diff options
166 files changed, 9615 insertions, 4184 deletions
@@ -1,4 +1,4 @@ -# mkin 1.2.0 (unreleased) +# mkin 1.2.0 (2022-11-17) - 'R/saem.R': 'logLik', 'update' and 'anova' methods for 'saem.mmkin' objects. diff --git a/_pkgdown.yml b/_pkgdown.yml index bb1ad052..8aa44ed4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,8 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: devel - version_label: info + mode: release + version_label: default template: bootswatch: spacelab diff --git a/custom_lsoda_call.patch b/custom_lsoda_call.patch new file mode 100644 index 00000000..d91a22c7 --- /dev/null +++ b/custom_lsoda_call.patch @@ -0,0 +1,1587 @@ +diff --git a/DESCRIPTION b/DESCRIPTION +index de0fab8..a006a44 100644 +--- a/DESCRIPTION ++++ b/DESCRIPTION +@@ -1,8 +1,8 @@ + Package: mkin + Type: Package + Title: Kinetic Evaluation of Chemical Degradation Data +-Version: 1.2.0 +-Date: 2022-11-16 ++Version: 1.3.0 ++Date: 2022-11-15 + Authors@R: c( + person("Johannes", "Ranke", role = c("aut", "cre", "cph"), + email = "johannes.ranke@jrwb.de", +@@ -22,8 +22,8 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, + Ranke et al. (2021) <doi:10.3390/environments8080071>. Please note that no + warranty is implied for correctness of results or fitness for a particular + purpose. +-Depends: R (>= 2.15.1), +-Imports: stats, graphics, methods, parallel, deSolve, R6, inline (>= 0.3.19), ++Depends: R (>= 2.15.1), deSolve ++Imports: stats, graphics, methods, parallel, R6, inline (>= 0.3.19), + numDeriv, lmtest, pkgbuild, nlme (>= 3.1-151), saemix (>= 3.1), rlang, vctrs + Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, + benchmarkme, tibble, stats4, readxl +diff --git a/NAMESPACE b/NAMESPACE +index 107ffc5..4a41acc 100644 +--- a/NAMESPACE ++++ b/NAMESPACE +@@ -147,7 +147,6 @@ export(status) + export(tex_listing) + export(transform_odeparms) + export(which.best) +-import(deSolve) + import(graphics) + import(nlme) + importFrom(R6,R6Class) +diff --git a/NEWS.md b/NEWS.md +index 22d5071..846c7c5 100644 +--- a/NEWS.md ++++ b/NEWS.md +@@ -1,11 +1,5 @@ + # mkin 1.2.0 (unreleased) + +-- 'R/saem.R': 'logLik', 'update' and 'anova' methods for 'saem.mmkin' objects. +- +-- 'R/saem.R': Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions. +- +-- 'R/status.R': New generic to show status information for fit array objects with methods for 'mmkin', 'mhmkin' and 'multistart' objects. +- + - 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. + + - 'R/mhmkin.R': 'anova.mhmkin' for conveniently comparing the resulting fits. +@@ -14,6 +8,12 @@ + + - 'R/multistart.R': New method for testing multiple start parameters for hierarchical model fits, with function 'llhist' and new generic 'parplot' for diagnostics, and new generics 'which.best' and 'best' for extracting the fit with the highest likelihood + ++- 'R/saem.R': 'logLik', 'update' and 'anova' methods for 'saem.mmkin' objects. ++ ++- 'R/saem.R': Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions. ++ ++- 'R/status.R': New generic to show status information for fit array objects with methods for 'mmkin', 'mhmkin' and 'multistart' objects. ++ + - 'R/summary.mmkin.R': Summary method for mmkin objects. + + - 'R/saem.R': Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported. +diff --git a/R/mkinfit.R b/R/mkinfit.R +index 693778f..0d9246d 100644 +--- a/R/mkinfit.R ++++ b/R/mkinfit.R +@@ -500,6 +500,15 @@ mkinfit <- function(mkinmod, observed, + } + } + ++ # Get native symbol before iterations info for speed ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ if (solution_type == "deSolve" & use_compiled[1] != FALSE) { ++ mkinmod$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = mkinmod$dll_info[["name"]])$address ++ mkinmod$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = mkinmod$dll_info[["name"]])$address ++ } ++ + # Get the error model and the algorithm for fitting + err_mod <- match.arg(error_model) + error_model_algorithm = match.arg(error_model_algorithm) +@@ -610,7 +619,8 @@ mkinfit <- function(mkinmod, observed, + solution_type = solution_type, + use_compiled = use_compiled, + method.ode = method.ode, +- atol = atol, rtol = rtol, ...) ++ atol = atol, rtol = rtol, ++ call_lsoda = call_lsoda, ...) + + observed_index <- cbind(as.character(observed$time), as.character(observed$name)) + observed$predicted <- out[observed_index] +@@ -892,7 +902,10 @@ mkinfit <- function(mkinmod, observed, + fit$calls <- calls + fit$time <- fit_time + +- # We also need the model and a model name for summary and plotting ++ # We also need the model and a model name for summary and plotting, ++ # but without address info that will become invalid ++ mkinmod$diffs_address <- NULL ++ mkinmod$initpar_address <- NULL + fit$mkinmod <- mkinmod + fit$mkinmod$name <- mkinmod_name + fit$obs_vars <- obs_vars +diff --git a/R/mkinmod.R b/R/mkinmod.R +index d8740ae..b1fb57c 100644 +--- a/R/mkinmod.R ++++ b/R/mkinmod.R +@@ -45,7 +45,9 @@ + #' @param dll_dir Directory where an DLL object, if generated internally by + #' [inline::cfunction()], should be saved. The DLL will only be stored in a + #' permanent location for use in future sessions, if 'dll_dir' and 'name' +-#' are specified. ++#' are specified. This is helpful if fit objects are cached e.g. by knitr, ++#' as the cache remains functional across sessions if the DLL is stored in ++#' a user defined location. + #' @param unload If a DLL from the target location in 'dll_dir' is already + #' loaded, should that be unloaded first? + #' @param overwrite If a file exists at the target DLL location in 'dll_dir', +diff --git a/R/mkinpredict.R b/R/mkinpredict.R +index 0dc9cf5..11a3b35 100644 +--- a/R/mkinpredict.R ++++ b/R/mkinpredict.R +@@ -19,26 +19,24 @@ + #' @param solution_type The method that should be used for producing the + #' predictions. This should generally be "analytical" if there is only one + #' observed variable, and usually "deSolve" in the case of several observed +-#' variables. The third possibility "eigen" is faster but not applicable to +-#' some models e.g. using FOMC for the parent compound. ++#' variables. The third possibility "eigen" is fast in comparison to uncompiled ++#' ODE models, but not applicable to some models, e.g. using FOMC for the ++#' parent compound. + #' @param method.ode The solution method passed via [mkinpredict] to [ode]] in +-#' case the solution type is "deSolve". The default "lsoda" is performant, but +-#' sometimes fails to converge. ++#' case the solution type is "deSolve" and we are not using compiled code. + #' @param use_compiled If set to \code{FALSE}, no compiled version of the + #' [mkinmod] model is used, even if is present. +-#' @param atol Absolute error tolerance, passed to [ode]. Default is 1e-8, +-#' lower than in [lsoda]. +-#' @param rtol Absolute error tolerance, passed to [ode]. Default is 1e-10, +-#' much lower than in [lsoda]. +-#' @param maxsteps Maximum number of steps, passed to [ode]. ++#' @param atol Absolute error tolerance, passed to the ode solver. ++#' @param rtol Absolute error tolerance, passed to the ode solver. ++#' @param maxsteps Maximum number of steps, passed to the ode solver. + #' @param map_output Boolean to specify if the output should list values for + #' the observed variables (default) or for all state variables (if set to + #' FALSE). Setting this to FALSE has no effect for analytical solutions, + #' as these always return mapped output. + #' @param na_stop Should it be an error if [ode] returns NaN values ++#' @param call_lsoda The address of the compiled function "call_lsoda" + #' @param \dots Further arguments passed to the ode solver in case such a + #' solver is used. +-#' @import deSolve + #' @return A matrix with the numeric solution in wide format + #' @author Johannes Ranke + #' @examples +@@ -116,9 +114,10 @@ mkinpredict.mkinmod <- function(x, + outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", + use_compiled = "auto", +- method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000, ++ method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L, + map_output = TRUE, + na_stop = TRUE, ++ call_lsoda = NULL, + ...) + { + +@@ -173,20 +172,80 @@ mkinpredict.mkinmod <- function(x, + if (solution_type == "deSolve") { + if (!is.null(x$cf) & use_compiled[1] != FALSE) { + +- out <- deSolve::ode( +- y = odeini, +- times = outtimes, +- func = "diffs", +- initfunc = "initpar", +- dllname = if (is.null(x$dll_info)) inline::getDynLib(x$cf)[["name"]] +- else x$dll_info[["name"]], +- parms = odeparms[x$parms], # Order matters when using compiled models +- method = method.ode, +- atol = atol, +- rtol = rtol, +- maxsteps = maxsteps, +- ... ++# out <- deSolve::ode( ++# y = odeini, ++# times = outtimes, ++# func = "diffs", ++# initfunc = "initpar", ++# dllname = x$dll_info[["name"]], ++# parms = odeparms[x$parms], # Order matters when using compiled models ++# method = method.ode, ++# atol = atol, ++# rtol = rtol, ++# maxsteps = maxsteps, ++# ... ++# ) ++# ++ # Prepare call to "call_lsoda" ++ # Simplified code from deSolve::lsoda() adapted to our use case ++ if (is.null(call_lsoda)) { ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ } ++ if (is.null(x$diffs_address)) { ++ x$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = x$dll_info[["name"]])$address ++ x$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = x$dll_info[["name"]])$address ++ } ++ rwork <- vector("double", 20) ++ rwork[] <- 0. ++ rwork[6] <- max(abs(diff(outtimes))) ++ ++ iwork <- vector("integer", 20) ++ iwork[] <- 0 ++ iwork[6] <- maxsteps ++ ++ n <- length(odeini) ++ lmat <- n^2 + 2 # from deSolve::lsoda(), for Jacobian type full, internal (2) ++ # hard-coded default values of lsoda(): ++ maxordn <- 12L ++ maxords <- 5L ++ lrn <- 20 + n * (maxordn + 1) + 3 * n # length in case non-stiff method ++ lrs <- 20 + n * (maxords + 1) + 3 * n + lmat # length in case stiff method ++ lrw <- max(lrn, lrs) # actual length: max of both ++ liw <- 20 + n ++ ++ on.exit(.C("unlock_solver", PACKAGE = "deSolve")) ++ ++ out_raw <- .Call(call_lsoda, ++ as.double(odeini), # y ++ as.double(outtimes), # times ++ x$diffs_address, # derivfunc ++ as.double(odeparms[x$parms]), # parms ++ rtol, atol, ++ NULL, NULL, # rho, tcrit ++ NULL, # jacfunc ++ x$initpar_address, # initfunc ++ NULL, # eventfunc ++ 0L, # verbose ++ 1L, # iTask ++ as.double(rwork), # rWork ++ as.integer(iwork), # iWork ++ 2L, # jT full Jacobian calculated internally ++ 0L, # nOut ++ as.integer(lrw), # lRw ++ as.integer(liw), # lIw ++ 1L, # Solver ++ NULL, # rootfunc ++ 0L, as.double(0), 0L, # nRoot, Rpar, Ipar ++ 0L, # Type ++ list(fmat = 0L, tmat = 0L, imat = 0L, ModelForc = NULL), # flist ++ list(), # elist ++ list(islag = 0L) # elag + ) ++ ++ out <- t(out_raw) ++ colnames(out) <- c("time", mod_vars) + } else { + mkindiff <- function(t, state, parms) { + +diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R +index 09cb84b..e193e5e 100644 +--- a/R/nlme.mmkin.R ++++ b/R/nlme.mmkin.R +@@ -186,10 +186,24 @@ nlme.mmkin <- function(model, data = "auto", + thisCall[["control"]] <- control + } + ++ # Provide the address of call_lsoda to the fitting function ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ if (model[[1]]$solution_type == "deSolve" & !is.null(model[[1]]$mkinmod$cf)) { ++ # The mkinmod stored in the first fit will be used by nlme ++ model[[1]]$mkinmod$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = model[[1]]$mkinmod$dll_info[["name"]])$address ++ model[[1]]$mkinmod$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = model[[1]]$mkinmod$dll_info[["name"]])$address ++ } ++ + fit_time <- system.time(val <- do.call("nlme.formula", thisCall)) + val$time <- fit_time + + val$mkinmod <- model[[1]]$mkinmod ++ # Don't return addresses that will become invalid ++ val$mkinmod$diffs_address <- NULL ++ val$mkinmod$initpar_address <- NULL ++ + val$data <- thisCall[["data"]] + val$mmkin <- model + if (is.list(start)) val$mean_dp_start <- start$fixed +diff --git a/R/read_spreadsheet.R b/R/read_spreadsheet.R +index 7ad09c3..a20af6d 100644 +--- a/R/read_spreadsheet.R ++++ b/R/read_spreadsheet.R +@@ -37,7 +37,7 @@ + #' and moisture normalisation factors in the sheet 'Datasets'? + #' @export + read_spreadsheet <- function(path, valid_datasets = "all", +- parent_only = FALSE, normalize = TRUE) ++ parent_only = TRUE, normalize = TRUE) + { + if (!requireNamespace("readxl", quietly = TRUE)) + stop("Please install the readxl package to use this function") +diff --git a/R/saem.R b/R/saem.R +index 696ea0e..5b8021d 100644 +--- a/R/saem.R ++++ b/R/saem.R +@@ -120,12 +120,12 @@ utils::globalVariables(c("predicted", "std")) + #' summary(f_saem_dfop_sfo, data = TRUE) + #' + #' # The following takes about 6 minutes +-#' #f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", +-#' # control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) ++#' f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", ++#' nbiter.saemix = c(200, 80)) + #' +-#' #saemix::compare.saemix(list( +-#' # f_saem_dfop_sfo$so, +-#' # f_saem_dfop_sfo_deSolve$so)) ++#' #anova( ++#' # f_saem_dfop_sfo, ++#' # f_saem_dfop_sfo_deSolve)) + #' + #' # If the model supports it, we can also use eigenvalue based solutions, which + #' # take a similar amount of time +@@ -580,6 +580,15 @@ saemix_model <- function(object, solution_type = "auto", + transform_rates <- object[[1]]$transform_rates + transform_fractions <- object[[1]]$transform_fractions + ++ # Get native symbol info for speed ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ if (solution_type == "deSolve" & !is.null(mkin_model$cf)) { ++ mkin_model$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = mkin_model$dll_info[["name"]])$address ++ mkin_model$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = mkin_model$dll_info[["name"]])$address ++ } ++ + # Define the model function + model_function <- function(psi, id, xidep) { + +@@ -613,7 +622,8 @@ saemix_model <- function(object, solution_type = "auto", + odeparms = odeparms, odeini = odeini, + solution_type = solution_type, + outtimes = sort(unique(i_time)), +- na_stop = FALSE ++ na_stop = FALSE, ++ call_lsoda = call_lsoda + ) + + out_index <- cbind(as.character(i_time), as.character(i_name)) +diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html +index 27e532a..6bfb63b 100644 +--- a/docs/dev/articles/mkin.html ++++ b/docs/dev/articles/mkin.html +@@ -34,7 +34,7 @@ + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> +- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> ++ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + </span> + </div> + +@@ -44,7 +44,7 @@ + <a href="../reference/index.html">Functions and data</a> + </li> + <li class="dropdown"> +- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> ++ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> +@@ -60,17 +60,11 @@ + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> +- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> +- </li> +- <li> +- <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> ++ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> +- <li> +- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> +- </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> +@@ -78,10 +72,7 @@ + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> +- <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> +- </li> +- <li> +- <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> ++ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> + </li> +@@ -112,7 +103,7 @@ + <h1 data-toc-skip>Introduction to mkin</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + +- <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-16)</h4> ++ <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-02-28)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> + <div class="hidden name"><code>mkin.rmd</code></div> +@@ -127,34 +118,34 @@ + </h2> + <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> + <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +-<span><span class="co"># Define the kinetic model</span></span> +-<span><span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span> +-<span> M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> +-<span> M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +-<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +-<span></span> +-<span></span> +-<span><span class="co"># Produce model predictions using some arbitrary parameters</span></span> +-<span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> +-<span><span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>,</span> +-<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>,</span> +-<span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>,</span> +-<span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>,</span> +-<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +-<span> <span class="va">sampling_times</span><span class="op">)</span></span> +-<span></span> +-<span><span class="co"># Generate a dataset by adding normally distributed errors with</span></span> +-<span><span class="co"># standard deviation 3, for two replicates at each sampling time</span></span> +-<span><span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>,</span> +-<span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>,</span> +-<span> n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span> +-<span></span> +-<span><span class="co"># Fit the model to the dataset</span></span> +-<span><span class="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +-<span></span> +-<span><span class="co"># Plot the results separately for parent and metabolites</span></span> +-<span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> ++<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> ++<span class="co"># Define the kinetic model</span> ++<span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>, ++ M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>, ++ M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, ++ use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> ++ ++ ++<span class="co"># Produce model predictions using some arbitrary parameters</span> ++<span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span> ++<span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, ++ <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>, ++ f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>, ++ f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>, ++ <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, ++ <span class="va">sampling_times</span><span class="op">)</span> ++ ++<span class="co"># Generate a dataset by adding normally distributed errors with</span> ++<span class="co"># standard deviation 3, for two replicates at each sampling time</span> ++<span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>, ++ sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>, ++ n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span> ++ ++<span class="co"># Fit the model to the dataset</span> ++<span class="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> ++ ++<span class="co"># Plot the results separately for parent and metabolites</span> ++<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div> + <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> + </div> + <div class="section level2"> +@@ -233,10 +224,10 @@ + <p>Ranke, J. 2021. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin" class="external-link">https://CRAN.R-project.org/package=mkin</a>.</p> + </div> + <div id="ref-ranke2012"> +-<p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin. <a href="https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf" class="external-link">https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf</a>.</p> ++<p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin.</p> + </div> + <div id="ref-ranke2015"> +-<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="https://jrwb.de/posters/piacenza_2015.pdf" class="external-link">https://jrwb.de/posters/piacenza_2015.pdf</a>.</p> ++<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf" class="external-link">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p> + </div> + <div id="ref-ranke2019"> + <p>Ranke, Johannes, and Stefan Meinecke. 2019. “Error Models for the Kinetic Evaluation of Chemical Degradation Data.” <em>Environments</em> 6 (12). <a href="https://doi.org/10.3390/environments6120124" class="external-link">https://doi.org/10.3390/environments6120124</a>.</p> +@@ -271,7 +262,7 @@ + + <div class="pkgdown"> + <p></p> +-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> ++<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + </div> + + </footer> +diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html +index afff038..e54bc38 100644 +--- a/docs/dev/articles/web_only/saem_benchmarks.html ++++ b/docs/dev/articles/web_only/saem_benchmarks.html +@@ -112,7 +112,7 @@ + <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + +- <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-16)</h4> ++ <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> + <div class="hidden name"><code>saem_benchmarks.rmd</code></div> +@@ -309,10 +309,10 @@ + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">2.156</td> +-<td align="right">4.647</td> +-<td align="right">4.296</td> +-<td align="right">4.951</td> ++<td align="right">2.11</td> ++<td align="right">4.632</td> ++<td align="right">4.264</td> ++<td align="right">4.93</td> + </tr></tbody> + </table> + <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> +@@ -332,10 +332,10 @@ + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">5.645</td> +-<td align="right">7.415</td> +-<td align="right">7.848</td> +-<td align="right">7.967</td> ++<td align="right">5.602</td> ++<td align="right">7.373</td> ++<td align="right">7.815</td> ++<td align="right">7.831</td> + </tr></tbody> + </table> + </div> +@@ -357,8 +357,8 @@ + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">24.182</td> +-<td align="right">783.932</td> ++<td align="right">24.014</td> ++<td align="right">749.699</td> + </tr></tbody> + </table> + </div> +@@ -379,7 +379,7 @@ + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">1322.5</td> ++<td align="right">1249.834</td> + </tr></tbody> + </table> + </div> +diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html +index 3353922..8448ebc 100644 +--- a/docs/dev/news/index.html ++++ b/docs/dev/news/index.html +@@ -89,13 +89,13 @@ + + <div class="section level2"> + <h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-unreleased">mkin 1.2.0 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-120-unreleased"></a></h2> +-<ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> +-<li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> +-<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> +-<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> ++<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> + <li><p>‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.</p></li> + <li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li> + <li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood</p></li> ++<li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> ++<li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> ++<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> + <li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li> + <li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> + <li><p>‘R/read_spreadsheet.R’: Conveniently read in data from a spreadsheet file.</p></li> +diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml +index 44bd60f..e0c11a8 100644 +--- a/docs/dev/pkgdown.yml ++++ b/docs/dev/pkgdown.yml +@@ -13,7 +13,7 @@ articles: + dimethenamid_2018: web_only/dimethenamid_2018.html + multistart: web_only/multistart.html + saem_benchmarks: web_only/saem_benchmarks.html +-last_built: 2022-11-16T14:17Z ++last_built: 2022-11-14T23:45Z + urls: + reference: https://pkgdown.jrwb.de/mkin/reference + article: https://pkgdown.jrwb.de/mkin/articles +diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html +index d0e192e..5d362f7 100644 +--- a/docs/dev/reference/mkinmod.html ++++ b/docs/dev/reference/mkinmod.html +@@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> +- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> ++ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + </span> + </div> + +@@ -30,7 +30,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" + <a href="../reference/index.html">Functions and data</a> + </li> + <li class="dropdown"> +- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> ++ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> +@@ -45,17 +45,11 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> +- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> +- </li> +- <li> +- <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> ++ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> +- <li> +- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> +- </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> +@@ -63,10 +57,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> +- <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> +- </li> +- <li> +- <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> ++ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul></li> + <li> +@@ -101,22 +92,22 @@ components.</p> + </div> + + <div id="ref-usage"> +- <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span> +-<span> <span class="va">...</span>,</span> +-<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> +-<span> name <span class="op">=</span> <span class="cn">NULL</span>,</span> +-<span> speclist <span class="op">=</span> <span class="cn">NULL</span>,</span> +-<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +-<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +-<span> dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span> +-<span> unload <span class="op">=</span> <span class="cn">FALSE</span>,</span> +-<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span></span> +-<span><span class="op">)</span></span> +-<span></span> +-<span><span class="co"># S3 method for mkinmod</span></span> +-<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +-<span></span> +-<span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> ++ <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinmod</span><span class="op">(</span> ++ <span class="va">...</span>, ++ use_of_ff <span class="op">=</span> <span class="st">"max"</span>, ++ name <span class="op">=</span> <span class="cn">NULL</span>, ++ speclist <span class="op">=</span> <span class="cn">NULL</span>, ++ quiet <span class="op">=</span> <span class="cn">FALSE</span>, ++ verbose <span class="op">=</span> <span class="cn">FALSE</span>, ++ dll_dir <span class="op">=</span> <span class="cn">NULL</span>, ++ unload <span class="op">=</span> <span class="cn">FALSE</span>, ++ overwrite <span class="op">=</span> <span class="cn">FALSE</span> ++<span class="op">)</span> ++ ++<span class="co"># S3 method for mkinmod</span> ++<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span> ++ ++<span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></code></pre></div> + </div> + + <div id="arguments"> +@@ -136,108 +127,72 @@ If the argument <code>use_of_ff</code> is set to "min" + additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively + fixing the flux to sink to zero. + In print.mkinmod, this argument is currently not used.</p></dd> +- +- + <dt>use_of_ff</dt> + <dd><p>Specification of the use of formation fractions in the + model equations and, if applicable, the coefficient matrix. If "max", + formation fractions are always used (default). If "min", a minimum use of + formation fractions is made, i.e. each first-order pathway to a metabolite + has its own rate constant.</p></dd> +- +- + <dt>name</dt> + <dd><p>A name for the model. Should be a valid R object name.</p></dd> +- +- + <dt>speclist</dt> + <dd><p>The specification of the observed variables and their + submodel types and pathways can be given as a single list using this + argument. Default is NULL.</p></dd> +- +- + <dt>quiet</dt> + <dd><p>Should messages be suppressed?</p></dd> +- +- + <dt>verbose</dt> + <dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if + applicable to give detailed information about the C function being built.</p></dd> +- +- + <dt>dll_dir</dt> + <dd><p>Directory where an DLL object, if generated internally by + <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a + permanent location for use in future sessions, if 'dll_dir' and 'name' + are specified.</p></dd> +- +- + <dt>unload</dt> + <dd><p>If a DLL from the target location in 'dll_dir' is already + loaded, should that be unloaded first?</p></dd> +- +- + <dt>overwrite</dt> + <dd><p>If a file exists at the target DLL location in 'dll_dir', + should this be overwritten?</p></dd> +- +- + <dt>x</dt> + <dd><p>An <code>mkinmod</code> object.</p></dd> +- +- + <dt>submodel</dt> + <dd><p>Character vector of length one to specify the submodel type. + See <code>mkinmod</code> for the list of allowed submodel names.</p></dd> +- +- + <dt>to</dt> + <dd><p>Vector of the names of the state variable to which a + transformation shall be included in the model.</p></dd> +- +- + <dt>sink</dt> + <dd><p>Should a pathway to sink be included in the model in addition to + the pathways to other state variables?</p></dd> +- +- + <dt>full_name</dt> + <dd><p>An optional name to be used e.g. for plotting fits + performed with the model. You can use non-ASCII characters here, but then + your R code will not be portable, <em>i.e.</em> may produce unintended plot + results on other operating systems or system configurations.</p></dd> +- + </dl></div> + <div id="value"> + <h2>Value</h2> +- +- +-<p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, ++ <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, + containing, among others,</p> + <dl><dt>diffs</dt> + <dd><p>A vector of string representations of differential equations, one for + each modelling variable.</p></dd> +- + <dt>map</dt> + <dd><p>A list containing named character vectors for each observed variable, + specifying the modelling variables by which it is represented.</p></dd> +- + <dt>use_of_ff</dt> + <dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> +- + <dt>deg_func</dt> + <dd><p>If generated, a function containing the solution of the degradation + model.</p></dd> +- + <dt>coefmat</dt> + <dd><p>The coefficient matrix, if the system of differential equations can be + represented by one.</p></dd> +- + <dt>cf</dt> + <dd><p>If generated, a compiled function calculating the derivatives as + returned by cfunction.</p></dd> +- +- + </dl><p>A list for use with <code>mkinmod</code>.</p> + </div> + <div id="details"> +@@ -275,16 +230,16 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + + <div id="ref-examples"> + <h2>Examples</h2> +- <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> +-<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span> +-<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +-<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> ++ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> ++<span class="r-in"><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span> ++<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order</span></span> ++<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> ++<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> ++<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span></span> ++<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span> + <span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> + <span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> + <span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> +@@ -297,32 +252,30 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + <span class="r-out co"><span class="r-pr">#></span> Differential equations:</span> + <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> + <span class="r-out co"><span class="r-pr">#></span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +-<span class="r-in"><span> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +-<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span> +-<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span> +-<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span></span> +-<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span></span> +-<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +-<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +-<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmpp1dECS/file32009e039f7a.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +-<span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> +-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +-<span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> +-<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> +-<span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +-<span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +-<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span> +-<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +-<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="co"># \dontrun{</span></span> ++<span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> ++<span class="r-in"></span> ++<span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> ++<span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> ++<span class="r-in"> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span> ++<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span> ++<span class="r-in"> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> ++<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> ++<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> ++<span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> ++<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp6NiOcv/fileb89c01ace19ec.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> ++<span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> ++<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> ++<span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> ++<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> ++<span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> ++<span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="co"># Show details of creating the C function</span></span> ++<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> ++<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> ++<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> + <span class="r-out co"><span class="r-pr">#></span> Program source:</span> + <span class="r-out co"><span class="r-pr">#></span> 1: #include <R.h></span> + <span class="r-out co"><span class="r-pr">#></span> 2: </span> +@@ -344,10 +297,10 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + <span class="r-out co"><span class="r-pr">#></span> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span> + <span class="r-out co"><span class="r-pr">#></span> 19: }</span> + <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span> +-<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span> +-<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="co"># The symbolic solution which is available in this case is not</span></span> ++<span class="r-in"><span class="co"># made for human reading but for speed of computation</span></span> ++<span class="r-in"><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span> + <span class="r-out co"><span class="r-pr">#></span> function (observed, odeini, odeparms) </span> + <span class="r-out co"><span class="r-pr">#></span> {</span> + <span class="r-out co"><span class="r-pr">#></span> predicted <- numeric(0)</span> +@@ -363,21 +316,21 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + <span class="r-out co"><span class="r-pr">#></span> })</span> + <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> + <span class="r-out co"><span class="r-pr">#></span> }</span> +-<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555d516c10></span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> +-<span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> +-<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +-<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +-<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +-<span class="r-in"><span></span></span> +-<span class="r-in"><span><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +-<span class="r-in"><span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +-<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +-<span class="r-in"><span><span class="co"># }</span></span></span> +-<span class="r-in"><span></span></span> ++<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555cd83c70></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> ++<span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> ++<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> ++<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> ++<span class="r-in"> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> ++<span class="r-in"> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> ++<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> ++<span class="r-in"></span> ++<span class="r-in"><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span> ++<span class="r-in"> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span> ++<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> ++<span class="r-in"><span class="co"># }</span></span> ++<span class="r-in"></span> + </code></pre></div> + </div> + </div> +@@ -392,7 +345,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + </div> + + <div class="pkgdown"> +- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> ++ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + </div> + + </footer></div> +diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html +index 0e645b5..3793091 100644 +--- a/docs/dev/reference/mkinpredict.html ++++ b/docs/dev/reference/mkinpredict.html +@@ -377,7 +377,7 @@ as these always return mapped output.</p></dd> + <span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> + <span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.2 0.021</span> + <span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.2 0.021</span> +-<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 41.0 0.205</span> ++<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.8 0.204</span> + <span class="r-in"><span></span></span> + <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> + <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> +diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html +index efba012..7082876 100644 +--- a/docs/dev/reference/read_spreadsheet.html ++++ b/docs/dev/reference/read_spreadsheet.html +@@ -64,10 +64,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><meta name= + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> +- <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> +- </li> +- <li> +- <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> ++ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul></li> + <li> +@@ -106,7 +103,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'.</p> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_spreadsheet</span><span class="op">(</span></span> + <span> <span class="va">path</span>,</span> + <span> valid_datasets <span class="op">=</span> <span class="st">"all"</span>,</span> +-<span> parent_only <span class="op">=</span> <span class="cn">FALSE</span>,</span> ++<span> parent_only <span class="op">=</span> <span class="cn">TRUE</span>,</span> + <span> normalize <span class="op">=</span> <span class="cn">TRUE</span></span> + <span><span class="op">)</span></span></code></pre></div> + </div> +diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html +index d2e930e..73382cb 100644 +--- a/docs/dev/reference/saem.html ++++ b/docs/dev/reference/saem.html +@@ -432,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p> + <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> + <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> + <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +-<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Nov 16 10:49:43 2022 </span> +-<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Nov 16 10:49:43 2022 </span> ++<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 15 00:45:58 2022 </span> ++<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 15 00:45:58 2022 </span> + <span class="r-out co"><span class="r-pr">#></span> </span> + <span class="r-out co"><span class="r-pr">#></span> Equations:</span> + <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> +@@ -448,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p> + <span class="r-out co"><span class="r-pr">#></span> </span> + <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> + <span class="r-out co"><span class="r-pr">#></span> </span> +-<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.935 s</span> ++<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.189 s</span> + <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> + <span class="r-out co"><span class="r-pr">#></span> </span> + <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> +diff --git a/log/build.log b/log/build.log +index a56a64d..245bd20 100644 +--- a/log/build.log ++++ b/log/build.log +@@ -5,4 +5,5 @@ + * creating vignettes ... OK + * checking for LF line-endings in source and make files and shell scripts + * checking for empty or unneeded directories +-* building ‘mkin_1.2.0.tar.gz’ ++* building ‘mkin_1.3.0.tar.gz’ ++ +diff --git a/log/check.log b/log/check.log +index 7aa4610..e7d4d32 100644 +--- a/log/check.log ++++ b/log/check.log +@@ -5,7 +5,7 @@ + * using options ‘--no-tests --as-cran’ + * checking for file ‘mkin/DESCRIPTION’ ... OK + * checking extension type ... Package +-* this is package ‘mkin’ version ‘1.2.0’ ++* this is package ‘mkin’ version ‘1.3.0’ + * package encoding: UTF-8 + * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers + Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ +@@ -37,11 +37,18 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ + * checking whether the namespace can be unloaded cleanly ... OK + * checking loading without being on the library search path ... OK + * checking use of S3 registration ... OK +-* checking dependencies in R code ... OK ++* checking dependencies in R code ... NOTE ++Package in Depends field not imported from: ‘deSolve’ ++ These packages need to be imported from (in the NAMESPACE file) ++ for when this namespace is loaded but not attached. + * checking S3 generic/method consistency ... OK + * checking replacement functions ... OK +-* checking foreign function calls ... OK +-* checking R code for possible problems ... [18s/18s] OK ++* checking foreign function calls ... NOTE ++Foreign function call to a different package: ++ .C("unlock_solver", ..., PACKAGE = "deSolve") ++See chapter ‘System and foreign language interfaces’ in the ‘Writing R ++Extensions’ manual. ++* checking R code for possible problems ... [17s/17s] OK + * checking Rd files ... OK + * checking Rd metadata ... OK + * checking Rd line widths ... OK +@@ -69,5 +76,9 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ + * checking for detritus in the temp directory ... OK + * DONE + +-Status: OK ++Status: 2 NOTEs ++See ++ ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ ++for details. ++ + +diff --git a/log/test.log b/log/test.log +index b305bf5..10c0aa7 100644 +--- a/log/test.log ++++ b/log/test.log +@@ -1,57 +1,57 @@ + ℹ Testing mkin + ✔ | F W S OK | Context + ✔ | 5 | AIC calculation +-✔ | 5 | Analytical solutions for coupled models [3.5s] ++✔ | 5 | Analytical solutions for coupled models [2.9s] + ✔ | 5 | Calculation of Akaike weights + ✔ | 3 | Export dataset for reading into CAKE +-✔ | 12 | Confidence intervals and p-values [1.1s] +-✔ | 1 12 | Dimethenamid data from 2018 [34.5s] ++✔ | 12 | Confidence intervals and p-values [1.0s] ++✔ | 1 12 | Dimethenamid data from 2018 [29.5s] + ──────────────────────────────────────────────────────────────────────────────── +-Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data ++Skip ('test_dmta.R:99'): Different backends get consistent results for SFO-SFO3+, dimethenamid data + Reason: Fitting this ODE model with saemix takes about 15 minutes on my system + ──────────────────────────────────────────────────────────────────────────────── +-✔ | 14 | Error model fitting [5.3s] ++✔ | 14 | Error model fitting [4.9s] + ✔ | 5 | Time step normalisation + ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +-✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ++✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7s] ++✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] + ✔ | 1 | Fitting the logistic model [0.2s] +-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.6s] +-✔ | 1 12 | Nonlinear mixed-effects models [0.4s] ++✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s] ++✔ | 1 12 | Nonlinear mixed-effects models [0.3s] + ──────────────────────────────────────────────────────────────────────────────── + Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits + Reason: Fitting with saemix takes around 10 minutes when using deSolve + ──────────────────────────────────────────────────────────────────────────────── + ✔ | 3 | Test dataset classes mkinds and mkindsg +-✔ | 10 | Special cases of mkinfit calls [0.6s] ++✔ | 10 | Special cases of mkinfit calls [0.5s] + ✔ | 3 | mkinfit features [0.7s] + ✔ | 8 | mkinmod model generation and printing [0.2s] +-✔ | 3 | Model predictions with mkinpredict [0.3s] +-✔ | 9 | Multistart method for saem.mmkin models [40.2s] +-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.6s] +-✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] +-✔ | 16 | Plotting [10.5s] ++✔ | 3 | Model predictions with mkinpredict [0.4s] ++✔ | 7 | Multistart method for saem.mmkin models [36.8s] ++✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] ++✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] ++✔ | 16 | Plotting [10.0s] + ✔ | 4 | Residuals extracted from mkinfit models +-✔ | 1 36 | saemix parent models [69.8s] ++✔ | 1 36 | saemix parent models [66.1s] + ──────────────────────────────────────────────────────────────────────────────── + Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem + Reason: This still takes almost 2.5 minutes although we do not solve ODEs + ──────────────────────────────────────────────────────────────────────────────── +-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] ++✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.1s] + ✔ | 11 | Processing of residue series +-✔ | 10 | Fitting the SFORB model [3.9s] ++✔ | 10 | Fitting the SFORB model [3.4s] + ✔ | 1 | Summaries of old mkinfit objects + ✔ | 5 | Summary [0.2s] +-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +-✔ | 9 | Hypothesis tests [8.5s] +-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] ++✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.6s] ++✔ | 9 | Hypothesis tests [6.1s] ++✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] + + ══ Results ═════════════════════════════════════════════════════════════════════ +-Duration: 225.9 s ++Duration: 206.2 s + + ── Skipped tests ────────────────────────────────────────────────────────────── + • Fitting this ODE model with saemix takes about 15 minutes on my system (1) + • Fitting with saemix takes around 10 minutes when using deSolve (1) + • This still takes almost 2.5 minutes although we do not solve ODEs (1) + +-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ] ++[ FAIL 0 | WARN 0 | SKIP 3 | PASS 267 ] +diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd +index 87ce901..612c3c2 100644 +--- a/man/mkinmod.Rd ++++ b/man/mkinmod.Rd +@@ -58,7 +58,9 @@ applicable to give detailed information about the C function being built.} + \item{dll_dir}{Directory where an DLL object, if generated internally by + \code{\link[inline:cfunction]{inline::cfunction()}}, should be saved. The DLL will only be stored in a + permanent location for use in future sessions, if 'dll_dir' and 'name' +-are specified.} ++are specified. This is helpful if fit objects are cached e.g. by knitr, ++as the cache remains functional across sessions if the DLL is stored in ++a user defined location.} + + \item{unload}{If a DLL from the target location in 'dll_dir' is already + loaded, should that be unloaded first?} +diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd +index 0797f25..d93c075 100644 +--- a/man/mkinpredict.Rd ++++ b/man/mkinpredict.Rd +@@ -18,9 +18,10 @@ mkinpredict(x, odeparms, odeini, outtimes, ...) + method.ode = "lsoda", + atol = 1e-08, + rtol = 1e-10, +- maxsteps = 20000, ++ maxsteps = 20000L, + map_output = TRUE, + na_stop = TRUE, ++ call_lsoda = NULL, + ... + ) + +@@ -60,23 +61,21 @@ solver is used.} + \item{solution_type}{The method that should be used for producing the + predictions. This should generally be "analytical" if there is only one + observed variable, and usually "deSolve" in the case of several observed +-variables. The third possibility "eigen" is faster but not applicable to +-some models e.g. using FOMC for the parent compound.} ++variables. The third possibility "eigen" is fast in comparison to uncompiled ++ODE models, but not applicable to some models, e.g. using FOMC for the ++parent compound.} + + \item{use_compiled}{If set to \code{FALSE}, no compiled version of the + \link{mkinmod} model is used, even if is present.} + + \item{method.ode}{The solution method passed via \link{mkinpredict} to \link{ode}] in +-case the solution type is "deSolve". The default "lsoda" is performant, but +-sometimes fails to converge.} ++case the solution type is "deSolve" and we are not using compiled code.} + +-\item{atol}{Absolute error tolerance, passed to \link{ode}. Default is 1e-8, +-lower than in \link{lsoda}.} ++\item{atol}{Absolute error tolerance, passed to the ode solver.} + +-\item{rtol}{Absolute error tolerance, passed to \link{ode}. Default is 1e-10, +-much lower than in \link{lsoda}.} ++\item{rtol}{Absolute error tolerance, passed to the ode solver.} + +-\item{maxsteps}{Maximum number of steps, passed to \link{ode}.} ++\item{maxsteps}{Maximum number of steps, passed to the ode solver.} + + \item{map_output}{Boolean to specify if the output should list values for + the observed variables (default) or for all state variables (if set to +@@ -84,6 +83,8 @@ FALSE). Setting this to FALSE has no effect for analytical solutions, + as these always return mapped output.} + + \item{na_stop}{Should it be an error if \link{ode} returns NaN values} ++ ++\item{call_lsoda}{The address of the compiled function "call_lsoda"} + } + \value{ + A matrix with the numeric solution in wide format +diff --git a/man/read_spreadsheet.Rd b/man/read_spreadsheet.Rd +index 41c3210..147d09b 100644 +--- a/man/read_spreadsheet.Rd ++++ b/man/read_spreadsheet.Rd +@@ -7,7 +7,7 @@ + read_spreadsheet( + path, + valid_datasets = "all", +- parent_only = FALSE, ++ parent_only = TRUE, + normalize = TRUE + ) + } +diff --git a/man/saem.Rd b/man/saem.Rd +index 1146335..3a5abad 100644 +--- a/man/saem.Rd ++++ b/man/saem.Rd +@@ -206,12 +206,12 @@ plot(f_saem_dfop_sfo) + summary(f_saem_dfop_sfo, data = TRUE) + + # The following takes about 6 minutes +-#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", +-# control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) ++f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", ++ nbiter.saemix = c(200, 80)) + +-#saemix::compare.saemix(list( +-# f_saem_dfop_sfo$so, +-# f_saem_dfop_sfo_deSolve$so)) ++#anova( ++# f_saem_dfop_sfo, ++# f_saem_dfop_sfo_deSolve)) + + # If the model supports it, we can also use eigenvalue based solutions, which + # take a similar amount of time +diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R +index c44cdac..5cfc61d 100644 +--- a/tests/testthat/test_dmta.R ++++ b/tests/testthat/test_dmta.R +@@ -11,13 +11,13 @@ names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) + dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]]) + dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL + ++# mkin ++dmta_dfop <- mmkin("DFOP", dmta_ds, quiet = TRUE, cores = n_cores) ++dmta_dfop_tc <- mmkin("DFOP", dmta_ds, error_model = "tc", quiet = TRUE, cores = n_cores) ++ + test_that("Different backends get consistent results for DFOP tc, dimethenamid data", { + + skip_on_cran() # Time constraints +- # mkin +- dmta_dfop <- mmkin("DFOP", dmta_ds, quiet = TRUE, cores = n_cores) +- dmta_dfop_tc <- mmkin("DFOP", dmta_ds, error_model = "tc", quiet = TRUE, cores = n_cores) +- + # nlme + expect_warning( + nlme_dfop_tc <- nlme(dmta_dfop_tc), +@@ -85,7 +85,8 @@ sfo_sfo3p <- mkinmod( + ) + + dmta_sfo_sfo3p_tc <- mmkin(list("SFO-SFO3+" = sfo_sfo3p), +- dmta_ds, error_model = "tc", quiet = TRUE, cores = n_cores) ++ dmta_ds, error_model = "tc", quiet = TRUE, ++ cores = n_cores) + + test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid data", { + +diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R +index 98d3fb6..c1a10d1 100644 +--- a/tests/testthat/test_multistart.R ++++ b/tests/testthat/test_multistart.R +@@ -1,7 +1,6 @@ + context("Multistart method for saem.mmkin models") + + test_that("multistart works for saem.mmkin models", { +- skip_on_cran() # Save CRAN time + set.seed(123456) + saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores, + no_random_effect = "parent_0") +@@ -10,13 +9,9 @@ test_that("multistart works for saem.mmkin models", { + best(saem_sfo_s_multi), + test = TRUE + ) +- # On winbuilder, sfo_saem_1 gives an AIC of 1310.8, while we get 1311.7 +- # locally on Linux and Windows. The other, well-determined fits +- # both give 1309.7 +- expect_equal(round(anova_sfo, 1)["sfo_saem_1_reduced", "AIC"], 1309.7) +- expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1309.7) +- expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, CRAN: 0.4 ++ expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.5) + ++ skip_on_cran() # Save CRAN time + set.seed(123456) + saem_biphasic_m_multi <- multistart(saem_biphasic_m, n = 8, + cores = n_cores) +diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R +index b89ea34..8eb052c 100644 +--- a/tests/testthat/test_nafta.R ++++ b/tests/testthat/test_nafta.R +@@ -4,7 +4,6 @@ test_that("Data for more than one compound are rejected", + expect_error(nafta(FOCUS_2006_D, cores = 1))) + + test_that("Test data from Appendix B are correctly evaluated", { +- skip_on_cran() + expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic", cores = 1)) + + # From Figure D.1 +@@ -26,7 +25,6 @@ test_that("Test data from Appendix B are correctly evaluated", { + }) + + test_that("Test data from Appendix D are correctly evaluated", { +- skip_on_cran() + # We are not interested in the warnings about non-normal residuals here + suppressWarnings( + res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555", +diff --git a/vignettes/mkin.html b/vignettes/mkin.html +index 0d5ed6f..38c44a0 100644 +--- a/vignettes/mkin.html ++++ b/vignettes/mkin.html +@@ -1599,7 +1599,7 @@ div.tocify { + + <h1 class="title toc-ignore">Introduction to mkin</h1> + <h4 class="author">Johannes Ranke</h4> +-<h4 class="date">Last change 15 February 2021 (rebuilt 2022-07-12)</h4> ++<h4 class="date">Last change 15 February 2021 (rebuilt 2022-11-15)</h4> + + </div> + +diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html +index 5f81f39..5376c1f 100644 +--- a/vignettes/web_only/benchmarks.html ++++ b/vignettes/web_only/benchmarks.html +@@ -1599,7 +1599,7 @@ div.tocify { + + <h1 class="title toc-ignore">Benchmark timings for mkin</h1> + <h4 class="author">Johannes Ranke</h4> +-<h4 class="date">Last change 14 July 2022 (rebuilt 2022-07-14)</h4> ++<h4 class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</h4> + + </div> + +@@ -1635,7 +1635,7 @@ FOMC_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub("SFO")) + DFOP_SFO <- mkinmod( +- parent = mkinsub("FOMC", "m1"), ++ parent = mkinsub("FOMC", "m1"), # erroneously used FOMC twice, not fixed for consistency + m1 = mkinsub("SFO")) + t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]] + t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), +@@ -1816,6 +1816,30 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), + <td align="right">1.770</td> + <td align="right">3.377</td> + </tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.1</td> ++<td align="left">1.1.2</td> ++<td align="right">1.957</td> ++<td align="right">3.633</td> ++</tr> ++<tr class="even"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.2.0</td> ++<td align="right">2.129</td> ++<td align="right">3.784</td> ++</tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.3.0</td> ++<td align="right">2.046</td> ++<td align="right">3.693</td> ++</tr> + </tbody> + </table> + </div> +@@ -1979,6 +2003,33 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), + <td align="right">5.758</td> + <td align="right">2.558</td> + </tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.1</td> ++<td align="left">1.1.2</td> ++<td align="right">1.503</td> ++<td align="right">6.147</td> ++<td align="right">2.803</td> ++</tr> ++<tr class="even"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.2.0</td> ++<td align="right">1.559</td> ++<td align="right">6.097</td> ++<td align="right">2.841</td> ++</tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.3.0</td> ++<td align="right">1.230</td> ++<td align="right">4.333</td> ++<td align="right">2.187</td> ++</tr> + </tbody> + </table> + </div> +@@ -2193,6 +2244,42 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), + <td align="right">1.744</td> + <td align="right">2.566</td> + </tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.1</td> ++<td align="left">1.1.2</td> ++<td align="right">0.861</td> ++<td align="right">1.295</td> ++<td align="right">1.507</td> ++<td align="right">3.102</td> ++<td align="right">1.961</td> ++<td align="right">2.852</td> ++</tr> ++<tr class="even"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.2.0</td> ++<td align="right">0.911</td> ++<td align="right">1.328</td> ++<td align="right">1.519</td> ++<td align="right">2.986</td> ++<td align="right">1.957</td> ++<td align="right">2.769</td> ++</tr> ++<tr class="odd"> ++<td align="left">Linux</td> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">4.2.2</td> ++<td align="left">1.3.0</td> ++<td align="right">0.693</td> ++<td align="right">0.996</td> ++<td align="right">1.121</td> ++<td align="right">2.174</td> ++<td align="right">1.427</td> ++<td align="right">2.026</td> ++</tr> + </tbody> + </table> + </div> +diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda +index 2d3deb2..c07def6 100644 +Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ +diff --git a/vignettes/web_only/saem_benchmarks.html b/vignettes/web_only/saem_benchmarks.html +index 4875bb1..714dc1f 100644 +--- a/vignettes/web_only/saem_benchmarks.html ++++ b/vignettes/web_only/saem_benchmarks.html +@@ -1599,7 +1599,7 @@ div.tocify { + + <h1 class="title toc-ignore">Benchmark timings for saem.mmkin</h1> + <h4 class="author">Johannes Ranke</h4> +-<h4 class="date">Last change 14 November 2022 (rebuilt 2022-11-14)</h4> ++<h4 class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</h4> + + </div> + +@@ -1781,10 +1781,20 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">2.996</td> +-<td align="right">5.207</td> +-<td align="right">5.317</td> +-<td align="right">5.171</td> ++<td align="right">2.110</td> ++<td align="right">4.632</td> ++<td align="right">4.264</td> ++<td align="right">4.930</td> ++</tr> ++<tr class="even"> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">Linux</td> ++<td align="left">1.3.0</td> ++<td align="left">3.2</td> ++<td align="right">2.394</td> ++<td align="right">4.748</td> ++<td align="right">4.883</td> ++<td align="right">4.937</td> + </tr> + </tbody> + </table> +@@ -1808,10 +1818,20 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">5.671</td> +-<td align="right">7.696</td> +-<td align="right">8.166</td> +-<td align="right">8.168</td> ++<td align="right">5.602</td> ++<td align="right">7.373</td> ++<td align="right">7.815</td> ++<td align="right">7.831</td> ++</tr> ++<tr class="even"> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">Linux</td> ++<td align="left">1.3.0</td> ++<td align="left">3.2</td> ++<td align="right">5.622</td> ++<td align="right">7.445</td> ++<td align="right">8.297</td> ++<td align="right">7.740</td> + </tr> + </tbody> + </table> +@@ -1836,8 +1856,16 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">24.883</td> +-<td align="right">818.157</td> ++<td align="right">24.014</td> ++<td align="right">749.699</td> ++</tr> ++<tr class="even"> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">Linux</td> ++<td align="left">1.3.0</td> ++<td align="left">3.2</td> ++<td align="right">24.480</td> ++<td align="right">519.087</td> + </tr> + </tbody> + </table> +@@ -1861,7 +1889,14 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF + <td align="left">Linux</td> + <td align="left">1.2.0</td> + <td align="left">3.2</td> +-<td align="right">1355.036</td> ++<td align="right">1249.834</td> ++</tr> ++<tr class="even"> ++<td align="left">Ryzen 7 1700</td> ++<td align="left">Linux</td> ++<td align="left">1.3.0</td> ++<td align="left">3.2</td> ++<td align="right">944.471</td> + </tr> + </tbody> + </table> +diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda +index 55fabf1..992b58c 100644 +Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ diff --git a/custom_lsoda_call_edited.patch b/custom_lsoda_call_edited.patch new file mode 100644 index 00000000..a79cbbcd --- /dev/null +++ b/custom_lsoda_call_edited.patch @@ -0,0 +1,116 @@ +--- a/R/mkinfit.R ++++ b/R/mkinfit.R + ++ # Get native symbol before iterations info for speed ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ if (solution_type == "deSolve" & use_compiled[1] != FALSE) { ++ mkinmod$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = mkinmod$dll_info[["name"]])$address ++ mkinmod$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = mkinmod$dll_info[["name"]])$address ++ } ++ + +@@ -610,7 +619,8 @@ mkinfit <- function(mkinmod, observed, + solution_type = solution_type, + use_compiled = use_compiled, + method.ode = method.ode, +- atol = atol, rtol = rtol, ...) ++ atol = atol, rtol = rtol, ++ call_lsoda = call_lsoda, ...) + +--- a/R/mkinpredict.R ++++ b/R/mkinpredict.R + +@@ -116,9 +114,10 @@ mkinpredict.mkinmod <- function(x, + outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", + use_compiled = "auto", +- method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000, ++ method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L, + map_output = TRUE, + na_stop = TRUE, ++ call_lsoda = NULL, + ...) + { + +@@ -173,20 +172,80 @@ mkinpredict.mkinmod <- function(x, + if (solution_type == "deSolve") { + if (!is.null(x$cf) & use_compiled[1] != FALSE) { + +- out <- deSolve::ode( +- y = odeini, +- times = outtimes, +- func = "diffs", +- initfunc = "initpar", +- dllname = if (is.null(x$dll_info)) inline::getDynLib(x$cf)[["name"]] +- else x$dll_info[["name"]], +- parms = odeparms[x$parms], # Order matters when using compiled models +- method = method.ode, +- atol = atol, +- rtol = rtol, +- maxsteps = maxsteps, +- ... ++ # Prepare call to "call_lsoda" ++ # Simplified code from deSolve::lsoda() adapted to our use case ++ if (is.null(call_lsoda)) { ++ call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve") ++ } ++ if (is.null(x$diffs_address)) { ++ x$diffs_address <- getNativeSymbolInfo("diffs", ++ PACKAGE = x$dll_info[["name"]])$address ++ x$initpar_address <- getNativeSymbolInfo("initpar", ++ PACKAGE = x$dll_info[["name"]])$address ++ } ++ rwork <- vector("double", 20) ++ rwork[] <- 0. ++ rwork[6] <- max(abs(diff(outtimes))) ++ ++ iwork <- vector("integer", 20) ++ iwork[] <- 0 ++ iwork[6] <- maxsteps ++ ++ n <- length(odeini) ++ lmat <- n^2 + 2 # from deSolve::lsoda(), for Jacobian type full, internal (2) ++ # hard-coded default values of lsoda(): ++ maxordn <- 12L ++ maxords <- 5L ++ lrn <- 20 + n * (maxordn + 1) + 3 * n # length in case non-stiff method ++ lrs <- 20 + n * (maxords + 1) + 3 * n + lmat # length in case stiff method ++ lrw <- max(lrn, lrs) # actual length: max of both ++ liw <- 20 + n ++ ++ on.exit(.C("unlock_solver", PACKAGE = "deSolve")) ++ ++ out_raw <- .Call(call_lsoda, ++ as.double(odeini), # y ++ as.double(outtimes), # times ++ x$diffs_address, # derivfunc ++ as.double(odeparms[x$parms]), # parms ++ rtol, atol, ++ NULL, NULL, # rho, tcrit ++ NULL, # jacfunc ++ x$initpar_address, # initfunc ++ NULL, # eventfunc ++ 0L, # verbose ++ 1L, # iTask ++ as.double(rwork), # rWork ++ as.integer(iwork), # iWork ++ 2L, # jT full Jacobian calculated internally ++ 0L, # nOut ++ as.integer(lrw), # lRw ++ as.integer(liw), # lIw ++ 1L, # Solver ++ NULL, # rootfunc ++ 0L, as.double(0), 0L, # nRoot, Rpar, Ipar ++ 0L, # Type ++ list(fmat = 0L, tmat = 0L, imat = 0L, ModelForc = NULL), # flist ++ list(), # elist ++ list(islag = 0L) # elag + ) ++ ++ out <- t(out_raw) ++ colnames(out) <- c("time", mod_vars) + } else { + mkindiff <- function(t, state, parms) { + diff --git a/docs/404.html b/docs/404.html index 89c41d21..36135992 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -61,19 +61,25 @@ <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="https://pkgdown.jrwb.de/mkin/articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 39cf7e1a..3c8ad547 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -116,207 +122,207 @@ <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## name time value</span> -<span class="co">## 1 parent 0 99.46</span> -<span class="co">## 2 parent 0 102.04</span> -<span class="co">## 3 parent 1 93.50</span> -<span class="co">## 4 parent 1 92.50</span> -<span class="co">## 5 parent 3 63.23</span> -<span class="co">## 6 parent 3 68.99</span> -<span class="co">## 7 parent 7 52.32</span> -<span class="co">## 8 parent 7 55.13</span> -<span class="co">## 9 parent 14 27.27</span> -<span class="co">## 10 parent 14 26.64</span> -<span class="co">## 11 parent 21 11.50</span> -<span class="co">## 12 parent 21 11.64</span> -<span class="co">## 13 parent 35 2.85</span> -<span class="co">## 14 parent 35 2.91</span> -<span class="co">## 15 parent 50 0.69</span> -<span class="co">## 16 parent 50 0.63</span> -<span class="co">## 17 parent 75 0.05</span> -<span class="co">## 18 parent 75 0.06</span> -<span class="co">## 19 parent 100 NA</span> -<span class="co">## 20 parent 100 NA</span> -<span class="co">## 21 parent 120 NA</span> -<span class="co">## 22 parent 120 NA</span> -<span class="co">## 23 m1 0 0.00</span> -<span class="co">## 24 m1 0 0.00</span> -<span class="co">## 25 m1 1 4.84</span> -<span class="co">## 26 m1 1 5.64</span> -<span class="co">## 27 m1 3 12.91</span> -<span class="co">## 28 m1 3 12.96</span> -<span class="co">## 29 m1 7 22.97</span> -<span class="co">## 30 m1 7 24.47</span> -<span class="co">## 31 m1 14 41.69</span> -<span class="co">## 32 m1 14 33.21</span> -<span class="co">## 33 m1 21 44.37</span> -<span class="co">## 34 m1 21 46.44</span> -<span class="co">## 35 m1 35 41.22</span> -<span class="co">## 36 m1 35 37.95</span> -<span class="co">## 37 m1 50 41.19</span> -<span class="co">## 38 m1 50 40.01</span> -<span class="co">## 39 m1 75 40.09</span> -<span class="co">## 40 m1 75 33.85</span> -<span class="co">## 41 m1 100 31.04</span> -<span class="co">## 42 m1 100 33.13</span> -<span class="co">## 43 m1 120 25.15</span> -<span class="co">## 44 m1 120 33.31</span></code></pre> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## name time value</span></span> +<span><span class="co">## 1 parent 0 99.46</span></span> +<span><span class="co">## 2 parent 0 102.04</span></span> +<span><span class="co">## 3 parent 1 93.50</span></span> +<span><span class="co">## 4 parent 1 92.50</span></span> +<span><span class="co">## 5 parent 3 63.23</span></span> +<span><span class="co">## 6 parent 3 68.99</span></span> +<span><span class="co">## 7 parent 7 52.32</span></span> +<span><span class="co">## 8 parent 7 55.13</span></span> +<span><span class="co">## 9 parent 14 27.27</span></span> +<span><span class="co">## 10 parent 14 26.64</span></span> +<span><span class="co">## 11 parent 21 11.50</span></span> +<span><span class="co">## 12 parent 21 11.64</span></span> +<span><span class="co">## 13 parent 35 2.85</span></span> +<span><span class="co">## 14 parent 35 2.91</span></span> +<span><span class="co">## 15 parent 50 0.69</span></span> +<span><span class="co">## 16 parent 50 0.63</span></span> +<span><span class="co">## 17 parent 75 0.05</span></span> +<span><span class="co">## 18 parent 75 0.06</span></span> +<span><span class="co">## 19 parent 100 NA</span></span> +<span><span class="co">## 20 parent 100 NA</span></span> +<span><span class="co">## 21 parent 120 NA</span></span> +<span><span class="co">## 22 parent 120 NA</span></span> +<span><span class="co">## 23 m1 0 0.00</span></span> +<span><span class="co">## 24 m1 0 0.00</span></span> +<span><span class="co">## 25 m1 1 4.84</span></span> +<span><span class="co">## 26 m1 1 5.64</span></span> +<span><span class="co">## 27 m1 3 12.91</span></span> +<span><span class="co">## 28 m1 3 12.96</span></span> +<span><span class="co">## 29 m1 7 22.97</span></span> +<span><span class="co">## 30 m1 7 24.47</span></span> +<span><span class="co">## 31 m1 14 41.69</span></span> +<span><span class="co">## 32 m1 14 33.21</span></span> +<span><span class="co">## 33 m1 21 44.37</span></span> +<span><span class="co">## 34 m1 21 46.44</span></span> +<span><span class="co">## 35 m1 35 41.22</span></span> +<span><span class="co">## 36 m1 35 37.95</span></span> +<span><span class="co">## 37 m1 50 41.19</span></span> +<span><span class="co">## 38 m1 50 40.01</span></span> +<span><span class="co">## 39 m1 75 40.09</span></span> +<span><span class="co">## 40 m1 75 33.85</span></span> +<span><span class="co">## 41 m1 100 31.04</span></span> +<span><span class="co">## 42 m1 100 33.13</span></span> +<span><span class="co">## 43 m1 120 25.15</span></span> +<span><span class="co">## 44 m1 120 33.31</span></span></code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## parent </span> -<span class="co">## "d_parent = - k_parent * parent" </span> -<span class="co">## m1 </span> -<span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## parent </span></span> +<span><span class="co">## "d_parent = - k_parent * parent" </span></span> +<span><span class="co">## m1 </span></span> +<span><span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></span></code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span> -<span class="co">## of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span></span> +<span><span class="co">## of zero were removed from the data</span></span></code></pre> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.2.0 </span> -<span class="co">## Date of fit: Wed May 18 20:42:29 2022 </span> -<span class="co">## Date of summary: Wed May 18 20:42:30 2022 </span> -<span class="co">## </span> -<span class="co">## Equations:</span> -<span class="co">## d_parent/dt = - k_parent * parent</span> -<span class="co">## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span> -<span class="co">## </span> -<span class="co">## Model predictions using solution type analytical </span> -<span class="co">## </span> -<span class="co">## Fitted using 401 model solutions performed in 0.144 s</span> -<span class="co">## </span> -<span class="co">## Error model: Constant variance </span> -<span class="co">## </span> -<span class="co">## Error model algorithm: OLS </span> -<span class="co">## </span> -<span class="co">## Starting values for parameters to be optimised:</span> -<span class="co">## value type</span> -<span class="co">## parent_0 100.7500 state</span> -<span class="co">## k_parent 0.1000 deparm</span> -<span class="co">## k_m1 0.1001 deparm</span> -<span class="co">## f_parent_to_m1 0.5000 deparm</span> -<span class="co">## </span> -<span class="co">## Starting values for the transformed parameters actually optimised:</span> -<span class="co">## value lower upper</span> -<span class="co">## parent_0 100.750000 -Inf Inf</span> -<span class="co">## log_k_parent -2.302585 -Inf Inf</span> -<span class="co">## log_k_m1 -2.301586 -Inf Inf</span> -<span class="co">## f_parent_qlogis 0.000000 -Inf Inf</span> -<span class="co">## </span> -<span class="co">## Fixed parameter values:</span> -<span class="co">## value type</span> -<span class="co">## m1_0 0 state</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## Warning(s): </span> -<span class="co">## Observations with value of zero were removed from the data</span> -<span class="co">## </span> -<span class="co">## Results:</span> -<span class="co">## </span> -<span class="co">## AIC BIC logLik</span> -<span class="co">## 204.4486 212.6365 -97.22429</span> -<span class="co">## </span> -<span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span> -<span class="co">## Estimate Std. Error Lower Upper</span> -<span class="co">## parent_0 99.60000 1.57000 96.4000 102.8000</span> -<span class="co">## log_k_parent -2.31600 0.04087 -2.3990 -2.2330</span> -<span class="co">## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770</span> -<span class="co">## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395</span> -<span class="co">## sigma 3.12600 0.35850 2.3960 3.8550</span> -<span class="co">## </span> -<span class="co">## Parameter correlation:</span> -<span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span> -<span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.174e-06</span> -<span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.492e-07</span> -<span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.220e-07</span> -<span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.307e-06</span> -<span class="co">## sigma -1.174e-06 -8.492e-07 8.220e-07 1.307e-06 1.000e+00</span> -<span class="co">## </span> -<span class="co">## Backtransformed parameters:</span> -<span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> -<span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span> -<span class="co">## for estimators of untransformed parameters.</span> -<span class="co">## Estimate t value Pr(>t) Lower Upper</span> -<span class="co">## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02</span> -<span class="co">## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01</span> -<span class="co">## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03</span> -<span class="co">## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01</span> -<span class="co">## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00</span> -<span class="co">## </span> -<span class="co">## FOCUS Chi2 error levels in percent:</span> -<span class="co">## err.min n.optim df</span> -<span class="co">## All data 6.398 4 15</span> -<span class="co">## parent 6.459 2 7</span> -<span class="co">## m1 4.690 2 8</span> -<span class="co">## </span> -<span class="co">## Resulting formation fractions:</span> -<span class="co">## ff</span> -<span class="co">## parent_m1 0.5145</span> -<span class="co">## parent_sink 0.4855</span> -<span class="co">## </span> -<span class="co">## Estimated disappearance times:</span> -<span class="co">## DT50 DT90</span> -<span class="co">## parent 7.023 23.33</span> -<span class="co">## m1 131.761 437.70</span> -<span class="co">## </span> -<span class="co">## Data:</span> -<span class="co">## time variable observed predicted residual</span> -<span class="co">## 0 parent 99.46 99.59848 -1.385e-01</span> -<span class="co">## 0 parent 102.04 99.59848 2.442e+00</span> -<span class="co">## 1 parent 93.50 90.23787 3.262e+00</span> -<span class="co">## 1 parent 92.50 90.23787 2.262e+00</span> -<span class="co">## 3 parent 63.23 74.07319 -1.084e+01</span> -<span class="co">## 3 parent 68.99 74.07319 -5.083e+00</span> -<span class="co">## 7 parent 52.32 49.91207 2.408e+00</span> -<span class="co">## 7 parent 55.13 49.91207 5.218e+00</span> -<span class="co">## 14 parent 27.27 25.01258 2.257e+00</span> -<span class="co">## 14 parent 26.64 25.01258 1.627e+00</span> -<span class="co">## 21 parent 11.50 12.53462 -1.035e+00</span> -<span class="co">## 21 parent 11.64 12.53462 -8.946e-01</span> -<span class="co">## 35 parent 2.85 3.14787 -2.979e-01</span> -<span class="co">## 35 parent 2.91 3.14787 -2.379e-01</span> -<span class="co">## 50 parent 0.69 0.71624 -2.624e-02</span> -<span class="co">## 50 parent 0.63 0.71624 -8.624e-02</span> -<span class="co">## 75 parent 0.05 0.06074 -1.074e-02</span> -<span class="co">## 75 parent 0.06 0.06074 -7.382e-04</span> -<span class="co">## 1 m1 4.84 4.80296 3.704e-02</span> -<span class="co">## 1 m1 5.64 4.80296 8.370e-01</span> -<span class="co">## 3 m1 12.91 13.02400 -1.140e-01</span> -<span class="co">## 3 m1 12.96 13.02400 -6.400e-02</span> -<span class="co">## 7 m1 22.97 25.04476 -2.075e+00</span> -<span class="co">## 7 m1 24.47 25.04476 -5.748e-01</span> -<span class="co">## 14 m1 41.69 36.69003 5.000e+00</span> -<span class="co">## 14 m1 33.21 36.69003 -3.480e+00</span> -<span class="co">## 21 m1 44.37 41.65310 2.717e+00</span> -<span class="co">## 21 m1 46.44 41.65310 4.787e+00</span> -<span class="co">## 35 m1 41.22 43.31313 -2.093e+00</span> -<span class="co">## 35 m1 37.95 43.31313 -5.363e+00</span> -<span class="co">## 50 m1 41.19 41.21832 -2.832e-02</span> -<span class="co">## 50 m1 40.01 41.21832 -1.208e+00</span> -<span class="co">## 75 m1 40.09 36.44704 3.643e+00</span> -<span class="co">## 75 m1 33.85 36.44704 -2.597e+00</span> -<span class="co">## 100 m1 31.04 31.98162 -9.416e-01</span> -<span class="co">## 100 m1 33.13 31.98162 1.148e+00</span> -<span class="co">## 120 m1 25.15 28.78984 -3.640e+00</span> -<span class="co">## 120 m1 33.31 28.78984 4.520e+00</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:21 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:21 2022 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Equations:</span></span> +<span><span class="co">## d_parent/dt = - k_parent * parent</span></span> +<span><span class="co">## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Model predictions using solution type analytical </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.154 s</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Error model: Constant variance </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Error model algorithm: OLS </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Starting values for parameters to be optimised:</span></span> +<span><span class="co">## value type</span></span> +<span><span class="co">## parent_0 100.7500 state</span></span> +<span><span class="co">## k_parent 0.1000 deparm</span></span> +<span><span class="co">## k_m1 0.1001 deparm</span></span> +<span><span class="co">## f_parent_to_m1 0.5000 deparm</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Starting values for the transformed parameters actually optimised:</span></span> +<span><span class="co">## value lower upper</span></span> +<span><span class="co">## parent_0 100.750000 -Inf Inf</span></span> +<span><span class="co">## log_k_parent -2.302585 -Inf Inf</span></span> +<span><span class="co">## log_k_m1 -2.301586 -Inf Inf</span></span> +<span><span class="co">## f_parent_qlogis 0.000000 -Inf Inf</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Fixed parameter values:</span></span> +<span><span class="co">## value type</span></span> +<span><span class="co">## m1_0 0 state</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Warning(s): </span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Results:</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## AIC BIC logLik</span></span> +<span><span class="co">## 204.4486 212.6365 -97.22429</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> +<span><span class="co">## Estimate Std. Error Lower Upper</span></span> +<span><span class="co">## parent_0 99.60000 1.57000 96.4000 102.8000</span></span> +<span><span class="co">## log_k_parent -2.31600 0.04087 -2.3990 -2.2330</span></span> +<span><span class="co">## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770</span></span> +<span><span class="co">## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395</span></span> +<span><span class="co">## sigma 3.12600 0.35850 2.3960 3.8550</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameter correlation:</span></span> +<span><span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span></span> +<span><span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06</span></span> +<span><span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07</span></span> +<span><span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07</span></span> +<span><span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06</span></span> +<span><span class="co">## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Backtransformed parameters:</span></span> +<span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> +<span><span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span></span> +<span><span class="co">## for estimators of untransformed parameters.</span></span> +<span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02</span></span> +<span><span class="co">## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01</span></span> +<span><span class="co">## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03</span></span> +<span><span class="co">## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01</span></span> +<span><span class="co">## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## FOCUS Chi2 error levels in percent:</span></span> +<span><span class="co">## err.min n.optim df</span></span> +<span><span class="co">## All data 6.398 4 15</span></span> +<span><span class="co">## parent 6.459 2 7</span></span> +<span><span class="co">## m1 4.690 2 8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Resulting formation fractions:</span></span> +<span><span class="co">## ff</span></span> +<span><span class="co">## parent_m1 0.5145</span></span> +<span><span class="co">## parent_sink 0.4855</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Estimated disappearance times:</span></span> +<span><span class="co">## DT50 DT90</span></span> +<span><span class="co">## parent 7.023 23.33</span></span> +<span><span class="co">## m1 131.761 437.70</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Data:</span></span> +<span><span class="co">## time variable observed predicted residual</span></span> +<span><span class="co">## 0 parent 99.46 99.59848 -1.385e-01</span></span> +<span><span class="co">## 0 parent 102.04 99.59848 2.442e+00</span></span> +<span><span class="co">## 1 parent 93.50 90.23787 3.262e+00</span></span> +<span><span class="co">## 1 parent 92.50 90.23787 2.262e+00</span></span> +<span><span class="co">## 3 parent 63.23 74.07319 -1.084e+01</span></span> +<span><span class="co">## 3 parent 68.99 74.07319 -5.083e+00</span></span> +<span><span class="co">## 7 parent 52.32 49.91207 2.408e+00</span></span> +<span><span class="co">## 7 parent 55.13 49.91207 5.218e+00</span></span> +<span><span class="co">## 14 parent 27.27 25.01258 2.257e+00</span></span> +<span><span class="co">## 14 parent 26.64 25.01258 1.627e+00</span></span> +<span><span class="co">## 21 parent 11.50 12.53462 -1.035e+00</span></span> +<span><span class="co">## 21 parent 11.64 12.53462 -8.946e-01</span></span> +<span><span class="co">## 35 parent 2.85 3.14787 -2.979e-01</span></span> +<span><span class="co">## 35 parent 2.91 3.14787 -2.379e-01</span></span> +<span><span class="co">## 50 parent 0.69 0.71624 -2.624e-02</span></span> +<span><span class="co">## 50 parent 0.63 0.71624 -8.624e-02</span></span> +<span><span class="co">## 75 parent 0.05 0.06074 -1.074e-02</span></span> +<span><span class="co">## 75 parent 0.06 0.06074 -7.382e-04</span></span> +<span><span class="co">## 1 m1 4.84 4.80296 3.704e-02</span></span> +<span><span class="co">## 1 m1 5.64 4.80296 8.370e-01</span></span> +<span><span class="co">## 3 m1 12.91 13.02400 -1.140e-01</span></span> +<span><span class="co">## 3 m1 12.96 13.02400 -6.400e-02</span></span> +<span><span class="co">## 7 m1 22.97 25.04476 -2.075e+00</span></span> +<span><span class="co">## 7 m1 24.47 25.04476 -5.748e-01</span></span> +<span><span class="co">## 14 m1 41.69 36.69003 5.000e+00</span></span> +<span><span class="co">## 14 m1 33.21 36.69003 -3.480e+00</span></span> +<span><span class="co">## 21 m1 44.37 41.65310 2.717e+00</span></span> +<span><span class="co">## 21 m1 46.44 41.65310 4.787e+00</span></span> +<span><span class="co">## 35 m1 41.22 43.31313 -2.093e+00</span></span> +<span><span class="co">## 35 m1 37.95 43.31313 -5.363e+00</span></span> +<span><span class="co">## 50 m1 41.19 41.21832 -2.832e-02</span></span> +<span><span class="co">## 50 m1 40.01 41.21832 -1.208e+00</span></span> +<span><span class="co">## 75 m1 40.09 36.44704 3.643e+00</span></span> +<span><span class="co">## 75 m1 33.85 36.44704 -2.597e+00</span></span> +<span><span class="co">## 100 m1 31.04 31.98162 -9.416e-01</span></span> +<span><span class="co">## 100 m1 33.13 31.98162 1.148e+00</span></span> +<span><span class="co">## 120 m1 25.15 28.78984 -3.640e+00</span></span> +<span><span class="co">## 120 m1 33.31 28.78984 4.520e+00</span></span></code></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -334,7 +340,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 7d36c77c..f02febc4 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-07-08)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -130,18 +136,18 @@ <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:00 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:00 2022 </span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:25 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:25 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 133 model solutions performed in 0.028 s</span></span> +<span><span class="co">## Fitted using 133 model solutions performed in 0.033 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -173,9 +179,9 @@ <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k_parent sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 6.186e-01 -1.712e-09</span></span> -<span><span class="co">## log_k_parent 6.186e-01 1.000e+00 -3.237e-09</span></span> -<span><span class="co">## sigma -1.712e-09 -3.237e-09 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 6.186e-01 -1.516e-09</span></span> +<span><span class="co">## log_k_parent 6.186e-01 1.000e+00 -3.124e-09</span></span> +<span><span class="co">## sigma -1.516e-09 -3.124e-09 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -217,7 +223,7 @@ <span><span class="co">## 30 parent 4.0 5.251 -1.2513</span></span></code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.SFO</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - SFO"</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.SFO</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - SFO"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> @@ -225,26 +231,29 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">m.L1.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="va">m.L1.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span></code></pre> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> -<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> <span><span class="co">## doubtful</span></span></code></pre> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:00 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:00 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:25 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:25 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 357 model solutions performed in 0.07 s</span></span> +<span><span class="co">## Fitted using 369 model solutions performed in 0.08 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -265,34 +274,39 @@ <span><span class="co">## Fixed parameter values:</span></span> <span><span class="co">## None</span></span> <span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Warning(s): </span></span> +<span><span class="co">## Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span> +<span><span class="co">## </span></span> <span><span class="co">## Results:</span></span> <span><span class="co">## </span></span> -<span><span class="co">## AIC BIC logLik</span></span> -<span><span class="co">## 95.88804 99.44953 -43.94402</span></span> +<span><span class="co">## AIC BIC logLik</span></span> +<span><span class="co">## 95.88781 99.44929 -43.9439</span></span> <span><span class="co">## </span></span> <span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> <span><span class="co">## Estimate Std. Error Lower Upper</span></span> <span><span class="co">## parent_0 92.47 1.2820 89.720 95.220</span></span> -<span><span class="co">## log_alpha 11.37 NaN NaN NaN</span></span> -<span><span class="co">## log_beta 13.72 NaN NaN NaN</span></span> -<span><span class="co">## sigma 2.78 0.4621 1.789 3.771</span></span> +<span><span class="co">## log_alpha 13.78 NaN NaN NaN</span></span> +<span><span class="co">## log_beta 16.13 NaN NaN NaN</span></span> +<span><span class="co">## sigma 2.78 0.4598 1.794 3.766</span></span> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.0000000 NaN NaN 0.0005548</span></span> +<span><span class="co">## parent_0 1.0000000 NaN NaN 0.0001671</span></span> <span><span class="co">## log_alpha NaN 1 NaN NaN</span></span> <span><span class="co">## log_beta NaN NaN 1 NaN</span></span> -<span><span class="co">## sigma 0.0005548 NaN NaN 1.0000000</span></span> +<span><span class="co">## sigma 0.0001671 NaN NaN 1.0000000</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> <span><span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span></span> <span><span class="co">## for estimators of untransformed parameters.</span></span> <span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 92.47 NA NA 89.720 95.220</span></span> -<span><span class="co">## alpha 87110.00 NA NA NA NA</span></span> -<span><span class="co">## beta 911100.00 NA NA NA NA</span></span> -<span><span class="co">## sigma 2.78 NA NA 1.789 3.771</span></span> +<span><span class="co">## parent_0 9.247e+01 NA NA 89.720 95.220</span></span> +<span><span class="co">## alpha 9.658e+05 NA NA NA NA</span></span> +<span><span class="co">## beta 1.010e+07 NA NA NA NA</span></span> +<span><span class="co">## sigma 2.780e+00 NA NA 1.794 3.766</span></span> <span><span class="co">## </span></span> <span><span class="co">## FOCUS Chi2 error levels in percent:</span></span> <span><span class="co">## err.min n.optim df</span></span> @@ -300,8 +314,8 @@ <span><span class="co">## parent 3.619 3 6</span></span> <span><span class="co">## </span></span> <span><span class="co">## Estimated disappearance times:</span></span> -<span><span class="co">## DT50 DT90 DT50back</span></span> -<span><span class="co">## parent 7.249 24.08 7.249</span></span></code></pre> +<span><span class="co">## DT50 DT90 DT50back</span></span> +<span><span class="co">## parent 7.25 24.08 7.25</span></span></code></pre> <p>We get a warning that the default optimisation algorithm <code>Port</code> did not converge, which is an indication that the model is overparameterised, <em>i.e.</em> contains too many parameters that are ill-defined as a consequence.</p> <p>And in fact, due to the higher number of parameters, and the lower number of degrees of freedom of the fit, the <span class="math inline">\(\chi^2\)</span> error level is actually higher for the FOMC model (3.6%) than for the SFO model (3.4%). Additionally, the parameters <code>log_alpha</code> and <code>log_beta</code> internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of <code>alpha</code> and <code>beta</code>. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of <code>log_alpha</code> and <code>log_beta</code> is 1.000, clearly indicating that the model is overparameterised.</p> <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke 2014)</span>.</p> @@ -310,7 +324,7 @@ <h2 id="laboratory-data-l2">Laboratory Data L2<a class="anchor" aria-label="anchor" href="#laboratory-data-l2"></a> </h2> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> -<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">FOCUS_2006_L2</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>,</span> <span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>,</span> @@ -321,9 +335,9 @@ <h3 id="sfo-fit-for-l2">SFO fit for L2<a class="anchor" aria-label="anchor" href="#sfo-fit-for-l2"></a> </h3> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> -<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - SFO"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> @@ -334,24 +348,24 @@ <h3 id="fomc-fit-for-l2">FOMC fit for L2<a class="anchor" aria-label="anchor" href="#fomc-fit-for-l2"></a> </h3> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - FOMC"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:01 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:01 2022 </span></span> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:26 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:26 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 239 model solutions performed in 0.044 s</span></span> +<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -386,10 +400,10 @@ <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.637e-09</span></span> -<span><span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07</span></span> -<span><span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.387e-07</span></span> -<span><span class="co">## sigma -7.637e-09 -1.617e-07 -1.387e-07 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09</span></span> +<span><span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07</span></span> +<span><span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07</span></span> +<span><span class="co">## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -415,17 +429,17 @@ <h3 id="dfop-fit-for-l2">DFOP fit for L2<a class="anchor" aria-label="anchor" href="#dfop-fit-for-l2"></a> </h3> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.DFOP</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - DFOP"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:01 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:01 2022 </span></span> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:27 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:27 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -434,7 +448,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 581 model solutions performed in 0.119 s</span></span> +<span><span class="co">## Fitted using 581 model solutions performed in 0.128 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -465,18 +479,18 @@ <span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> <span><span class="co">## Estimate Std. Error Lower Upper</span></span> <span><span class="co">## parent_0 93.950 9.998e-01 91.5900 96.3100</span></span> -<span><span class="co">## log_k1 3.113 1.845e+03 -4360.0000 4367.0000</span></span> +<span><span class="co">## log_k1 3.112 1.842e+03 -4353.0000 4359.0000</span></span> <span><span class="co">## log_k2 -1.088 6.285e-02 -1.2370 -0.9394</span></span> <span><span class="co">## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638</span></span> <span><span class="co">## sigma 1.414 2.886e-01 0.7314 2.0960</span></span> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 6.784e-07 -5.188e-10 2.665e-01 -5.800e-10</span></span> -<span><span class="co">## log_k1 6.784e-07 1.000e+00 1.114e-04 -2.191e-04 -1.029e-05</span></span> -<span><span class="co">## log_k2 -5.188e-10 1.114e-04 1.000e+00 -7.903e-01 5.080e-09</span></span> -<span><span class="co">## g_qlogis 2.665e-01 -2.191e-04 -7.903e-01 1.000e+00 -7.991e-09</span></span> -<span><span class="co">## sigma -5.800e-10 -1.029e-05 5.080e-09 -7.991e-09 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10</span></span> +<span><span class="co">## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05</span></span> +<span><span class="co">## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09</span></span> +<span><span class="co">## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09</span></span> +<span><span class="co">## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -484,7 +498,7 @@ <span><span class="co">## for estimators of untransformed parameters.</span></span> <span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100</span></span> -<span><span class="co">## k1 22.4800 5.544e-04 4.998e-01 0.0000 Inf</span></span> +<span><span class="co">## k1 22.4800 5.553e-04 4.998e-01 0.0000 Inf</span></span> <span><span class="co">## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909</span></span> <span><span class="co">## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591</span></span> <span><span class="co">## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960</span></span> @@ -496,7 +510,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Estimated disappearance times:</span></span> <span><span class="co">## DT50 DT90 DT50back DT50_k1 DT50_k2</span></span> -<span><span class="co">## parent 0.5335 5.311 1.599 0.03083 2.058</span></span></code></pre> +<span><span class="co">## parent 0.5335 5.311 1.599 0.03084 2.058</span></span></code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion.</p> </div> </div> @@ -504,7 +518,7 @@ <h2 id="laboratory-data-l3">Laboratory Data L3<a class="anchor" aria-label="anchor" href="#laboratory-data-l3"></a> </h2> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">FOCUS_2006_L3</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>,</span> <span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">97.8</span>, <span class="fl">60</span>, <span class="fl">51</span>, <span class="fl">43</span>, <span class="fl">35</span>, <span class="fl">22</span>, <span class="fl">15</span>, <span class="fl">12</span><span class="op">)</span><span class="op">)</span></span> @@ -513,11 +527,11 @@ <h3 id="fit-multiple-models">Fit multiple models<a class="anchor" aria-label="anchor" href="#fit-multiple-models"></a> </h3> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="co"># Only use one core here, not to offend the CRAN checks</span></span> <span><span class="va">mm.L3</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L3"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L3_mkin</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> @@ -526,12 +540,12 @@ </h3> <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:02 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:02 2022 </span></span> +<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:27 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:28 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -540,7 +554,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 376 model solutions performed in 0.072 s</span></span> +<span><span class="co">## Fitted using 376 model solutions performed in 0.078 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -578,11 +592,11 @@ <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.632e-08</span></span> -<span><span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.145e-07</span></span> -<span><span class="co">## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.021e-06</span></span> -<span><span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.925e-07</span></span> -<span><span class="co">## sigma -9.632e-08 7.145e-07 1.021e-06 -7.925e-07 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08</span></span> +<span><span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07</span></span> +<span><span class="co">## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06</span></span> +<span><span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07</span></span> +<span><span class="co">## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -614,8 +628,8 @@ <span><span class="co">## 60 parent 22.0 23.26 -1.25919</span></span> <span><span class="co">## 91 parent 15.0 15.18 -0.18181</span></span> <span><span class="co">## 120 parent 12.0 10.19 1.81395</span></span></code></pre> -<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> @@ -625,33 +639,33 @@ <h2 id="laboratory-data-l4">Laboratory Data L4<a class="anchor" aria-label="anchor" href="#laboratory-data-l4"></a> </h2> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">FOCUS_2006_L4</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>,</span> <span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span><span class="op">)</span><span class="op">)</span></span> <span><span class="va">FOCUS_2006_L4_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L4</span><span class="op">)</span></span></code></pre></div> <p>Fits of the SFO and FOMC models, plots and summaries are produced below:</p> -<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="co"># Only use one core here, not to offend the CRAN checks</span></span> <span><span class="va">mm.L4</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L4"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L4_mkin</span><span class="op">)</span>,</span> <span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:02 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:02 2022 </span></span> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:28 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:29 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 142 model solutions performed in 0.026 s</span></span> +<span><span class="co">## Fitted using 142 model solutions performed in 0.029 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -683,9 +697,9 @@ <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k_parent sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 5.938e-01 3.440e-07</span></span> -<span><span class="co">## log_k_parent 5.938e-01 1.000e+00 5.885e-07</span></span> -<span><span class="co">## sigma 3.440e-07 5.885e-07 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 5.938e-01 3.387e-07</span></span> +<span><span class="co">## log_k_parent 5.938e-01 1.000e+00 5.830e-07</span></span> +<span><span class="co">## sigma 3.387e-07 5.830e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -704,19 +718,19 @@ <span><span class="co">## Estimated disappearance times:</span></span> <span><span class="co">## DT50 DT90</span></span> <span><span class="co">## parent 106 352</span></span></code></pre> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.1 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Jul 8 17:34:02 2022 </span></span> -<span><span class="co">## Date of summary: Fri Jul 8 17:34:02 2022 </span></span> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.0 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 17 14:04:28 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 17 14:04:29 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 224 model solutions performed in 0.041 s</span></span> +<span><span class="co">## Fitted using 224 model solutions performed in 0.046 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -751,10 +765,10 @@ <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07</span></span> -<span><span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 4.066e-08</span></span> -<span><span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 6.818e-08</span></span> -<span><span class="co">## sigma -2.563e-07 4.066e-08 6.818e-08 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07</span></span> +<span><span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08</span></span> +<span><span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08</span></span> +<span><span class="co">## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -803,7 +817,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex b56e91e1..b6130527 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index c3a39708..292a72a4 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -102,6 +108,10 @@ <dd> </dd><dt><a href="web_only/dimethenamid_2018.html">Example evaluations of the dimethenamid data from 2018</a></dt> <dd> + </dd><dt><a href="web_only/multistart.html">Short demo of the multistart method</a></dt> + <dd> + </dd><dt><a href="web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></dt> + <dd> </dd></dl></div> </div> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index a32f4b41..da499501 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> @@ -120,34 +126,34 @@ </h2> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="co"># Define the kinetic model</span> -<span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>, - M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>, - M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> - - -<span class="co"># Produce model predictions using some arbitrary parameters</span> -<span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span> -<span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, - <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>, - f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>, - f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>, - <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, - <span class="va">sampling_times</span><span class="op">)</span> - -<span class="co"># Generate a dataset by adding normally distributed errors with</span> -<span class="co"># standard deviation 3, for two replicates at each sampling time</span> -<span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>, - sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>, - n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span> - -<span class="co"># Fit the model to the dataset</span> -<span class="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> - -<span class="co"># Plot the results separately for parent and metabolites</span> -<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="co"># Define the kinetic model</span></span> +<span><span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span> +<span> M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> +<span> M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span></span> +<span><span class="co"># Produce model predictions using some arbitrary parameters</span></span> +<span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> +<span><span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>,</span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>,</span> +<span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>,</span> +<span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>,</span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> <span class="va">sampling_times</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># Generate a dataset by adding normally distributed errors with</span></span> +<span><span class="co"># standard deviation 3, for two replicates at each sampling time</span></span> +<span><span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>,</span> +<span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span> +<span></span> +<span><span class="co"># Fit the model to the dataset</span></span> +<span><span class="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># Plot the results separately for parent and metabolites</span></span> +<span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div class="section level2"> @@ -264,7 +270,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex d1e7048d..63246387 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/twa.html b/docs/articles/twa.html index dad8ee44..41340e88 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> @@ -168,7 +174,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 0dafb98a..ea20ecd9 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -120,88 +126,88 @@ </h2> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span> -<span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> - t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>, - <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>, - Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>, - <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>, - <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>, - <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>, - <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span> - -<span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span></span> +<span><span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,</span> +<span> <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,</span> +<span> Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</span> +<span> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</span> +<span> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</span> +<span> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</span> +<span> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> <h2 id="parent-and-one-metabolite">Parent and one metabolite<a class="anchor" aria-label="anchor" href="#parent-and-one-metabolite"></a> </h2> <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span> -<span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span> -<span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span> -<span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span> -<span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span> -<span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span> -<span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span> -<span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span> -<span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span> -<span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span> -<span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span> -<span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span> +<span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span> +<span><span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span></span> +<span><span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></span></code></pre> <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> </div> <div class="section level2"> @@ -209,56 +215,58 @@ </h2> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span> -<span class="co">## Observations with value of zero were removed from the data</span></code></pre> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> +<code class="sourceCode R"><span><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span></code></pre> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span></code></pre> <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 96.838397 1.994270 48.5583 4.0284e-42 92.826435 100.850359</span> -<span class="co">## k_Z0 2.215406 0.118459 18.7018 1.0416e-23 1.989466 2.467005</span> -<span class="co">## k_Z1 0.478300 0.028257 16.9267 6.2409e-22 0.424702 0.538662</span> -<span class="co">## k_Z2 0.451616 0.042137 10.7178 1.6305e-14 0.374328 0.544863</span> -<span class="co">## k_Z3 0.058693 0.015245 3.8499 1.7803e-04 0.034805 0.098976</span> -<span class="co">## f_Z2_to_Z3 0.471509 0.058352 8.0804 9.6622e-11 0.357739 0.588317</span> -<span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></code></pre> -<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## $ff</span> -<span class="co">## Z2_Z3 Z2_sink </span> -<span class="co">## 0.47151 0.52849 </span> -<span class="co">## </span> -<span class="co">## $distimes</span> -<span class="co">## DT50 DT90</span> -<span class="co">## Z0 0.31288 1.0394</span> -<span class="co">## Z1 1.44919 4.8141</span> -<span class="co">## Z2 1.53481 5.0985</span> -<span class="co">## Z3 11.80971 39.2310</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span> +<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span> +<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span> +<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span> +<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span> +<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span> +<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z2_Z3 Z2_sink </span></span> +<span><span class="co">## 0.4715 0.5285 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90</span></span> +<span><span class="co">## Z0 0.31288 1.0394</span></span> +<span><span class="co">## Z1 1.44917 4.8141</span></span> +<span><span class="co">## Z2 1.53478 5.0984</span></span> +<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div class="section level2"> @@ -266,107 +274,105 @@ </h2> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> -<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div> -<pre><code><span class="co">## NULL</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> +<pre><code><span><span class="co">## NULL</span></span></code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span></code></pre> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span> -<span class="co">## data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span></span> +<span><span class="co">## data</span></span></code></pre> <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span> -<span class="co">## the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span></span> +<span><span class="co">## the data</span></span></code></pre> <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>, - k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, - fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span> -<span class="co">## from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,</span> +<span> k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span></span> +<span><span class="co">## from the data</span></span></code></pre> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> <div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> <div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## $ff</span> -<span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span> -<span class="co">## 1.00000 0.53656 0.46344 1.00000 </span> -<span class="co">## </span> -<span class="co">## $SFORB</span> -<span class="co">## Z0_b1 Z0_b2 Z3_b1 Z3_b2 </span> -<span class="co">## 2.4471376 0.0075126 0.0800073 0.0000000 </span> -<span class="co">## </span> -<span class="co">## $distimes</span> -<span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span> -<span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.264 NA NA</span> -<span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span> -<span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span> -<span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span></span> +<span><span class="co">## 1.00000 0.53656 0.46344 1.00000 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $SFORB</span></span> +<span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span> +<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span> +<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span> +<span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span> +<span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span> +<span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> <div class="section level2"> @@ -398,7 +404,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex 229bae82..bc6efaf7 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex e13ad9aa..55c1b645 100644 --- 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a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex 77965455..d95cac25 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex 250d0df5..cb333a1c 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 5a01c03e..db807f14 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index df1e06db..b8ec5059 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -128,205 +134,205 @@ <h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a> </h3> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 465.21753 56.27506 32.06401 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 64.4304</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span> -<span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span> -<span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> -<span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> -<span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> -<span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> -<span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span> -<span class="co">## k2 2.95e-12 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span> -<span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 67.7 2.25e+02 6.77e+01</span> -<span class="co">## IORE 58.2 1.07e+03 3.22e+02</span> -<span class="co">## DFOP 55.5 4.28e+11 2.35e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 321.51</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 465.21753 56.27506 32.06401 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 64.4304</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span></span> +<span><span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span></span> +<span><span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span></span> +<span><span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span></span> +<span><span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> +<span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> +<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> +<span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> +<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> +<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 321.51</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a> </h3> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 94.81123 10.10936 7.55871 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 11.77879</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span> -<span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span> -<span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span> -<span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span> -<span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span> -<span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span> -<span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span> -<span class="co">## k2 9.41e-12 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span> -<span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 86.6 2.88e+02 8.66e+01</span> -<span class="co">## IORE 85.5 7.17e+02 2.16e+02</span> -<span class="co">## DFOP 83.6 1.21e+11 7.36e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 215.87</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 94.81123 10.10936 7.55871 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 11.77879</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span></span> +<span><span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span></span> +<span><span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span> +<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span> +<span><span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span> +<span><span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> +<span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> +<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> +<span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> +<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> +<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 215.87</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a> </h3> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 188.45361 51.00699 42.46931 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 58.39888</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span> -<span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span> -<span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span> -<span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span> -<span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span> -<span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span> -<span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span> -<span class="co">## k2 4.40e-11 5.00e-01 0.0000 Inf</span> -<span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span> -<span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 38.6 1.28e+02 3.86e+01</span> -<span class="co">## IORE 34.0 1.77e+02 5.32e+01</span> -<span class="co">## DFOP 34.1 7.43e+09 1.58e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 53.17</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 188.45361 51.00699 42.46931 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 58.39888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span></span> +<span><span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span></span> +<span><span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span></span> +<span><span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span></span> +<span><span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span></span> +<span><span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> +<span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> +<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> +<span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> +<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> +<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 53.17</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a> </h3> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 3661.661 3195.030 3174.145 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 3334.194</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span> -<span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span> -<span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span> -<span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span> -<span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span> -<span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span> -<span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span> -<span class="co">## k2 2.81e-10 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span> -<span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 94.3 3.13e+02 9.43e+01</span> -<span class="co">## IORE 96.7 1.51e+03 4.55e+02</span> -<span class="co">## DFOP 96.4 4.87e+09 2.46e+09</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 454.55</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3661.661 3195.030 3174.145 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 3334.194</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span> +<span><span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span></span> +<span><span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span></span> +<span><span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span></span> +<span><span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span></span> +<span><span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> +<span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> +<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> +<span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> +<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> +<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 454.55</span></span></code></pre> </div> </div> <div class="section level2"> @@ -337,52 +343,52 @@ </h3> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 1996.9408 444.9237 547.5616 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 477.4924</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span> -<span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span> -<span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span> -<span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span> -<span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span> -<span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span> -<span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span> -<span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span> -<span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span> -<span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 86.3 287 86.3</span> -<span class="co">## IORE 53.4 668 201.0</span> -<span class="co">## DFOP 55.6 517 253.0</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 201.03</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 1996.9408 444.9237 547.5616 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 477.4924</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span> +<span><span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span></span> +<span><span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span> +<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span> +<span><span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span> +<span><span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span> +<span><span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span></span> +<span><span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span></span> +<span><span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span></span> +<span><span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.3 287 86.3</span></span> +<span><span class="co">## IORE 53.4 668 201.0</span></span> +<span><span class="co">## DFOP 55.6 517 253.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 201.03</span></span></code></pre> </div> </div> <div class="section level2"> @@ -392,160 +398,165 @@ <h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a> </h3> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> <div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 839.35238 88.57064 9.93363 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 105.5678</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span> -<span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span> -<span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span> -<span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span> -<span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span> -<span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span> -<span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span> -<span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span> -<span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span> -<span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 16.9 5.63e+01 1.69e+01</span> -<span class="co">## IORE 11.6 3.37e+02 1.01e+02</span> -<span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 101.43</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 839.35238 88.57064 9.93363 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 105.5678</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span></span> +<span><span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span></span> +<span><span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span> +<span><span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span> +<span><span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span> +<span><span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span></span> +<span><span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span></span> +<span><span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span></span> +<span><span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> +<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 101.43</span></span></code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> <div class="section level3"> <h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a> </h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 35.64867 23.22334 35.64867 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 28.54188</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span> -<span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span> -<span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span> -<span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span> -<span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span> -<span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span> -<span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span> -<span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span> -<span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span> -<span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 17.8 59.2 17.8</span> -<span class="co">## IORE 18.4 49.2 14.8</span> -<span class="co">## DFOP 17.8 59.2 17.8</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 14.8</span></code></pre> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 35.64867 23.22334 35.64867 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 28.54188</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span></span> +<span><span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span></span> +<span><span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span></span> +<span><span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span></span> +<span><span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span></span> +<span><span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> +<span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> +<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 17.8 59.2 17.8</span></span> +<span><span class="co">## IORE 18.4 49.2 14.8</span></span> +<span><span class="co">## DFOP 17.8 59.2 17.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 14.8</span></span></code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> <div class="section level3"> <h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> </h3> -<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 899.4089 336.4348 899.4089 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 413.4841</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span> -<span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span> -<span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span> -<span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span> -<span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span> -<span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span> -<span class="co">## k1 0.0495 6.32e-03 0.0241 0.1018</span> -<span class="co">## k2 0.0495 2.41e-03 0.0272 0.0901</span> -<span class="co">## g 0.4487 5.00e-01 NA NA</span> -<span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 14.0 46.5 14.00</span> -<span class="co">## IORE 16.4 29.4 8.86</span> -<span class="co">## DFOP 14.0 46.5 14.00</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 8.86</span></code></pre> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 899.4089 336.4348 899.4089 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 413.4841</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span> +<span><span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span></span> +<span><span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span></span> +<span><span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span></span> +<span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> +<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> +<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> +<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 14.0 46.5 14.00</span></span> +<span><span class="co">## IORE 16.4 29.4 8.86</span></span> +<span><span class="co">## DFOP 14.0 46.5 14.00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.86</span></span></code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> @@ -555,53 +566,53 @@ <div class="section level3"> <h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> </h3> -<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> <div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 579.6805 204.7932 144.7783 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 251.6944</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span> -<span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span> -<span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span> -<span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span> -<span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span> -<span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span> -<span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span> -<span class="co">## k2 9.93e-13 5.00e-01 0.0000 Inf</span> -<span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span> -<span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span> -<span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span> -<span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 41148171</span></code></pre> +<code class="sourceCode R"><span><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 579.6805 204.7932 144.7783 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 251.6944</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span> +<span><span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span></span> +<span><span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span></span> +<span><span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span></span> +<span><span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span></span> +<span><span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span></span> +<span><span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span></span> +<span><span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span></span> +<span><span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span></span> +<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span> +<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41148170</span></span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> @@ -612,380 +623,379 @@ <div class="section level3"> <h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> </h3> -<div class="sourceCode" id="cb58"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> -<span class="co">## matrix</span> - -<span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> -<span class="co">## matrix</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 695.4440 220.0685 695.4440 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 270.4679</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span> -<span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span> -<span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.823 NA NA NA</span> -<span class="co">## k__iore_parent 2.436 NA NA NA</span> -<span class="co">## N_parent 0.263 NA NA NA</span> -<span class="co">## sigma 3.965 NA NA NA</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 100.521 NA NA NA</span> -<span class="co">## k1 0.124 NA NA NA</span> -<span class="co">## k2 0.124 NA NA NA</span> -<span class="co">## g 0.793 NA NA NA</span> -<span class="co">## sigma 7.048 NA NA NA</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 5.58 18.5 5.58</span> -<span class="co">## IORE 6.49 13.2 3.99</span> -<span class="co">## DFOP 5.58 18.5 5.58</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 3.99</span></code></pre> +<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 695.4440 220.0685 695.4440 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 270.4679</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span></span> +<span><span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span></span> +<span><span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.823 NA NA NA</span></span> +<span><span class="co">## k__iore_parent 2.436 NA NA NA</span></span> +<span><span class="co">## N_parent 0.263 NA NA NA</span></span> +<span><span class="co">## sigma 3.965 NA NA NA</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> +<span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> +<span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> +<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 5.58 18.5 5.58</span></span> +<span><span class="co">## IORE 6.49 13.2 3.99</span></span> +<span><span class="co">## DFOP 5.58 18.5 5.58</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 3.99</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> </h3> -<div class="sourceCode" id="cb65"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 58.90242 19.06353 58.90242 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 51.51756</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span> -<span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span> -<span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span> -<span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span> -<span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span> -<span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.6840 NaN NaN NaN</span> -<span class="co">## k1 0.0589 NaN NA NA</span> -<span class="co">## k2 0.0589 NaN NA NA</span> -<span class="co">## g 0.6473 NaN NA NA</span> -<span class="co">## sigma 3.4323 NaN NaN NaN</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 11.8 39.1 11.80</span> -<span class="co">## IORE 12.9 31.4 9.46</span> -<span class="co">## DFOP 11.8 39.1 11.80</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 9.46</span></code></pre> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 58.90242 19.06353 58.90242 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 51.51756</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span></span> +<span><span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span></span> +<span><span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span></span> +<span><span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span></span> +<span><span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span></span> +<span><span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 NaN NaN NaN</span></span> +<span><span class="co">## k1 0.0589 NaN NA NA</span></span> +<span><span class="co">## k2 0.0589 NaN NA NA</span></span> +<span><span class="co">## g 0.6473 NaN NA NA</span></span> +<span><span class="co">## sigma 3.4323 NaN NaN NaN</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 11.8 39.1 11.80</span></span> +<span><span class="co">## IORE 12.9 31.4 9.46</span></span> +<span><span class="co">## DFOP 11.8 39.1 11.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 9.46</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 174.5971 142.3951 174.5971 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 172.131</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span> -<span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span> -<span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span> -<span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span> -<span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span> -<span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span> -<span class="co">## k1 0.00258 NA 4.24e-04 0.01573</span> -<span class="co">## k2 0.00258 NA 1.76e-03 0.00379</span> -<span class="co">## g 0.16452 NA NA NA</span> -<span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 269 892 269</span> -<span class="co">## IORE 261 560 169</span> -<span class="co">## DFOP 269 892 269</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 168.51</span></code></pre> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 174.5971 142.3951 174.5971 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 172.131</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span> +<span><span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span></span> +<span><span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span></span> +<span><span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span></span> +<span><span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span></span> +<span><span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> +<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> +<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> +<span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 269 892 269</span></span> +<span><span class="co">## IORE 261 560 169</span></span> +<span><span class="co">## DFOP 269 892 269</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 168.51</span></span></code></pre> </div> </div> <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 48.43249 28.67746 27.26248 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 32.83337</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span> -<span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span> -<span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.00e+02 NA NaN NaN</span> -<span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span> -<span class="co">## N_parent 3.31e+00 NA NaN NaN</span> -<span class="co">## sigma 1.20e+00 NA 0.796 1.6</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span> -<span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span> -<span class="co">## k2 5.03e-12 5.00e-01 0.00000 Inf</span> -<span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span> -<span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span> -<span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span> -<span class="co">## DFOP 3.69e+10 3.57e+11 1.38e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 6697.44</span></code></pre> +<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 48.43249 28.67746 27.26248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 32.83337</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span> +<span><span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span></span> +<span><span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 NA NaN NaN</span></span> +<span><span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span></span> +<span><span class="co">## N_parent 3.31e+00 NA NaN NaN</span></span> +<span><span class="co">## sigma 1.20e+00 NA 0.796 1.6</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> +<span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> +<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> +<span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> +<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> +<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 6697.44</span></span></code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> <div class="section level2"> <h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> </h2> -<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 245.5248 135.0132 245.5248 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 165.9335</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span> -<span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span> -<span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span> -<span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span> -<span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span> -<span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span> -<span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span> -<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span> -<span class="co">## g 0.21241 5.00e-01 NA NA</span> -<span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 72.8 242 72.8</span> -<span class="co">## IORE 76.3 137 41.3</span> -<span class="co">## DFOP 72.8 242 72.8</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 41.33</span></code></pre> +<code class="sourceCode R"><span><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 245.5248 135.0132 245.5248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 165.9335</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span> +<span><span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span></span> +<span><span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span></span> +<span><span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span></span> +<span><span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span></span> +<span><span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> +<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 72.8 242 72.8</span></span> +<span><span class="co">## IORE 76.3 137 41.3</span></span> +<span><span class="co">## DFOP 72.8 242 72.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41.33</span></span></code></pre> <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 106.91629 68.55574 106.91629 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 84.25618</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span> -<span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span> -<span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span> -<span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span> -<span class="co">## N_parent 0.00 5.00e-01 -1.07695 1.08</span> -<span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span> -<span class="co">## k1 4.86e-03 NA 8.62e-04 2.74e-02</span> -<span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span> -<span class="co">## g 1.88e-01 NA 0.00e+00 1.00e+00</span> -<span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 143 474 143.0</span> -<span class="co">## IORE 131 236 71.2</span> -<span class="co">## DFOP 143 474 143.0</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 71.18</span></code></pre> +<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 106.91629 68.55574 106.91629 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 84.25618</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span> +<span><span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span></span> +<span><span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> +<span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> +<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> +<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 143 474 143.0</span></span> +<span><span class="co">## IORE 131 236 71.2</span></span> +<span><span class="co">## DFOP 143 474 143.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 71.18</span></span></code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> <div class="section level2"> <h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> </h2> -<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></code></pre> -<pre><code><span class="co">## to the terminal degradation rate found with the DFOP model.</span></code></pre> -<pre><code><span class="co">## The representative half-life obtained from the DFOP model may be used</span></code></pre> -<div class="sourceCode" id="cb112"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> <div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 3831.804 2062.008 1550.980 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 2247.348</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span> -<span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span> -<span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span> -<span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span> -<span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span> -<span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span> -<span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span> -<span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span> -<span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span> -<span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 4.35 14.4 4.35</span> -<span class="co">## IORE 1.48 32.1 9.67</span> -<span class="co">## DFOP 0.67 21.4 8.93</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 8.93</span></code></pre> +<code class="sourceCode R"><span><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> +<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> +<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> +<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3831.804 2062.008 1550.980 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 2247.348</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span></span> +<span><span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span></span> +<span><span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span></span> +<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span></span> +<span><span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span></span> +<span><span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span></span> +<span><span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span></span> +<span><span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span></span> +<span><span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 4.35 14.4 4.35</span></span> +<span><span class="co">## IORE 1.48 32.1 9.67</span></span> +<span><span class="co">## DFOP 0.67 21.4 8.93</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.93</span></span></code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> <div class="section level2"> @@ -1022,7 +1032,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex a53c48b2..75611a70 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png Binary files differindex fb211a8e..b6faeff9 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png Binary files differindex 9aedbf16..6b9ba98c 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png Binary files differindex 034eed46..db90244b 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png Binary files differindex 86cd9755..a33372e8 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png Binary files differindex 10225504..d64ea98d 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 0b14fea2..64c68ea0 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-07-22)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -149,7 +155,7 @@ <span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> <span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, <span class="co"># erroneously used FOMC twice, not fixed for consistency</span></span> <span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> <span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>,</span> @@ -336,8 +342,16 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.962</td> -<td align="right">3.606</td> +<td align="right">1.957</td> +<td align="right">3.633</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">2.140</td> +<td align="right">3.774</td> </tr> </tbody> </table> @@ -506,9 +520,18 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.465</td> -<td align="right">6.184</td> -<td align="right">2.752</td> +<td align="right">1.503</td> +<td align="right">6.147</td> +<td align="right">2.803</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.554</td> +<td align="right">6.193</td> +<td align="right">2.843</td> </tr> </tbody> </table> @@ -728,12 +751,24 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">0.857</td> -<td align="right">1.298</td> -<td align="right">1.504</td> +<td align="right">0.861</td> +<td align="right">1.295</td> +<td align="right">1.507</td> +<td align="right">3.102</td> +<td align="right">1.961</td> +<td align="right">2.852</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.913</td> +<td align="right">1.345</td> +<td align="right">1.539</td> <td align="right">3.011</td> -<td align="right">1.888</td> -<td align="right">2.756</td> +<td align="right">1.987</td> +<td align="right">2.802</td> </tr> </tbody> </table> @@ -758,7 +793,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 0b78bb2e..d17d7aeb 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2022-10-29</h4> + <h4 data-toc-skip class="date">2022-11-17</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -163,10 +169,10 @@ <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.188</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.628 0.306</span></span> -<span><span class="co">## 2 Eigenvalue based 1 2.064 0.388</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 38.894 7.312</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.218</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.550 0.338</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.950 0.425</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 33.041 7.203</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div class="section level2"> @@ -193,11 +199,11 @@ <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.00 0.441</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 30.68 13.530</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.1.2 on</p> -<pre><code><span><span class="co">## R version 4.2.1 (2022-06-23)</span></span> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.510</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 26.247 13.386</span></span></code></pre> +<p>Here we get a performance benefit of a factor of 26 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 1.2.0 on</p> +<pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> <span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre> <pre><code><span><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></span></code></pre> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index b020a7b0..8c37edd6 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 1 July 2022, built on 08 Jul 2022</h4> + <h4 data-toc-skip class="date">Last change 1 July 2022, built on 17 Nov 2022</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -155,20 +161,20 @@ <span> error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p>The plot of the individual SFO fits shown below suggests that at least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 and log k2, as well as of the logit of the g parameter of the DFOP model). Here, this procedure does not result in parameters that represent the degradation well, because in some datasets the fitted value for k2 is extremely close to zero, leading to a log k2 value that dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual fits enter the population curve with the same weight. This is where nonlinear mixed-effects models can help out by treating all datasets with equally by fitting a parameter distribution model together with the degradation model and the error model (see below).</p> <p>The remaining trend of the residuals to be higher for higher predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by the fact that they did not converge:</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> @@ -178,7 +184,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK OK OK C OK + DFOP OK OK C OK C OK OK: No warnings C: Optimisation did not converge: @@ -222,7 +228,7 @@ f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001 <p>While the SFO variants converge fast, the additional parameters introduced by this lead to convergence warnings for the DFOP model. The model comparison clearly show that adding correlations between random effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -231,41 +237,32 @@ f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001 <p>The saemix package provided the first Open Source implementation of the Stochastic Approximation to the Expectation Maximisation (SAEM) algorithm. SAEM fits of degradation models can be conveniently performed using an interface to the saemix package available in current development versions of the mkin package.</p> <p>The corresponding SAEM fits of the four combinations of degradation and error models are fitted below. As there is no convergence criterion implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.</p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></code></pre></div> -<pre><code>Loading required package: npde</code></pre> -<pre><code>Package saemix, version 3.0 - please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre> -<pre><code> -Attaching package: 'saemix'</code></pre> -<pre><code>The following objects are masked from 'package:npde': - - kurtosis, skewness</code></pre> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> +<span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_10k</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10000</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_const-1.png" width="700"></p> <p>Obviously the selected number of iterations is sufficient to reach convergence. This can also be said for the SFO fit using the two-component error model.</p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -286,23 +283,21 @@ DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 -a.1 1.82141 1.60516 2.0377 -SD.DMTA_0 1.64787 0.45729 2.8384 +a.1 1.82141 1.65974 1.9831 +SD.DMTA_0 1.64787 0.45779 2.8379 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50524 2.5712 -SD.g 1.10266 0.32354 1.8818</code></pre> +SD.k2 0.03296 -2.50143 2.5673 +SD.g 1.10266 0.32371 1.8816</code></pre> <p>While the other parameters converge to credible values, the variance of k2 (<code>omega2.k2</code>) converges to a very small value. The printout of the <code>saem.mmkin</code> model shows that the estimated standard deviation of k2 across the population of soils (<code>SD.k2</code>) is ill-defined, indicating overparameterisation of this model.</p> <p>When the DFOP model is fitted with the two-component error model, we also observe that the estimated variance of k2 becomes very small, while being ill-defined, as illustrated by the excessive confidence interval of <code>SD.k2</code>.</p> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span></code></pre></div> -<pre><code>Likelihood cannot be computed by Importance Sampling.</code></pre> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> +<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> -<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -318,21 +313,21 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - estimate lower upper -DMTA_0 9.82e+01 96.27937 100.1783 -k1 6.41e-02 0.03333 0.0948 -k2 8.56e-03 0.00608 0.0110 -g 9.55e-01 0.91440 0.9947 -a.1 1.07e+00 0.86542 1.2647 -b.1 2.96e-02 0.02258 0.0367 -SD.DMTA_0 2.04e+00 0.40629 3.6678 -SD.k1 5.98e-01 0.25796 0.9373 -SD.k2 5.28e-04 -58.93251 58.9336 -SD.g 1.04e+00 0.36509 1.7083</code></pre> + estimate lower upper +DMTA_0 98.27617 96.3088 100.2436 +k1 0.06437 0.0337 0.0950 +k2 0.00880 0.0063 0.0113 +g 0.95249 0.9100 0.9949 +a.1 1.06161 0.8625 1.2607 +b.1 0.02967 0.0226 0.0367 +SD.DMTA_0 2.06075 0.4187 3.7028 +SD.k1 0.59357 0.2561 0.9310 +SD.k2 0.00292 -10.2960 10.3019 +SD.g 1.05725 0.3808 1.7337</code></pre> <p>Doubling the number of iterations in the first phase of the algorithm leads to a slightly lower likelihood, and therefore to slightly higher AIC and BIC values. With even more iterations, the algorithm stops with an error message. This is related to the variance of k2 approximating zero and has been submitted as a <a href="https://github.com/saemixdevelopment/saemixextension/issues/29" class="external-link">bug to the saemix package</a>, as the algorithm does not converge in this case.</p> <p>An alternative way to fit DFOP in combination with the two-component error model is to use the model formulation with transformed parameters as used per default in mkin. When using this option, convergence is slower, but eventually the algorithm stops as well with the same error message.</p> <p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and the version with increased iterations can be compared using the model comparison function of the saemix package:</p> -<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span></span> <span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> @@ -340,7 +335,7 @@ SD.g 1.04e+00 0.36509 1.7083</code></pre> <span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> <span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></span></code></pre></div> @@ -348,10 +343,10 @@ SD.g 1.04e+00 0.36509 1.7083</code></pre> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.72 663.63 -DFOP tc more iterations NaN NaN</code></pre> +DFOP tc 665.65 663.57 +DFOP tc more iterations 665.88 663.80</code></pre> <p>In order to check the influence of the likelihood calculation algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from the three methods are compared.</p> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span><span class="va">AIC_parent_saemix_methods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> @@ -361,11 +356,11 @@ DFOP tc more iterations NaN NaN</code></pre> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -665.72 665.88 665.15 </code></pre> +665.65 665.68 665.11 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value.</p> <p>In order to illustrate that the comparison of the three method depends on the degree of convergence obtained in the fit, the same comparison is shown below for the fit using the defaults for the number of iterations and the number of MCMC chains.</p> <p>When using OpenBlas for linear algebra, there is a large difference in the values obtained with Gaussian quadrature, so the larger number of iterations makes a lot of difference. When using the LAPACK version coming with Debian Bullseye, the AIC based on Gaussian quadrature is almost the same as the one obtained with the other methods, also when using defaults for the fit.</p> -<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> @@ -376,14 +371,14 @@ DFOP tc more iterations NaN NaN</code></pre> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -668.91 663.61 667.40 </code></pre> +669.77 669.36 670.95 </code></pre> </div> </div> <div class="section level3"> <h3 id="comparison">Comparison<a class="anchor" aria-label="anchor" href="#comparison"></a> </h3> <p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains).</p> -<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="st">"Degradation model"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> @@ -408,7 +403,7 @@ DFOP tc more iterations NaN NaN</code></pre> <td align="left">SFO</td> <td align="left">const</td> <td align="right">796.60</td> -<td align="right">794.17</td> +<td align="right">796.60</td> <td align="right">796.38</td> </tr> <tr class="even"> @@ -422,15 +417,15 @@ DFOP tc more iterations NaN NaN</code></pre> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">704.95</td> +<td align="right">671.98</td> <td align="right">705.75</td> </tr> <tr class="even"> <td align="left">DFOP</td> <td align="left">tc</td> <td align="right">671.91</td> -<td align="right">665.15</td> -<td align="right">665.72</td> +<td align="right">665.11</td> +<td align="right">665.65</td> </tr> </tbody> </table> @@ -445,15 +440,15 @@ DFOP tc more iterations NaN NaN</code></pre> <div class="section level2"> <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h2> -<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.1 (2022-06-23) +<pre><code>R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 11 (bullseye) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.13.so locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -464,28 +459,27 @@ locale: [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: -[1] parallel stats graphics grDevices utils datasets methods -[8] base +[1] stats graphics grDevices utils datasets methods base other attached packages: -[1] nlme_3.1-158 mkin_1.1.1 knitr_1.39 +[1] nlme_3.1-160 mkin_1.2.0 knitr_1.40 loaded via a namespace (and not attached): - [1] deSolve_1.32 zoo_1.8-10 tidyselect_1.1.2 xfun_0.31 - [5] bslib_0.3.1 purrr_0.3.4 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.4.1 generics_0.1.3 htmltools_0.5.2 yaml_2.3.5 -[13] utf8_1.2.2 rlang_1.0.3 pkgdown_2.0.5 saemix_3.0 -[17] jquerylib_0.1.4 pillar_1.7.0 glue_1.6.2 lifecycle_1.0.1 -[21] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 ragg_1.2.2 -[25] memoise_2.0.1 evaluate_0.15 npde_3.2 fastmap_1.1.0 -[29] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.0 -[33] cachem_1.0.6 desc_1.4.1 jsonlite_1.8.0 systemfonts_1.0.4 -[37] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.3.6 -[41] digest_0.6.29 stringi_1.7.6 dplyr_1.0.9 grid_4.2.1 -[45] rprojroot_2.0.3 cli_3.3.0 tools_4.2.1 magrittr_2.0.3 -[49] sass_0.4.1 tibble_3.1.7 crayon_1.5.1 pkgconfig_2.0.3 -[53] ellipsis_0.3.2 rmarkdown_2.14 R6_2.5.1 mclust_5.4.10 -[57] compiler_4.2.1 </code></pre> + [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.33 + [5] bslib_0.4.0 purrr_0.3.5 lattice_0.20-45 colorspace_2.0-3 + [9] vctrs_0.5.0 generics_0.1.3 htmltools_0.5.3 yaml_2.3.6 +[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.6 saemix_3.2 +[17] jquerylib_0.1.4 pillar_1.8.1 glue_1.6.2 DBI_1.1.3 +[21] lifecycle_1.0.3 stringr_1.4.1 munsell_0.5.0 gtable_0.3.1 +[25] ragg_1.2.2 memoise_2.0.1 evaluate_0.18 npde_3.2 +[29] fastmap_1.1.0 lmtest_0.9-40 parallel_4.2.2 fansi_1.0.3 +[33] highr_0.9 scales_1.2.1 cachem_1.0.6 desc_1.4.2 +[37] jsonlite_1.8.3 systemfonts_1.0.4 fs_1.5.2 textshaping_0.3.6 +[41] gridExtra_2.3 ggplot2_3.4.0 digest_0.6.30 stringi_1.7.8 +[45] dplyr_1.0.10 grid_4.2.2 rprojroot_2.0.3 cli_3.4.1 +[49] tools_4.2.2 magrittr_2.0.3 sass_0.4.2 tibble_3.1.8 +[53] pkgconfig_2.0.3 assertthat_0.2.1 rmarkdown_2.16 R6_2.5.1 +[57] mclust_6.0.0 compiler_4.2.2 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -522,7 +516,7 @@ loaded via a namespace (and not attached): <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html new file mode 100644 index 00000000..720c6742 --- /dev/null +++ b/docs/articles/web_only/multistart.html @@ -0,0 +1,200 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<title>Short demo of the multistart method • mkin</title> +<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" 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href="../../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> +<li> + <a href="../../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> +<li> + <a href="../../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with 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href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> + + + + </header><script src="multistart_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <h1 data-toc-skip>Short demo of the multistart method</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + + <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-17)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> + <div class="hidden name"><code>multistart.rmd</code></div> + + </div> + + + +<p>The dimethenamid data from 2018 from seven soils is used as example data in this vignette.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +<p>First, we check the DFOP model with the two-component error model and random effects for all degradation parameters.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<p>We see that not all variability parameters are identifiable. The <code>illparms</code> function tells us that the confidence interval for the standard deviation of ‘log_k2’ includes zero. We check this assessment using multiple runs with different starting values.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p> +<p>This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> +<span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p> +<p>The results confirm that all remaining parameters can be determined with sufficient certainty.</p> +<p>We can also analyse the log-likelihoods obtained in the multiple runs:</p> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/llhist.html">llhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p> +<p>The parameter histograms can be further improved by excluding the result with the low likelihood.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-6-1.png" width="700"></p> +<p>We can use the <code>anova</code> method to compare the models, including a likelihood ratio test if the models are nested.</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85 </span></span> +<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89 0 1 1</span></span></code></pre> +<p>While AIC and BIC are lower for the reduced model, the likelihood ratio test does not indicate a significant difference between the fits.</p> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + </div> + +</div> + + + + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer> +</div> + + + + + + + </body> +</html> diff --git a/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo 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data-toc-skip>Benchmark timings for saem.mmkin</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + + <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-17)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> + <div class="hidden name"><code>saem_benchmarks.rmd</code></div> + + </div> + + + +<p>Each system is characterized by operating system type, CPU type, mkin version, saemix version and R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p> +<p>For the initial mmkin fits, we use all available cores.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<div class="section level2"> +<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> +</h2> +<p>Please refer to the vignette <code>dimethenamid_2018</code> for an explanation of the following preprocessing.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> +</h2> +<div class="section level3"> +<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> +</h3> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">parent_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> +<span><span class="va">parent_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="va">parent_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">sfo_const</td> +<td align="right">5</td> +<td align="right">796.3</td> +<td align="right">795.3</td> +<td align="right">-393.2</td> +</tr> +<tr class="even"> +<td align="left">sfo_tc</td> +<td align="right">6</td> +<td align="right">798.3</td> +<td align="right">797.1</td> +<td align="right">-393.2</td> +</tr> +<tr class="odd"> +<td align="left">dfop_const</td> +<td align="right">9</td> +<td align="right">709.4</td> +<td align="right">707.5</td> +<td align="right">-345.7</td> +</tr> +<tr class="even"> +<td align="left">sforb_const</td> +<td align="right">9</td> +<td align="right">710.0</td> +<td align="right">708.1</td> +<td align="right">-346.0</td> +</tr> +<tr class="odd"> +<td align="left">hs_const</td> +<td align="right">9</td> +<td align="right">713.7</td> +<td align="right">711.8</td> +<td align="right">-347.8</td> +</tr> +<tr class="even"> +<td align="left">dfop_tc</td> +<td align="right">10</td> +<td align="right">669.8</td> +<td align="right">667.7</td> +<td align="right">-324.9</td> +</tr> +<tr class="odd"> +<td align="left">sforb_tc</td> +<td align="right">10</td> +<td align="right">662.8</td> +<td align="right">660.7</td> +<td align="right">-321.4</td> +</tr> +<tr class="even"> +<td align="left">hs_tc</td> +<td align="right">10</td> +<td align="right">667.3</td> +<td align="right">665.2</td> +<td align="right">-323.6</td> +</tr> +</tbody> +</table> +<p>The above model comparison suggests to use the SFORB model with two-component error. For comparison, we keep the DFOP model with two-component error, as it competes with SFORB for biphasic curves.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre> +<p>For these two models, random effects for the transformed parameters <code>k2</code> and <code>k_DMTA_bound_free</code> could not be quantified.</p> +</div> +<div class="section level3"> +<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> +</h3> +<p>We remove parameters that were found to be ill-defined in the parent only fits.</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">one_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> +<span> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">one_met_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">one_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +<div class="section level3"> +<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a> +</h3> +<p>For the case of three metabolites, we only keep the SFORB model in order to limit the time for compiling this vignette, and as fitting in parallel may disturb the benchmark. Again, we do not include random effects that were ill-defined in previous fits of subsets of the degradation model.</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">three_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> +<span> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> M27 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> M31 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">three_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +</div> +<div class="section level2"> +<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> +</h2> +<p>Benchmarks for all available error models are shown. They are intended for improving mkin, not for comparing CPUs or operating systems. All trademarks belong to their respective owners.</p> +<div class="section level3"> +<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> +</h3> +<p>Constant variance for SFO, DFOP, SFORB and HS.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t1</th> +<th align="right">t2</th> +<th align="right">t3</th> +<th align="right">t4</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">2.14</td> +<td align="right">4.626</td> +<td align="right">4.328</td> +<td align="right">4.998</td> +</tr></tbody> +</table> +<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t5</th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">5.678</td> +<td align="right">7.441</td> +<td align="right">8</td> +<td align="right">7.98</td> +</tr></tbody> +</table> +</div> +<div class="section level3"> +<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a> +</h3> +<p>Two-component error for DFOP-SFO and SFORB-SFO.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t9</th> +<th align="right">t10</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">24.465</td> +<td align="right">800.266</td> +</tr></tbody> +</table> +</div> +<div class="section level3"> +<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a> +</h3> +<p>Two-component error for SFORB-SFO3-plus</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t11</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">1289.198</td> +</tr></tbody> +</table> +</div> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> + </nav> +</div> + +</div> + + + + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer> +</div> + + + + + + + </body> +</html> diff --git a/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index ab436c86..6560ab17 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -109,13 +115,13 @@ <p>Ranke J (2022). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.1.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.0, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2022}, - note = {R package version 1.1.2}, + note = {R package version 1.2.0}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/index.html b/docs/index.html index 67e1702a..9048bc38 100644 --- a/docs/index.html +++ b/docs/index.html @@ -44,7 +44,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -73,19 +73,25 @@ <a href="articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> diff --git a/docs/news/index.html b/docs/news/index.html index faaab288..90768141 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -82,13 +88,18 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2> -<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> -<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> -<li><p>‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li> -<li><p>‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li> +<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> +<ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> +<li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> +<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> +<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> +<li><p>‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.</p></li> <li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li> +<li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood</p></li> <li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li> +<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> +<li><p>‘R/read_spreadsheet.R’: Conveniently read in data from a spreadsheet file.</p></li> +<li><p>‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.</p></li> </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 7db87468..14c22439 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,9 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-08-10T13:56Z + multistart: web_only/multistart.html + saem_benchmarks: web_only/saem_benchmarks.html +last_built: 2022-11-17T13:56Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index c46824e6..48e3b7e2 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -18,7 +18,7 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,11 +95,11 @@ same dataset.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -101,14 +107,21 @@ same dataset.</p> <dl><dt>object</dt> <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one column.</p></dd> + + <dt>...</dt> <dd><p>For compatibility with the generic method</p></dd> + + <dt>k</dt> <dd><p>As in the generic method</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>As in the generic method (a numeric value for single fits, or a + + +<p>As in the generic method (a numeric value for single fits, or a dataframe if there are several fits in the column).</p> </div> <div id="author"> @@ -118,52 +131,50 @@ dataframe if there are several fits in the column).</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># skip, as it takes > 10 s on winbuilder</span></span> -<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span> -<span class="r-in"> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> -<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> -<span class="r-in"> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span> -<span class="r-in"> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># We get a single number for a single fit</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># skip, as it takes > 10 s on winbuilder</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> +<span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span></span> +<span class="r-in"><span> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># We get a single number for a single fit</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="co"># or when extracting an mkinfit object</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="co"># or when extracting an mkinfit object</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># For FOCUS A, the models fit almost equally well, so the higher the number</span></span> -<span class="r-in"> <span class="co"># of parameters, the higher (worse) the AIC</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS A, the models fit almost equally well, so the higher the number</span></span></span> +<span class="r-in"><span> <span class="co"># of parameters, the higher (worse) the AIC</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28198</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28198</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df BIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59975</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># For FOCUS C, the more complex models fit better</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS C, the more complex models fit better</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 59.29336</span> <span class="r-out co"><span class="r-pr">#></span> FOMC 4 44.68652</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 29.02372</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df BIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 59.88504</span> <span class="r-out co"><span class="r-pr">#></span> FOMC 4 45.47542</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 30.00984</span> -<span class="r-in"> </span> -<span class="r-in"></span> +<span class="r-in"><span> </span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -178,7 +189,7 @@ dataframe if there are several fits in the column).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 4a0b599b..f1edaab2 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,21 +95,21 @@ specified as well.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">CAKE_export</span><span class="op">(</span> - <span class="va">ds</span>, - map <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>, - links <span class="op">=</span> <span class="cn">NA</span>, - filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>, - path <span class="op">=</span> <span class="st">"."</span>, - overwrite <span class="op">=</span> <span class="cn">FALSE</span>, - study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>, - description <span class="op">=</span> <span class="st">""</span>, - time_unit <span class="op">=</span> <span class="st">"days"</span>, - res_unit <span class="op">=</span> <span class="st">"% AR"</span>, - comment <span class="op">=</span> <span class="st">""</span>, - date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>, - optimiser <span class="op">=</span> <span class="st">"IRLS"</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">CAKE_export</span><span class="op">(</span></span> +<span> <span class="va">ds</span>,</span> +<span> map <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span> +<span> links <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>,</span> +<span> path <span class="op">=</span> <span class="st">"."</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>,</span> +<span> description <span class="op">=</span> <span class="st">""</span>,</span> +<span> time_unit <span class="op">=</span> <span class="st">"days"</span>,</span> +<span> res_unit <span class="op">=</span> <span class="st">"% AR"</span>,</span> +<span> comment <span class="op">=</span> <span class="st">""</span>,</span> +<span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> optimiser <span class="op">=</span> <span class="st">"IRLS"</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -111,38 +117,65 @@ specified as well.</p> <dl><dt>ds</dt> <dd><p>A named list of datasets in long format as compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>map</dt> <dd><p>A character vector with CAKE compartment names (Parent, A1, ...), named with the names used in the list of datasets.</p></dd> + + <dt>links</dt> <dd><p>An optional character vector of target compartments, named with the names of the source compartments. In order to make this easier, the names are used as in the datasets supplied.</p></dd> + + <dt>filename</dt> <dd><p>Where to write the result. Should end in .csf in order to be compatible with CAKE.</p></dd> + + <dt>path</dt> <dd><p>An optional path to the output file.</p></dd> + + <dt>overwrite</dt> <dd><p>If TRUE, existing files are overwritten.</p></dd> + + <dt>study</dt> <dd><p>The name of the study.</p></dd> + + <dt>description</dt> <dd><p>An optional description.</p></dd> + + <dt>time_unit</dt> <dd><p>The time unit for the residue data.</p></dd> + + <dt>res_unit</dt> <dd><p>The unit used for the residues.</p></dd> + + <dt>comment</dt> <dd><p>An optional comment.</p></dd> + + <dt>date</dt> <dd><p>The date of file creation.</p></dd> + + <dt>optimiser</dt> <dd><p>Can be OLS or IRLS.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="author"> <h2>Author</h2> @@ -161,7 +194,7 @@ compatible with CAKE.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 6e2ec0ba..a22c2f73 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,7 +103,7 @@ constrained by data protection regulations.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">D24_2014</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">D24_2014</span></span></code></pre></div> </div> <div id="format"> @@ -124,7 +130,7 @@ specific pieces of information in the comments.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span> <span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 </span> <span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span> @@ -145,8 +151,8 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span> <span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span> <span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Mississippi </span> <span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: D24 </span> <span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span> @@ -166,11 +172,11 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> 11 183 11.3</span> <span class="r-out co"><span class="r-pr">#></span> 12 273 9.9</span> <span class="r-out co"><span class="r-pr">#></span> 13 365 6.3</span> -<span class="r-in"><span class="va">m_D24</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span> -<span class="r-in"> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span> -<span class="r-in"> DCA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">m_D24</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> DCA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> <span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> <span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> @@ -186,11 +192,11 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> d_D24/dt = - k_D24 * D24</span> <span class="r-out co"><span class="r-pr">#></span> d_DCP/dt = + f_D24_to_DCP * k_D24 * D24 - k_DCP * DCP</span> <span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span> -<span class="r-in"><span class="va">m_D24_2</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span> -<span class="r-in"> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span> -<span class="r-in"> DCA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">m_D24_2</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> DCA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24_2</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> <span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> <span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> @@ -209,7 +215,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2</span> <span class="r-out co"><span class="r-pr">#></span> * time))) * D24 - k_DCP * DCP</span> <span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -224,7 +230,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 41a7d256..4a8cb640 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,26 +95,37 @@ two exponential decline functions.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>k1</dt> <dd><p>First kinetic constant.</p></dd> + + <dt>k2</dt> <dd><p>Second kinetic constant.</p></dd> + + <dt>g</dt> <dd><p>Fraction of the starting value declining according to the first kinetic constant.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="references"> <h2>References</h2> @@ -136,10 +153,10 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">5</span>, <span class="fl">0.5</span>, <span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">4</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">5</span>, <span class="fl">0.5</span>, <span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">4</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="DFOP.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -154,7 +171,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index e00391e8..1f528615 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,19 +101,30 @@ <h2>Arguments</h2> <dl><dt>x</dt> <dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd> + + <dt>i</dt> <dd><p>Row index selecting the fits for specific models</p></dd> + + <dt>j</dt> <dd><p>Column index selecting the fits to specific datasets</p></dd> + + <dt>...</dt> <dd><p>Not used, only there to satisfy the generic method definition</p></dd> + + <dt>drop</dt> <dd><p>If FALSE, the method always returns an mmkin object, otherwise either a list of mkinfit objects or a single mkinfit object.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p> + + +<p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p> </div> <div id="author"> <h2>Author</h2> @@ -116,11 +133,11 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span> -<span class="r-in"> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span> -<span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> <span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -129,7 +146,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> -<span class="r-in"> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> <span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -139,7 +156,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> FOMC OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> -<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> <span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -148,14 +165,14 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> SFO OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="co"># This extracts an mkinfit object with lots of components</span></span> -<span class="r-in"> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"> <span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="co"># This extracts an mkinfit object with lots of components</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $par</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.666193 2.549849 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $objective</span> <span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> @@ -168,7 +185,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $evaluations</span> <span class="r-out co"><span class="r-pr">#></span> function gradient </span> -<span class="r-out co"><span class="r-pr">#></span> 25 72 </span> +<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $message</span> <span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> @@ -187,7 +204,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 93602958..e6052063 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,7 +101,7 @@ in this fit.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span></span></code></pre></div> </div> <div id="format"> @@ -137,7 +143,7 @@ in this fit.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span><span class="op">)</span></span></span> </code></pre></div> </div> </div> @@ -152,7 +158,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 31c14505..76c72fd5 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,7 +101,7 @@ in this fit.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span></span></code></pre></div> </div> <div id="format"> @@ -134,7 +140,7 @@ in this fit.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> </div> @@ -149,7 +155,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 83ab4e56..de4908e6 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,7 +101,7 @@ in this fit.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">FOCUS_2006_HS_ref_A_to_F</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_HS_ref_A_to_F</span></span></code></pre></div> </div> <div id="format"> @@ -137,7 +143,7 @@ in this fit.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_HS_ref_A_to_F</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_HS_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> </div> @@ -152,7 +158,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index f47cba8d..1ba63264 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,7 +101,7 @@ in this fit.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">FOCUS_2006_SFO_ref_A_to_F</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span></span></code></pre></div> </div> <div id="format"> @@ -131,7 +137,7 @@ in this fit.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> </div> @@ -146,7 +152,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index aeeaf723..385c0f2b 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,12 +93,12 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">FOCUS_2006_A</span> - <span class="va">FOCUS_2006_B</span> - <span class="va">FOCUS_2006_C</span> - <span class="va">FOCUS_2006_D</span> - <span class="va">FOCUS_2006_E</span> - <span class="va">FOCUS_2006_F</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_A</span></span> +<span> <span class="va">FOCUS_2006_B</span></span> +<span> <span class="va">FOCUS_2006_C</span></span> +<span> <span class="va">FOCUS_2006_D</span></span> +<span> <span class="va">FOCUS_2006_E</span></span> +<span> <span class="va">FOCUS_2006_F</span></span></code></pre></div> </div> <div id="format"> @@ -119,7 +125,7 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">FOCUS_2006_C</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_2006_C</span></span></span> <span class="r-out co"><span class="r-pr">#></span> name time value</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 0 85.1</span> <span class="r-out co"><span class="r-pr">#></span> 2 parent 1 57.9</span> @@ -144,7 +150,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 7274cadc..e288c955 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,24 +95,33 @@ a decreasing rate constant.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">alpha</span>, <span class="va">beta</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">alpha</span>, <span class="va">beta</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>alpha</dt> <dd><p>Shape parameter determined by coefficient of variation of rate constant values.</p></dd> + + <dt>beta</dt> <dd><p>Location parameter.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="details"> <h2>Details</h2> @@ -117,8 +132,8 @@ in the original equation.</p> <div id="note"> <h2>Note</h2> <p>The solution of the FOMC kinetic model reduces to the -<code><a href="SFO.solution.html">SFO.solution</a></code> for large values of <code>alpha</code> and -<code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> +<code><a href="SFO.solution.html">SFO.solution</a></code> for large values of <code>alpha</code> and <code>beta</code> +with \(k = \frac{\beta}{\alpha}\).</p> </div> <div id="references"> <h2>References</h2> @@ -149,10 +164,10 @@ Technology</em> <b>24</b>, 1032-1038</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">10</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">10</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="FOMC.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -167,7 +182,7 @@ Technology</em> <b>24</b>, 1032-1038</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 03b30958..21bd919a 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,27 +95,38 @@ between them.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">HS.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">HS.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>k1</dt> <dd><p>First kinetic constant.</p></dd> + + <dt>k2</dt> <dd><p>Second kinetic constant.</p></dd> + + <dt>tb</dt> <dd><p>Break point. Before this time, exponential decline according to <code>k1</code> is calculated, after this time, exponential decline proceeds according to <code>k2</code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="references"> <h2>References</h2> @@ -137,10 +154,10 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">HS.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">2</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">HS.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">2</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="HS.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -155,7 +172,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 0116760d..57e2e1f4 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,24 +95,33 @@ a concentration dependent rate constant.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>k__iore</dt> <dd><p>Rate constant. Note that this depends on the concentration units used.</p></dd> + + <dt>N</dt> <dd><p>Exponent describing the nonlinearity of the rate equation</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="note"> <h2>Note</h2> @@ -133,29 +148,29 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="IORE.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit.fomc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">fit.iore</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">fit.iore.deS</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>, </span> -<span class="r-in"> row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit.fomc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">fit.iore</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">fit.iore.deS</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>,</span></span> +<span class="r-in"><span> row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> fit.fomc.par fit.iore.par fit.iore.deS.par</span> -<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874891</span> +<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874890</span> <span class="r-out co"><span class="r-pr">#></span> model par 2 0.05192238 -4.826631 -4.826631</span> <span class="r-out co"><span class="r-pr">#></span> model par 3 0.65096665 1.949403 1.949403</span> <span class="r-out co"><span class="r-pr">#></span> model par 4 1.85744396 1.857444 1.857444</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span>fomc <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, iore <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, </span> -<span class="r-in"> iore.deS <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span>fomc <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, iore <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>,</span></span> +<span class="r-in"><span> iore.deS <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back</span> <span class="r-out co"><span class="r-pr">#></span> fomc 1.785233 15.1479 4.559973</span> <span class="r-out co"><span class="r-pr">#></span> iore 1.785233 15.1479 4.559973</span> <span class="r-out co"><span class="r-pr">#></span> iore.deS 1.785233 15.1479 4.559973</span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -170,7 +185,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 06b5bd6f..3d00e9f6 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,8 +93,8 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">NAFTA_SOP_Appendix_B</span> - <span class="va">NAFTA_SOP_Appendix_D</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Appendix_B</span></span> +<span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div> </div> <div id="format"> @@ -118,12 +124,12 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> <span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> <span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> <span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> <span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> <span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> @@ -162,7 +168,7 @@ <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> <span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="NAFTA_SOP_2015-1.png" alt="" width="700" height="433"></span> </code></pre></div> </div> @@ -178,7 +184,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index a9f4e36f..04f38b78 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,7 +93,7 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">NAFTA_SOP_Attachment</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Attachment</span></span></code></pre></div> </div> <div id="format"> @@ -109,10 +115,10 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> <span class="r-msg co"><span class="r-pr">#></span> The half-life obtained from the IORE model may be used</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> <span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> <span class="r-out co"><span class="r-pr">#></span> 465.21753 56.27506 32.06401 </span> @@ -151,7 +157,7 @@ <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> <span class="r-out co"><span class="r-pr">#></span> [1] 321.51</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="NAFTA_SOP_Attachment-1.png" alt="" width="700" height="433"></span> </code></pre></div> </div> @@ -167,7 +173,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 17a35806..ca982688 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex f06a860e..de2d61aa 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex 1af5d4b4..774715e0 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 12d337a4..37e0e95e 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex cb419daa..76f25647 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex bc6979e9..48f5bbd8 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 3607a5ac..3aabc1d6 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,21 +93,28 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">SFO.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>k</dt> <dd><p>Kinetic rate constant.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="references"> <h2>References</h2> @@ -129,10 +142,10 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFO.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFO.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="SFO.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -147,7 +160,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 9b4c391c..89c932b6 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,26 +101,37 @@ and no substance in the bound fraction.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k_12</span>, <span class="va">k_21</span>, <span class="va">k_1output</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k_12</span>, <span class="va">k_21</span>, <span class="va">k_1output</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>k_12</dt> <dd><p>Kinetic constant describing transfer from free to bound.</p></dd> + + <dt>k_21</dt> <dd><p>Kinetic constant describing transfer from bound to free.</p></dd> + + <dt>k_1output</dt> <dd><p>Kinetic constant describing degradation of the free fraction.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable, which is the sum of free and + + +<p>The value of the response variable, which is the sum of free and bound fractions at time <code>t</code>.</p> </div> <div id="references"> @@ -143,10 +160,10 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.5</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.5</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="SFORB.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -161,7 +178,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 3a129533..4332ba05 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -19,7 +19,7 @@ may depend on the predicted value and is specified as a standard deviation."><!- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ may depend on the predicted value and is specified as a standard deviation."><!- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,16 +97,16 @@ may depend on the predicted value and is specified as a standard deviation.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">add_err</span><span class="op">(</span> - <span class="va">prediction</span>, - <span class="va">sdfunc</span>, - secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>, - n <span class="op">=</span> <span class="fl">10</span>, - LOD <span class="op">=</span> <span class="fl">0.1</span>, - reps <span class="op">=</span> <span class="fl">2</span>, - digits <span class="op">=</span> <span class="fl">1</span>, - seed <span class="op">=</span> <span class="cn">NA</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span> +<span> <span class="va">prediction</span>,</span> +<span> <span class="va">sdfunc</span>,</span> +<span> secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> +<span> n <span class="op">=</span> <span class="fl">10</span>,</span> +<span> LOD <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> reps <span class="op">=</span> <span class="fl">2</span>,</span> +<span> digits <span class="op">=</span> <span class="fl">1</span>,</span> +<span> seed <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -108,29 +114,46 @@ may depend on the predicted value and is specified as a standard deviation.</p> <dl><dt>prediction</dt> <dd><p>A prediction from a kinetic model as produced by <code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd> + + <dt>sdfunc</dt> <dd><p>A function taking the predicted value as its only argument and returning a standard deviation that should be used for generating the random error terms for this value.</p></dd> + + <dt>secondary</dt> <dd><p>The names of state variables that should have an initial value of zero</p></dd> + + <dt>n</dt> <dd><p>The number of datasets to be generated.</p></dd> + + <dt>LOD</dt> <dd><p>The limit of detection (LOD). Values that are below the LOD after adding the random error will be set to NA.</p></dd> + + <dt>reps</dt> <dd><p>The number of replicates to be generated within the datasets.</p></dd> + + <dt>digits</dt> <dd><p>The number of digits to which the values will be rounded.</p></dd> + + <dt>seed</dt> <dd><p>The seed used for the generation of random numbers. If NA, the seed is not set.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the + + +<p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> <div id="references"> @@ -147,53 +170,53 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># The kinetic model</span></span> -<span class="r-in"><span class="va">m_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The kinetic model</span></span></span> +<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Generate a prediction for a specific set of parameters</span></span> -<span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span> -<span class="r-in"><span class="co"># from 2015</span></span> -<span class="r-in"><span class="va">d_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span> -<span class="r-in"> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span> -<span class="r-in"><span class="co"># of 10, and generate three datasets</span></span> -<span class="r-in"><span class="va">d_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Name the datasets for nicer plotting</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span> -<span class="r-in"><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span> -<span class="r-in"><span class="co"># checks</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span> +<span class="r-in"><span><span class="co"># from 2015</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span> +<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span> +<span class="r-in"><span><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span></span> +<span class="r-in"><span><span class="co"># checks</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span> -<span class="r-in"><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span> -<span class="r-in"><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span> +<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span> +<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span> -<span class="r-in"><span class="co"># and plot.mmkin is used</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span> +<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -208,7 +231,7 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html new file mode 100644 index 00000000..02be017b --- /dev/null +++ b/docs/reference/anova.saem.mmkin.html @@ -0,0 +1,168 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Anova method for saem.mmkin objects — anova.saem.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Anova method for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/anova.saem.mmkin.R" class="external-link"><code>R/anova.saem.mmkin.R</code></a></small> + <div class="hidden name"><code>anova.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> <span class="va">...</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span>,</span> +<span> test <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> model.names <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <a href="saem.html">saem.mmkin</a> object</p></dd> + + +<dt>...</dt> +<dd><p>further such objects</p></dd> + + +<dt>method</dt> +<dd><p>Method for likelihood calculation: "is" (importance sampling), +"lin" (linear approximation), or "gq" (Gaussian quadrature). Passed +to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + + +<dt>test</dt> +<dd><p>Should a likelihood ratio test be performed? If TRUE, +the alternative models are tested against the first model. Should +only be done for nested models.</p></dd> + + +<dt>model.names</dt> +<dd><p>Optional character vector of model names</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>an "anova" data frame; the traditional (S3) result of anova()</p> + </div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 1694d5f7..c1e1b4ed 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,13 +97,19 @@ by Burnham and Anderson (2004).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mkinfit</span> -<span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -108,9 +120,12 @@ by Burnham and Anderson (2004).</p> or an mkinfit object. In the latter case, further mkinfit objects fitted to the same data should be specified as dots arguments.</p></dd> + + <dt>...</dt> <dd><p>Not used in the method for <a href="mmkin.html">mmkin</a> column objects, further <a href="mkinfit.html">mkinfit</a> objects in the method for mkinfit objects.</p></dd> + </dl></div> <div id="references"> <h2>References</h2> @@ -121,22 +136,22 @@ Inference: Understanding AIC and BIC in Model Selection. <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_dfop</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">aw_sfo_dfop</span> <span class="op"><-</span> <span class="fu">aw</span><span class="op">(</span><span class="va">f_sfo</span>, <span class="va">f_dfop</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">aw_sfo_dfop</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_dfop</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="op"><-</span> <span class="fu">aw</span><span class="op">(</span><span class="va">f_sfo</span>, <span class="va">f_dfop</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">aw_sfo_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1</span> -<span class="r-in"><span class="va">aw_sfo_dfop</span> <span class="co"># SFO gets more weight as it has less parameters and a similar fit</span></span> +<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="co"># SFO gets more weight as it has less parameters and a similar fit</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.5970258 0.4029742</span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS D"</span> <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS D"</span> <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.4808722 0.1945539 0.3245740</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1</span> -<span class="r-in"><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.5970258 0.4029742</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -151,7 +166,7 @@ Inference: Understanding AIC and BIC in Model Selection. </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 5469f8f8..8d7c272f 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -51,19 +51,25 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -101,66 +107,91 @@ method of Venzon and Moolgavkar (1988).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span> - <span class="va">object</span>, - <span class="va">parm</span>, - level <span class="op">=</span> <span class="fl">0.95</span>, - alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>, - <span class="va">cutoff</span>, - method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"quadratic"</span>, <span class="st">"profile"</span><span class="op">)</span>, - transformed <span class="op">=</span> <span class="cn">TRUE</span>, - backtransform <span class="op">=</span> <span class="cn">TRUE</span>, - cores <span class="op">=</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>, - rel_tol <span class="op">=</span> <span class="fl">0.01</span>, - quiet <span class="op">=</span> <span class="cn">FALSE</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> <span class="va">parm</span>,</span> +<span> level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>,</span> +<span> <span class="va">cutoff</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"quadratic"</span>, <span class="st">"profile"</span><span class="op">)</span>,</span> +<span> transformed <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> backtransform <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> cores <span class="op">=</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> rel_tol <span class="op">=</span> <span class="fl">0.01</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + <dt>parm</dt> <dd><p>A vector of names of the parameters which are to be given confidence intervals. If missing, all parameters are considered.</p></dd> + + <dt>level</dt> <dd><p>The confidence level required</p></dd> + + <dt>alpha</dt> <dd><p>The allowed error probability, overrides 'level' if specified.</p></dd> + + <dt>cutoff</dt> <dd><p>Possibility to specify an alternative cutoff for the difference in the log-likelihoods at the confidence boundary. Specifying an explicit cutoff value overrides arguments 'level' and 'alpha'</p></dd> + + <dt>method</dt> <dd><p>The 'quadratic' method approximates the likelihood function at the optimised parameters using the second term of the Taylor expansion, using a second derivative (hessian) contained in the object. The 'profile' method searches the parameter space for the cutoff of the confidence intervals by means of a likelihood ratio test.</p></dd> + + <dt>transformed</dt> <dd><p>If the quadratic approximation is used, should it be applied to the likelihood based on the transformed parameters?</p></dd> + + <dt>backtransform</dt> <dd><p>If we approximate the likelihood in terms of the transformed parameters, should we backtransform the parameters with their confidence intervals?</p></dd> + + <dt>cores</dt> <dd><p>The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.</p></dd> + + <dt>rel_tol</dt> <dd><p>If the method is 'profile', what should be the accuracy of the lower and upper bounds, relative to the estimate obtained from the quadratic method?</p></dd> + + <dt>quiet</dt> <dd><p>Should we suppress the message "Profiling the likelihood"</p></dd> + + <dt>...</dt> <dd><p>Not used</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A matrix with columns giving lower and upper confidence limits for + + +<p>A matrix with columns giving lower and upper confidence limits for each parameter.</p> </div> <div id="references"> @@ -175,178 +206,178 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 71.8242430 93.1600766</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.2109541 0.4440528</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.9778868 7.3681380</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"profile"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"profile"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 73.0641834 92.1392181</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.2170293 0.4235348</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.1307772 8.0628314</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Set the number of cores for the profiling method for further examples</span></span> -<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"NOT_CRAN"</span><span class="op">)</span>, <span class="st">"true"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span></span> -<span class="r-in"><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> -<span class="r-in"> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fl">1</span></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span> -<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Set the number of cores for the profiling method for further examples</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"NOT_CRAN"</span><span class="op">)</span>, <span class="st">"true"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 3.409 0.000 3.411 </span> -<span class="r-in"><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span> -<span class="r-in"><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span> -<span class="r-in"><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile_no_parent_0</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> 3.931 0.000 3.932 </span> +<span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> +<span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> +<span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile_no_parent_0</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.317 0.152 0.847 </span> -<span class="r-in"><span class="va">ci_profile</span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.219 0.000 2.219 </span> +<span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040762501 5.549764e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046786482 5.500879e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003892605 6.702778e-03</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> -<span class="r-in"><span class="va">ci_quadratic_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ci_quadratic_transformed</span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841640 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.041033378 5.596269e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046777902 5.511931e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.004012217 6.897547e-03</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> -<span class="r-in"><span class="va">ci_quadratic_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ci_quadratic_untransformed</span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841645 102.79312449</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040485331 0.05535491</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046611582 0.05494364</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003835483 0.00668582</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> -<span class="r-in"><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span> -<span class="r-in"><span class="co"># intervals based on the internal parameter transformation are less</span></span> -<span class="r-in"><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span> -<span class="r-in"><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span> -<span class="r-in"><span class="va">rel_diffs_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span> -<span class="r-in"><span class="va">rel_diffs_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span> -<span class="r-in"><span class="va">rel_diffs_transformed</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed</span></span> +<span class="r-in"><span><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span></span> +<span class="r-in"><span><span class="co"># intervals based on the internal parameter transformation are less</span></span></span> +<span class="r-in"><span><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span></span> +<span class="r-in"><span><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> sigma FALSE FALSE</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_transformed</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_transformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006650 0.008380</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.000183 0.002010</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.030700 0.029100</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_untransformed</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_untransformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006800 0.002570</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.003740 0.001180</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.014700 0.002530</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> -<span class="r-in"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Investigate a case with formation fractions</span></span> -<span class="r-in"><span class="va">f_d_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ci_profile_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Investigate a case with formation fractions</span></span></span> +<span class="r-in"><span><span class="va">f_d_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_profile_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> -<span class="r-in"><span class="va">ci_profile_ff</span></span> +<span class="r-in"><span><span class="va">ci_profile_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090911032 1.071578e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003892606 6.702775e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.471328495 5.611550e-01</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> -<span class="r-in"><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ci_quadratic_transformed_ff</span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833565 102.79311648</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> -<span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833570 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> -<span class="r-in"><span class="va">rel_diffs_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span> -<span class="r-in"><span class="va">rel_diffs_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span> -<span class="r-in"><span class="co"># the profile based interval when using the internal parameter</span></span> -<span class="r-in"><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span> -<span class="r-in"><span class="co"># without internal parameter transformation.</span></span> -<span class="r-in"><span class="va">rel_diffs_transformed_ff</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed_ff</span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span></span> +<span class="r-in"><span><span class="co"># the profile based interval when using the internal parameter</span></span></span> +<span class="r-in"><span><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span></span> +<span class="r-in"><span><span class="co"># without internal parameter transformation.</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> k_parent TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> -<span class="r-in"><span class="va">rel_diffs_transformed_ff</span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598534 0.0009001862</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283050 0.0290588375</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881765 0.0027780058</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> -<span class="r-in"><span class="va">rel_diffs_untransformed_ff</span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217231</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102157 0.0023732283</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740682 0.0025291807</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995207 0.0023457708</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span> -<span class="r-in"><span class="co"># therefore we use the quadratic approximation</span></span> -<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> -<span class="r-in"><span class="va">f_tc_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">DFOP_par_c</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> -<span class="r-in"> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> +<span class="r-in"><span><span class="co"># therefore we use the quadratic approximation</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">f_tc_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">DFOP_par_c</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> +<span class="r-in"><span> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596210088 106.19935874</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605436 0.04490756</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568746 0.01087674</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021466645 0.62023879</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015168549 0.37975352</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897574 0.33388069</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943815 0.73583258</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283808 0.83992121</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411010 0.07662004</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59621 106.1994</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -361,7 +392,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index b85acb7a..b93f1c4a 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,59 +93,64 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">create_deg_func</span><span class="op">(</span><span class="va">spec</span>, use_of_ff <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"min"</span>, <span class="st">"max"</span><span class="op">)</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">create_deg_func</span><span class="op">(</span><span class="va">spec</span>, use_of_ff <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"min"</span>, <span class="st">"max"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>spec</dt> <dd><p>List of model specifications as contained in mkinmod objects</p></dd> + + <dt>use_of_ff</dt> <dd><p>Minimum or maximum use of formation fractions</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Degradation function to be attached to mkinmod objects</p> + + +<p>Degradation function to be attached to mkinmod objects</p> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># to avoid warnings</span></span> -<span class="r-in"><span class="va">fit_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> -<span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># to avoid warnings</span></span></span> +<span class="r-in"><span><span class="va">fit_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.401 1.00 0.401 0.000 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.211 3.02 1.210 0.002 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.445 1.000 0.444 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.693 1.557 0.692 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> -<span class="r-in"> <span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> -<span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.84 1.000 0.839 0.001 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 3.19 3.798 3.188 0.001 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.871 1.000 0.871 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.519 1.744 1.519 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -154,7 +165,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex 6e5d357d..c8b05bf5 100644 --- a/docs/reference/dimethenamid_2018-1.png +++ b/docs/reference/dimethenamid_2018-1.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 431e5c34..6d8c0157 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,7 +103,7 @@ constrained by data protection regulations.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dimethenamid_2018</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">dimethenamid_2018</span></span></code></pre></div> </div> <div id="format"> @@ -120,7 +126,7 @@ specific pieces of information in the comments.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 7 mkinds objects</span> <span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 </span> <span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span> @@ -145,29 +151,29 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> Flaach NA 20</span> <span class="r-out co"><span class="r-pr">#></span> BBA 2.2 NA 20</span> <span class="r-out co"><span class="r-pr">#></span> BBA 2.3 NA 20</span> -<span class="r-in"><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> -<span class="r-in"> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> -<span class="r-in"> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> -<span class="r-in"> <span class="va">ds_i</span></span> -<span class="r-in"><span class="op">}</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> -<span class="r-in"><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> -<span class="r-in"><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> -<span class="r-in"><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="co"># We don't use DFOP for the parent compound, as this gives numerical</span></span> -<span class="r-in"><span class="co"># instabilities in the fits</span></span> -<span class="r-in"><span class="va">sfo_sfo3p</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> DMTA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M23 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M27 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M31 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-in"><span class="va">dmta_sfo_sfo3p_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO3+"</span> <span class="op">=</span> <span class="va">sfo_sfo3p</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># We don't use DFOP for the parent compound, as this gives numerical</span></span></span> +<span class="r-in"><span><span class="co"># instabilities in the fits</span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo3p</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> DMTA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M23 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M27 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M31 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_sfo_sfo3p_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO3+"</span> <span class="op">=</span> <span class="va">sfo_sfo3p</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> <span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -176,35 +182,33 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> SFO-SFO3+ OK OK OK OK OK OK </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> -<span class="r-in"><span class="co"># The default (test_log_parms = FALSE) gives an undue</span></span> -<span class="r-in"><span class="co"># influence of ill-defined rate constants that have</span></span> -<span class="r-in"><span class="co"># extremely small values:</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># The default (test_log_parms = FALSE) gives an undue</span></span></span> +<span class="r-in"><span><span class="co"># influence of ill-defined rate constants that have</span></span></span> +<span class="r-in"><span><span class="co"># extremely small values:</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># If we disregards ill-defined rate constants, the results</span></span></span> +<span class="r-in"><span><span class="co"># look more plausible, but the truth is likely to be in</span></span></span> +<span class="r-in"><span><span class="co"># between these variants</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># If we disregards ill-defined rate constants, the results</span></span> -<span class="r-in"><span class="co"># look more plausible, but the truth is likely to be in</span></span> -<span class="r-in"><span class="co"># between these variants</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># We can also specify a default value for the failing</span></span> -<span class="r-in"><span class="co"># log parameters, to mimic FOCUS guidance</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span class="r-in"> default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span> -<span class="r-plt img"><img src="dimethenamid_2018-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span> -<span class="r-in"><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span> -<span class="r-in"><span class="co"># nlme reaches maxIter = 50 without convergence</span></span> -<span class="r-in"><span class="va">f_dmta_saem_tc</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># I am commenting out the convergence plot as rendering them</span></span> -<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the</span></span> -<span class="r-in"><span class="co"># graphics device used)</span></span> -<span class="r-in"><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Jun 30 10:21:01 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Jun 30 10:21:01 2022 </span> +<span class="r-in"><span><span class="co"># We can also specify a default value for the failing</span></span></span> +<span class="r-in"><span><span class="co"># log parameters, to mimic FOCUS guidance</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> +<span class="r-in"><span> default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span></span> +<span class="r-in"><span><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span></span> +<span class="r-in"><span><span class="co"># nlme reaches maxIter = 50 without convergence</span></span></span> +<span class="r-in"><span><span class="va">f_dmta_saem_tc</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># I am commenting out the convergence plot as rendering them</span></span></span> +<span class="r-in"><span><span class="co"># with pkgdown fails (at least without further tweaks to the</span></span></span> +<span class="r-in"><span><span class="co"># graphics device used)</span></span></span> +<span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 13:57:51 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 13:57:51 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +221,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 1845.619 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 802.957 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -235,78 +239,88 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 2276 2272 -1120</span> +<span class="r-out co"><span class="r-pr">#></span> 2276 2273 -1120</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3098 84.1383 92.4813</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0510 -3.5659 -2.5361</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0567 -4.9178 -3.1955</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8592 -4.2571 -3.4614</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9685 -4.4683 -3.4686</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1382 -0.2120 0.4885</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1429 -0.2616 0.5473</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3192 83.8656 92.7729</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0315 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0237 -0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0392 -0.0048 0.0040 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0303 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.2733 -1.1098 7.6564</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6422 0.2777 1.0066</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0131 0.3797 1.6465</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4511 0.1510 0.7513</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5695 0.1923 0.9466</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9255 0.8288 1.0221</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1365 0.1191 0.1538</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.30980 84.138334 92.48126</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04731 0.028272 0.07918</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01731 0.007315 0.04095</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02108 0.014164 0.03139</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01890 0.011467 0.03116</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14626 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12029 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11135 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.31924 83.865625 92.77286</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1463</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1203</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1113</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6221</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1461</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.67</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.05 133.05</span> -<span class="r-out co"><span class="r-pr">#></span> M27 32.88 109.21</span> -<span class="r-out co"><span class="r-pr">#></span> M31 36.67 121.81</span> -<span class="r-in"><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span> -<span class="r-in"><span class="co"># includes zero, we could try an alternative model without</span></span> -<span class="r-in"><span class="co"># such random effects</span></span> -<span class="r-in"><span class="co"># f_dmta_saem_tc_2 <- saem(dmta_sfo_sfo3p_tc,</span></span> -<span class="r-in"><span class="co"># covariance.model = diag(c(0, rep(1, 7))))</span></span> -<span class="r-in"><span class="co"># saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")</span></span> -<span class="r-in"><span class="co"># This does not perform better judged by AIC and BIC</span></span> -<span class="r-in"><span class="co"># saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)</span></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.68 48.76</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> +<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> +<span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> +<span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> +<span class="r-in"><span><span class="co"># such random effects</span></span></span> +<span class="r-in"><span><span class="co"># f_dmta_saem_tc_2 <- saem(dmta_sfo_sfo3p_tc,</span></span></span> +<span class="r-in"><span><span class="co"># covariance.model = diag(c(0, rep(1, 7))))</span></span></span> +<span class="r-in"><span><span class="co"># saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")</span></span></span> +<span class="r-in"><span><span class="co"># This does not perform better judged by AIC and BIC</span></span></span> +<span class="r-in"><span><span class="co"># saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -321,7 +335,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 883c9e5d..1f49092e 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -50,19 +50,25 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -98,24 +104,26 @@ advantage that the SFORB model can also be used for metabolites.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>fit</dt> -<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, -or another object that has list components -mkinmod containing an <a href="mkinmod.html">mkinmod</a> degradation model, and two numeric vectors, -bparms.optim and bparms.fixed, that contain parameter values -for that model.</p></dd> +<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, or +another object that has list components mkinmod containing an <a href="mkinmod.html">mkinmod</a> +degradation model, and two numeric vectors, bparms.optim and bparms.fixed, +that contain parameter values for that model.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A list with a matrix of dissipation times named distimes, -and, if applicable, a vector of formation fractions named ff -and, if the SFORB model was in use, a vector of eigenvalues -of these SFORB models, equivalent to DFOP rate constants</p> + + +<p>A list with a matrix of dissipation times named distimes, and, if +applicable, a vector of formation fractions named ff and, if the SFORB model +was in use, a vector of eigenvalues of these SFORB models, equivalent to +DFOP rate constants</p> </div> <div id="details"> <h2>Details</h2> @@ -134,36 +142,36 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back</span> <span class="r-out co"><span class="r-pr">#></span> parent 1.785233 15.1479 4.559973</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> <span class="r-out co"><span class="r-pr">#></span> parent 1.886925 21.25106 6.397207 1.508293 38.83438</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="va">fit_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="va">fit_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_free </span> <span class="r-out co"><span class="r-pr">#></span> 1 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $SFORB</span> -<span class="r-out co"><span class="r-pr">#></span> parent_b1 parent_b2 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.4595574 0.0178488 </span> +<span class="r-out co"><span class="r-pr">#></span> parent_b1 parent_b2 parent_g </span> +<span class="r-out co"><span class="r-pr">#></span> 0.4595574 0.0178488 0.8539454 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_parent_b1 DT50_parent_b2</span> <span class="r-out co"><span class="r-pr">#></span> parent 1.886925 21.25106 6.397208 1.508293 38.83438</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -178,7 +186,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex 50c09278..b7b4d63b 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 69a8baf4..08d2de00 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -45,7 +45,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -72,19 +72,25 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -143,7 +149,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">experimental_data_for_UBA_2019</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div> </div> <div id="format"> @@ -182,48 +188,48 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Model definitions</span></span> -<span class="r-in"><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span> -<span class="r-in"><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Model definitions</span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span> -<span class="r-in"><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">sfo_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span> -<span class="r-in"> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span> -<span class="r-in"><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">dfop_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span> -<span class="r-in"> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span> -<span class="r-in"><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">d_1_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_1_2</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_1_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">d_1_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_1_2</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_1_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="experimental_data_for_UBA-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -238,7 +244,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 27da5718..caeb25a1 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,56 +95,73 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for numeric</span> -<span class="fu">f_time_norm_focus</span><span class="op">(</span> - <span class="va">object</span>, - moisture <span class="op">=</span> <span class="cn">NA</span>, - field_moisture <span class="op">=</span> <span class="cn">NA</span>, - temperature <span class="op">=</span> <span class="va">object</span>, - Q10 <span class="op">=</span> <span class="fl">2.58</span>, - walker <span class="op">=</span> <span class="fl">0.7</span>, - f_na <span class="op">=</span> <span class="cn">NA</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="co"># S3 method for mkindsg</span> -<span class="fu">f_time_norm_focus</span><span class="op">(</span> - <span class="va">object</span>, - study_moisture_ref_source <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>, - Q10 <span class="op">=</span> <span class="fl">2.58</span>, - walker <span class="op">=</span> <span class="fl">0.7</span>, - f_na <span class="op">=</span> <span class="cn">NA</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> field_moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> temperature <span class="op">=</span> <span class="va">object</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkindsg</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> study_moisture_ref_source <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An object containing information used for the calculations</p></dd> + + <dt>...</dt> <dd><p>Currently not used</p></dd> + + <dt>moisture</dt> <dd><p>Numeric vector of moisture contents in \% w/w</p></dd> + + <dt>field_moisture</dt> <dd><p>Numeric vector of moisture contents at field capacity (pF2) in \% w/w</p></dd> + + <dt>temperature</dt> <dd><p>Numeric vector of temperatures in °C</p></dd> + + <dt>Q10</dt> <dd><p>The Q10 value used for temperature normalisation</p></dd> + + <dt>walker</dt> <dd><p>The Walker exponent used for moisture normalisation</p></dd> + + <dt>f_na</dt> <dd><p>The factor to use for NA values. If set to NA, only factors for complete cases will be returned.</p></dd> + + <dt>study_moisture_ref_source</dt> <dd><p>Source for the reference value used to calculate the study moisture. If 'auto', preference is given to a reference moisture given in the meta information, otherwise the focus soil moisture for the soil class is used</p></dd> + </dl></div> <div id="references"> <h2>References</h2> @@ -160,10 +183,10 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span> <span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span> <span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span> <span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span> @@ -176,9 +199,9 @@ Version 1.1, 18 December 2014 <span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span> <span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span> <span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span> -<span class="r-in"><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span> -<span class="r-in"><span class="co"># temperature only normalisation as in the EU evaluation</span></span> -<span class="r-in"><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span></span> +<span class="r-in"><span><span class="co"># temperature only normalisation as in the EU evaluation</span></span></span> +<span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span> </code></pre></div> </div> @@ -194,7 +217,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 6b64ba73..088c7bc3 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -18,7 +18,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,7 +95,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">focus_soil_moisture</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">focus_soil_moisture</span></span></code></pre></div> </div> <div id="format"> @@ -105,7 +111,7 @@ Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-wa <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">focus_soil_moisture</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">focus_soil_moisture</span></span></span> <span class="r-out co"><span class="r-pr">#></span> pF1 pF2 pF2.5</span> <span class="r-out co"><span class="r-pr">#></span> Sand 24 12 7</span> <span class="r-out co"><span class="r-pr">#></span> Loamy sand 24 14 9</span> @@ -133,7 +139,7 @@ Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-wa </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index c63a968c..dc6fee5e 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,12 +93,14 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_deg_func</span><span class="op">(</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_deg_func</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> </div> <div id="value"> <h2>Value</h2> - <p>A function that was likely previously assigned from within + + +<p>A function that was likely previously assigned from within nlme.mmkin</p> </div> @@ -108,7 +116,7 @@ nlme.mmkin</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index cbdbfde2..52f130e6 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -100,6 +106,9 @@ without parameter transformations is used.</p> <span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> +<span><span class="co"># S3 method for illparms.mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> <span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -109,6 +118,9 @@ without parameter transformations is used.</p> <span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> +<span><span class="co"># S3 method for illparms.saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> <span><span class="co"># S3 method for mhmkin</span></span> <span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -149,8 +161,7 @@ tested?</p></dd> <p>For <a href="mkinfit.html">mkinfit</a> or <a href="saem.html">saem</a> objects, a character vector of parameter names. For <a href="mmkin.html">mmkin</a> or <a href="mhmkin.html">mhmkin</a> objects, a matrix like object of class -'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable -printing method.</p> +'illparms.mmkin' or 'illparms.mhmkin'.</p> </div> <div id="details"> <h2>Details</h2> @@ -161,6 +172,11 @@ effects expressed as standard deviations include zero, and if the confidence intervals for the error model parameters include zero.</p> </div> + <div id="note"> + <h2>Note</h2> + <p>All return objects have printing methods. For the single fits, printing +does not output anything in the case no ill-defined parameters are found.</p> + </div> <div id="ref-examples"> <h2>Examples</h2> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 58ae56b0..7c3a2e33 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -18,7 +18,7 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,9 +95,9 @@ transformations.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> - -<span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -99,10 +105,13 @@ transformations.</p> <dl><dt>x</dt> <dd><p>A numeric vector. Naturally, the forward transformation is only sensible for vectors with all elements being greater than zero.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The result of the forward or backward transformation. The returned + + +<p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> </div> @@ -123,39 +132,39 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># Order matters</span></span> -<span class="r-in"><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Order matters</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] -1.628174 -2.820079</span> -<span class="r-in"><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1.628174 2.820079</span> -<span class="r-in"><span class="co"># Equal entries give ilr transformations with zeros as elements</span></span> -<span class="r-in"><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># Equal entries give ilr transformations with zeros as elements</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0 0</span> -<span class="r-in"><span class="co"># Almost equal entries give small numbers</span></span> -<span class="r-in"><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.3</span>, <span class="fl">0.4</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># Almost equal entries give small numbers</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.3</span>, <span class="fl">0.4</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] -0.2034219 0.1174457</span> -<span class="r-in"><span class="co"># Only the ratio between the numbers counts, not their sum</span></span> -<span class="r-in"><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># Only the ratio between the numbers counts, not their sum</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> -<span class="r-in"><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fl">2.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fl">2.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> -<span class="r-in"><span class="co"># Inverse transformation of larger numbers gives unequal elements</span></span> -<span class="r-in"><span class="fu">invilr</span><span class="op">(</span><span class="op">-</span><span class="fl">10</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># Inverse transformation of larger numbers gives unequal elements</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="op">-</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 7.213536e-07 9.999993e-01</span> -<span class="r-in"><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 7.207415e-07 9.991507e-01 8.486044e-04</span> -<span class="r-in"><span class="co"># The sum of the elements of the inverse ilr is 1</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># The sum of the elements of the inverse ilr is 1</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1</span> -<span class="r-in"><span class="co"># This is why we do not need all elements of the inverse transformation to go back:</span></span> -<span class="r-in"><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span></span> -<span class="r-in"><span class="va">b</span> <span class="op"><-</span> <span class="fu">invilr</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span> <span class="co"># Four elements</span></span> +<span class="r-in"><span><span class="co"># This is why we do not need all elements of the inverse transformation to go back:</span></span></span> +<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">invilr</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span> <span class="co"># Four elements</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 4</span> -<span class="r-in"><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fl">1</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="co"># Gives c(0.1, 0.3, 0.5)</span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fl">1</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="co"># Gives c(0.1, 0.3, 0.5)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.1 0.3 0.5</span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -170,7 +179,7 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 956648d2..665912f7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -107,11 +113,15 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p><p>Generic functions introduced by the package</p> </th> </tr></tbody><tbody><tr><td> - <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i><convergence.mmkin></i>)</a></code> </p> + <p><code><a href="parms.html">parms()</a></code> </p> + </td> + <td><p>Extract model parameters</p></td> + </tr><tr><td> + <p><code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> </p> </td> - <td><p>Method to get convergence information</p></td> + <td><p>Method to get status information for fit array objects</p></td> </tr><tr><td> - <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p> + <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p> </td> <td><p>Method to get the names of ill-defined parameters</p></td> </tr><tr><td> @@ -119,6 +129,10 @@ degradation models and one or more error models</p></td> </td> <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> + </tr><tr><td> + <p><code><a href="aw.html">aw()</a></code> </p> + </td> + <td><p>Calculate Akaike weights for model averaging</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p><p>Functions working with mkinfit objects</p> @@ -132,10 +146,6 @@ with mkinfit</p></td> </td> <td><p>Summary method for class "mkinfit"</p></td> </tr><tr><td> - <p><code><a href="parms.html">parms()</a></code> </p> - </td> - <td><p>Extract model parameters from mkinfit models</p></td> - </tr><tr><td> <p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p> </td> <td><p>Confidence intervals for parameters of mkinfit objects</p></td> @@ -156,10 +166,6 @@ with mkinfit</p></td> </td> <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> </tr><tr><td> - <p><code><a href="aw.html">aw()</a></code> </p> - </td> - <td><p>Calculate Akaike weights for model averaging</p></td> - </tr><tr><td> <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p> </td> <td><p>Export a list of datasets format to a CAKE study file</p></td> @@ -189,11 +195,15 @@ of an mmkin object</p></td> <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> </th> </tr></tbody><tbody><tr><td> + <p><code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> </p> + </td> + <td><p>Read datasets and relevant meta information from a spreadsheet file</p></td> + </tr><tr><td> <p><code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> </p> </td> <td><p>Create an nlme model for an mmkin row object</p></td> </tr><tr><td> - <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> + <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> <code><a href="saem.html">parms(<i><saem.mmkin></i>)</a></code> </p> </td> <td><p>Fit nonlinear mixed models with SAEM</p></td> </tr><tr><td> @@ -214,6 +224,14 @@ degradation models and one or more error models</p></td> </td> <td><p>Summary method for class "saem.mmkin"</p></td> </tr><tr><td> + <p><code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>Anova method for saem.mmkin objects</p></td> + </tr><tr><td> + <p><code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>logLik method for saem.mmkin objects</p></td> + </tr><tr><td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> @@ -233,6 +251,18 @@ degradation models and one or more error models</p></td> <p><code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> </p> </td> <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> + </tr><tr><td> + <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p> + </td> + <td><p>Perform a hierarchical model fit with multiple starting values</p></td> + </tr><tr><td> + <p><code><a href="llhist.html">llhist()</a></code> </p> + </td> + <td><p>Plot the distribution of log likelihoods from multistart objects</p></td> + </tr><tr><td> + <p><code><a href="parplot.html">parplot()</a></code> </p> + </td> + <td><p>Plot parameter variability of multistart objects</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> @@ -322,10 +352,18 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p> </th> </tr></tbody><tbody><tr><td> + <p><code><a href="tex_listing.html">tex_listing()</a></code> </p> + </td> + <td><p>Wrap the output of a summary function in tex listing environment</p></td> + </tr><tr><td> <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p> </td> <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td> </tr><tr><td> + <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> + </td> + <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> + </tr><tr><td> <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p> </td> <td><p>Function to calculate maximum time weighted average concentrations from diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index ae621adc..1547f3af 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,27 +93,36 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for saem.mmkin</span> -<span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">object</span>, level <span class="op">=</span> <span class="fl">0.95</span>, backtransform <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">object</span>, level <span class="op">=</span> <span class="fl">0.95</span>, backtransform <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>The fitted saem.mmkin object</p></dd> + + <dt>level</dt> <dd><p>The confidence level. Must be the default of 0.95 as this is what is available in the saemix object</p></dd> + + <dt>backtransform</dt> <dd><p>In case the model was fitted with mkin transformations, should we backtransform the parameters where a one to one correlation between transformed and backtransformed parameters exists?</p></dd> + + <dt>...</dt> <dd><p>For compatibility with the generic method</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object with 'intervals.saem.mmkin' and 'intervals.lme' in the + + +<p>An object with 'intervals.saem.mmkin' and 'intervals.lme' in the class attribute</p> </div> @@ -123,7 +138,7 @@ class attribute</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html new file mode 100644 index 00000000..cc58e481 --- /dev/null +++ b/docs/reference/llhist.html @@ -0,0 +1,151 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot the distribution of log likelihoods from multistart objects — llhist • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot the distribution of log likelihoods from multistart objects — llhist"><meta property="og:description" content="Produces a histogram of log-likelihoods. In addition, the likelihood of the +original fit is shown as a red vertical line."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot the distribution of log likelihoods from multistart objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/llhist.R" class="external-link"><code>R/llhist.R</code></a></small> + <div class="hidden name"><code>llhist.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Produces a histogram of log-likelihoods. In addition, the likelihood of the +original fit is shown as a red vertical line.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">llhist</span><span class="op">(</span><span class="va">object</span>, breaks <span class="op">=</span> <span class="st">"Sturges"</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The <a href="multistart.html">multistart</a> object</p></dd> + + +<dt>breaks</dt> +<dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd> + + +<dt>lpos</dt> +<dd><p>Positioning of the legend.</p></dd> + + +<dt>main</dt> +<dd><p>Title of the plot</p></dd> + + +<dt>...</dt> +<dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd> + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div> + </div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex a1a65a61..d897c363 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex c441f2ed..0847bbec 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index ee9b37e4..254b568f 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -20,7 +20,7 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -93,18 +99,21 @@ compares the likelihoods using the likelihood ratio test </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mkinfit</span> -<span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>A model object with a defined loftest method</p></dd> + + <dt>...</dt> <dd><p>Not used</p></dd> + </dl></div> <div id="details"> <h2>Details</h2> @@ -120,12 +129,12 @@ of replicate samples.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We see a clear pattern in the residuals</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We see a clear pattern in the residuals</span></span></span> <span class="r-plt img"><img src="loftest-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We have a clear lack of fit</span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We have a clear lack of fit</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> @@ -135,13 +144,13 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -7 46.487 7.027e-08 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># We try a different model (the one that was used to generate the data)</span></span> -<span class="r-in"><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># We don't see systematic deviations, but heteroscedastic residuals</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># We try a different model (the one that was used to generate the data)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># We don't see systematic deviations, but heteroscedastic residuals</span></span></span> <span class="r-plt img"><img src="loftest-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># therefore we should consider adapting the error model, although we have</span></span> -<span class="r-in"><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># no lack of fit</span></span> +<span class="r-in"><span><span class="co"># therefore we should consider adapting the error model, although we have</span></span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># no lack of fit</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> @@ -149,12 +158,12 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> <span class="r-out co"><span class="r-pr">#></span> 1 10 -40.710 </span> <span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -5 3.485 0.6257</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># This is the anova model used internally for the comparison</span></span> -<span class="r-in"><span class="va">test_data_anova</span> <span class="op"><-</span> <span class="va">test_data</span></span> -<span class="r-in"><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span> -<span class="r-in"><span class="va">anova_fit</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="va">time</span>, data <span class="op">=</span> <span class="va">test_data_anova</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># This is the anova model used internally for the comparison</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span> <span class="op"><-</span> <span class="va">test_data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="va">time</span>, data <span class="op">=</span> <span class="va">test_data_anova</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Call:</span> <span class="r-out co"><span class="r-pr">#></span> lm(formula = value ~ time, data = test_data_anova)</span> @@ -181,18 +190,18 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 </span> <span class="r-out co"><span class="r-pr">#></span> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span> <span class="co"># We get the same likelihood and degrees of freedom</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span> <span class="co"># We get the same likelihood and degrees of freedom</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 'log Lik.' -40.71015 (df=10)</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="va">test_data_2</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> -<span class="r-in"><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">test_data_2</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">sfo_lin_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span> <span class="co"># not a good model, we try parallel formation</span></span> +<span class="r-in"><span><span class="va">sfo_lin_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span> <span class="co"># not a good model, we try parallel formation</span></span></span> <span class="r-plt img"><img src="loftest-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> @@ -202,15 +211,15 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> 2 7 -171.927 -21 156.64 < 2.2e-16 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">sfo_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span> <span class="co"># much better for metabolites</span></span> +<span class="r-in"><span><span class="va">sfo_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span> <span class="co"># much better for metabolites</span></span></span> <span class="r-plt img"><img src="loftest-4.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> @@ -220,15 +229,15 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> 2 7 -156.331 -21 125.45 < 2.2e-16 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">dfop_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># No visual lack of fit</span></span> +<span class="r-in"><span><span class="va">dfop_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># No visual lack of fit</span></span></span> <span class="r-plt img"><img src="loftest-5.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># no lack of fit found by the test</span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># no lack of fit found by the test</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> @@ -236,13 +245,13 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> <span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> <span class="r-out co"><span class="r-pr">#></span> 2 9 -102.763 -19 18.313 0.5016</span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># The anova model used for comparison in the case of transformation products</span></span> -<span class="r-in"><span class="va">test_data_anova_2</span> <span class="op"><-</span> <span class="va">dfop_par_fit</span><span class="op">$</span><span class="va">data</span></span> -<span class="r-in"><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span><span class="op">)</span></span> -<span class="r-in"><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span> -<span class="r-in"><span class="va">anova_fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">observed</span> <span class="op">~</span> <span class="va">time</span><span class="op">:</span><span class="va">variable</span> <span class="op">-</span> <span class="fl">1</span>, data <span class="op">=</span> <span class="va">test_data_anova_2</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit_2</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The anova model used for comparison in the case of transformation products</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span> <span class="op"><-</span> <span class="va">dfop_par_fit</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">observed</span> <span class="op">~</span> <span class="va">time</span><span class="op">:</span><span class="va">variable</span> <span class="op">-</span> <span class="fl">1</span>, data <span class="op">=</span> <span class="va">test_data_anova_2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Call:</span> <span class="r-out co"><span class="r-pr">#></span> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2)</span> @@ -287,7 +296,7 @@ of replicate samples.</p> <span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 </span> <span class="r-out co"><span class="r-pr">#></span> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -302,7 +311,7 @@ of replicate samples.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 9c34d890..76fa4645 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -21,7 +21,7 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,20 +101,25 @@ the error model.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>...</dt> <dd><p>For compatibility with the generic method</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated + + +<p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> </div> @@ -130,24 +141,24 @@ and the fitted error model parameters.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span></span> -<span class="r-in"> <span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="va">d_t</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nw</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">sfo_sfo</span>, <span class="va">d_t</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># no weighting (weights are unity)</span></span> -<span class="r-in"> <span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nw</span>, <span class="va">f_obs</span>, <span class="va">f_tc</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="va">d_t</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nw</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">sfo_sfo</span>, <span class="va">d_t</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># no weighting (weights are unity)</span></span></span> +<span class="r-in"><span> <span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nw</span>, <span class="va">f_obs</span>, <span class="va">f_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> f_nw 5 204.4486</span> <span class="r-out co"><span class="r-pr">#></span> f_obs 6 205.8727</span> <span class="r-out co"><span class="r-pr">#></span> f_tc 6 141.9656</span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -162,7 +173,7 @@ and the fitted error model parameters.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html new file mode 100644 index 00000000..36ba6957 --- /dev/null +++ b/docs/reference/logLik.saem.mmkin.html @@ -0,0 +1,138 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>logLik method for saem.mmkin objects — logLik.saem.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="logLik method for saem.mmkin objects — logLik.saem.mmkin"><meta property="og:description" content="logLik method for saem.mmkin objects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>logLik method for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> + <div class="hidden name"><code>logLik.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>logLik method for saem.mmkin objects</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The fitted <a href="saem.html">saem.mmkin</a> object</p></dd> + + +<dt>...</dt> +<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + + +<dt>method</dt> +<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + +</dl></div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index b09d3a69..a63b1b1b 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,25 +95,36 @@ an increasing rate constant, supposedly caused by microbial growth</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">logistic.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">kmax</span>, <span class="va">k0</span>, <span class="va">r</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">logistic.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">kmax</span>, <span class="va">k0</span>, <span class="va">r</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> + + <dt>parent_0</dt> <dd><p>Starting value for the response variable at time zero.</p></dd> + + <dt>kmax</dt> <dd><p>Maximum rate constant.</p></dd> + + <dt>k0</dt> <dd><p>Minimum rate constant effective at time zero.</p></dd> + + <dt>r</dt> <dd><p>Growth rate of the increase in the rate constant.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The value of the response variable at time <code>t</code>.</p> + + +<p>The value of the response variable at time <code>t</code>.</p> </div> <div id="note"> <h2>Note</h2> @@ -140,57 +157,57 @@ Version 1.1, 18 December 2014 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># Reproduce the plot on page 57 of FOCUS (2014)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.2</span><span class="op">)</span>,</span> -<span class="r-in"> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span>,</span> -<span class="r-in"> xlab <span class="op">=</span> <span class="st">"Time"</span>, ylab <span class="op">=</span> <span class="st">"Residue"</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.4</span><span class="op">)</span>,</span> -<span class="r-in"> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span>, col <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.8</span><span class="op">)</span>,</span> -<span class="r-in"> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">3</span>, col <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.001</span>, <span class="fl">0.2</span><span class="op">)</span>,</span> -<span class="r-in"> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">4</span>, col <span class="op">=</span> <span class="fl">4</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.08</span>, <span class="fl">0.2</span><span class="op">)</span>,</span> -<span class="r-in"> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">5</span>, col <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></span><span class="op">(</span><span class="st">"topright"</span>, inset <span class="op">=</span> <span class="fl">0.05</span>,</span> -<span class="r-in"> legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"k0 = "</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.0001</span>, <span class="fl">0.0001</span>, <span class="fl">0.0001</span>, <span class="fl">0.001</span>, <span class="fl">0.08</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="st">", r = "</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.2</span>, <span class="fl">0.4</span>, <span class="fl">0.8</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> lty <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">5</span>, col <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Reproduce the plot on page 57 of FOCUS (2014)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> xlab <span class="op">=</span> <span class="st">"Time"</span>, ylab <span class="op">=</span> <span class="st">"Residue"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span>, col <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.8</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">3</span>, col <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.001</span>, <span class="fl">0.2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">4</span>, col <span class="op">=</span> <span class="fl">4</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.08</span>, <span class="fl">0.2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> from <span class="op">=</span> <span class="fl">0</span>, to <span class="op">=</span> <span class="fl">100</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">5</span>, col <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></span><span class="op">(</span><span class="st">"topright"</span>, inset <span class="op">=</span> <span class="fl">0.05</span>,</span></span> +<span class="r-in"><span> legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"k0 = "</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.0001</span>, <span class="fl">0.0001</span>, <span class="fl">0.0001</span>, <span class="fl">0.001</span>, <span class="fl">0.08</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="st">", r = "</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.2</span>, <span class="fl">0.4</span>, <span class="fl">0.8</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> lty <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">5</span>, col <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="logistic.solution-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># Fit with synthetic data</span></span> -<span class="r-in"> <span class="va">logistic</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"logistic"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">parms_logistic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>kmax <span class="op">=</span> <span class="fl">0.08</span>, k0 <span class="op">=</span> <span class="fl">0.0001</span>, r <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">d_logistic</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">logistic</span>,</span> -<span class="r-in"> <span class="va">parms_logistic</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">d_2_1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_logistic</span>,</span> -<span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="sigma_twocomp.html">sigma_twocomp</a></span><span class="op">(</span><span class="va">x</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span>,</span> -<span class="r-in"> n <span class="op">=</span> <span class="fl">1</span>, reps <span class="op">=</span> <span class="fl">2</span>, digits <span class="op">=</span> <span class="fl">5</span>, LOD <span class="op">=</span> <span class="fl">0.1</span>, seed <span class="op">=</span> <span class="fl">123456</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">m</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"logistic"</span>, <span class="va">d_2_1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Fit with synthetic data</span></span></span> +<span class="r-in"><span> <span class="va">logistic</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"logistic"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">parms_logistic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>kmax <span class="op">=</span> <span class="fl">0.08</span>, k0 <span class="op">=</span> <span class="fl">0.0001</span>, r <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">d_logistic</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">logistic</span>,</span></span> +<span class="r-in"><span> <span class="va">parms_logistic</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">d_2_1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_logistic</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="sigma_twocomp.html">sigma_twocomp</a></span><span class="op">(</span><span class="va">x</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span>, reps <span class="op">=</span> <span class="fl">2</span>, digits <span class="op">=</span> <span class="fl">5</span>, LOD <span class="op">=</span> <span class="fl">0.1</span>, seed <span class="op">=</span> <span class="fl">123456</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">m</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"logistic"</span>, <span class="va">d_2_1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="logistic.solution-2.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02</span> <span class="r-out co"><span class="r-pr">#></span> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08</span> -<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08</span> +<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 109.9341588</span> <span class="r-out co"><span class="r-pr">#></span> kmax 0.1041853</span> -<span class="r-out co"><span class="r-pr">#></span> k0 0.4448750</span> -<span class="r-out co"><span class="r-pr">#></span> r 1.1821121</span> +<span class="r-out co"><span class="r-pr">#></span> k0 0.4448749</span> +<span class="r-out co"><span class="r-pr">#></span> r 1.1821120</span> <span class="r-out co"><span class="r-pr">#></span> sigma 7.3256566</span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span></span></span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_k0 DT50_kmax</span> -<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.854 10.83349</span> -<span class="r-in"></span> +<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.853 10.83349</span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -205,7 +222,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index bc8dab67..a053a032 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -21,7 +21,7 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,11 +101,11 @@ and can be expressed by fixing the parameters of the other.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -107,11 +113,16 @@ and can be expressed by fixing the parameters of the other.</p> <dl><dt>object</dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object, or an <code><a href="mmkin.html">mmkin</a></code> column object containing two fits to the same data.</p></dd> + + <dt>object_2</dt> <dd><p>Optionally, another mkinfit object fitted to the same data.</p></dd> + + <dt>...</dt> <dd><p>Argument to <code><a href="mkinfit.html">mkinfit</a></code>, passed to <code><a href="update.mkinfit.html">update.mkinfit</a></code> for creating the alternative fitted object.</p></dd> + </dl></div> <div id="details"> <h2>Details</h2> @@ -125,11 +136,11 @@ lower number of fitted parameters (null hypothesis).</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="va">sfo_fit</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="va">sfo_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> @@ -139,7 +150,7 @@ lower number of fitted parameters (null hypothesis).</p> <span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">sfo_fit</span>, <span class="va">dfop_fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">sfo_fit</span>, <span class="va">dfop_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> @@ -149,14 +160,14 @@ lower number of fitted parameters (null hypothesis).</p> <span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The following two examples are commented out as they fail during</span></span> -<span class="r-in"><span class="co"># generation of the static help pages by pkgdown</span></span> -<span class="r-in"><span class="co">#lrtest(dfop_fit, error_model = "tc")</span></span> -<span class="r-in"><span class="co">#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># However, this equivalent syntax also works for static help pages</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following two examples are commented out as they fail during</span></span></span> +<span class="r-in"><span><span class="co"># generation of the static help pages by pkgdown</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, error_model = "tc")</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># However, this equivalent syntax also works for static help pages</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model tc</span> @@ -166,7 +177,7 @@ lower number of fitted parameters (null hypothesis).</p> <span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -1 15.731 7.302e-05 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, fixed_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, fixed_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> @@ -176,7 +187,7 @@ lower number of fitted parameters (null hypothesis).</p> <span class="r-out co"><span class="r-pr">#></span> 2 4 -57.340 -1 29.776 4.851e-08 ***</span> <span class="r-out co"><span class="r-pr">#></span> ---</span> <span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -191,7 +202,7 @@ lower number of fitted parameters (null hypothesis).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 69da881b..3c8e1662 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -23,7 +23,7 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -50,19 +50,25 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -98,49 +104,72 @@ soil section of the FOCUS guidance.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="va">windows</span><span class="op">)</span> - -<span class="fu">max_twa_sfo</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k</span>, <span class="va">t</span><span class="op">)</span> - -<span class="fu">max_twa_fomc</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">alpha</span>, <span class="va">beta</span>, <span class="va">t</span><span class="op">)</span> - -<span class="fu">max_twa_dfop</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">t</span><span class="op">)</span> - -<span class="fu">max_twa_hs</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span>, <span class="va">t</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="va">windows</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_sfo</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_fomc</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">alpha</span>, <span class="va">beta</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_dfop</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_hs</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span>, <span class="va">t</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>fit</dt> <dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>windows</dt> <dd><p>The width of the time windows for which the TWAs should be calculated.</p></dd> + + <dt>M0</dt> <dd><p>The initial concentration for which the maximum time weighted average over the decline curve should be calculated. The default is to use a value of 1, which means that a relative maximum time weighted average factor (f_twa) is calculated.</p></dd> + + <dt>k</dt> <dd><p>The rate constant in the case of SFO kinetics.</p></dd> + + <dt>t</dt> <dd><p>The width of the time window.</p></dd> + + <dt>alpha</dt> <dd><p>Parameter of the FOMC model.</p></dd> + + <dt>beta</dt> <dd><p>Parameter of the FOMC model.</p></dd> + + <dt>k1</dt> <dd><p>The first rate constant of the DFOP or the HS kinetics.</p></dd> + + <dt>k2</dt> <dd><p>The second rate constant of the DFOP or the HS kinetics.</p></dd> + + <dt>g</dt> <dd><p>Parameter of the DFOP model.</p></dd> + + <dt>tb</dt> <dd><p>Parameter of the HS model.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>For <code>max_twa_parent</code>, a numeric vector, named using the + + +<p>For <code>max_twa_parent</code>, a numeric vector, named using the <code>windows</code> argument. For the other functions, a numeric vector of length one (also known as 'a number').</p> </div> @@ -159,12 +188,12 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 7 21 </span> <span class="r-out co"><span class="r-pr">#></span> 34.71343 18.22124 </span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -179,7 +208,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 97ac647e..0460e376 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -19,7 +19,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,7 +97,7 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">mccall81_245T</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div> </div> <div id="format"> @@ -122,80 +128,80 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span> -<span class="r-in"> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span> -<span class="r-in"> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074929 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993439 1.356073 9.756988e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340365 1.562627 6.949413e-02</span> -<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439498 1.488441 7.867788e-02</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558786 5.123989 6.233156e-05</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> <span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061401 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013878 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.706607296 3.322649e+00</span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span> -<span class="r-in"> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span> -<span class="r-in"> <span class="co"># the sink in the model generation</span></span> -<span class="r-in"> <span class="va">SFO_SFO_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span> -<span class="r-in"> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span></span> +<span class="r-in"><span> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span></span> +<span class="r-in"><span> <span class="co"># the sink in the model generation</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653038 48.028439 4.993108e-19 99.271020197</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343667 23.643268 3.573556e-14 0.039650977</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050583e-01 0.1177237899 3.440751 1.679257e-03 0.218746592</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872895e-08 0.005377082</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198824 2.039410e-12 0.547975622</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.084390e+02</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 4.743877e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 7.500560e-01</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 8.295499e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.921231e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.318272e+00</span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="co"># }</span></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -210,7 +216,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index bea9f2d8..dedb8660 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,36 +93,47 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mean_degparms</span><span class="op">(</span> - <span class="va">object</span>, - random <span class="op">=</span> <span class="cn">FALSE</span>, - test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, - conf.level <span class="op">=</span> <span class="fl">0.6</span>, - default_log_parms <span class="op">=</span> <span class="cn">NA</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_degparms</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> random <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> +<span> default_log_parms <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> + + <dt>random</dt> <dd><p>Should a list with fixed and random effects be returned?</p></dd> + + <dt>test_log_parms</dt> <dd><p>If TRUE, log parameters are only considered in the mean calculations if their untransformed counterparts (most likely rate constants) pass the t-test for significant difference from zero.</p></dd> + + <dt>conf.level</dt> <dd><p>Possibility to adjust the required confidence level for parameter that are tested if requested by 'test_log_parms'.</p></dd> + + <dt>default_log_parms</dt> <dd><p>If set to a numeric value, this is used as a default value for the tested log parameters that failed the t-test.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>If random is FALSE (default), a named vector containing mean values + + +<p>If random is FALSE (default), a named vector containing mean values of the fitted degradation model parameters. If random is TRUE, a list with fixed and random effects, in the format required by the start argument of nlme for the case of a single grouping variable ds.</p> @@ -134,7 +151,7 @@ nlme for the case of a single grouping variable ds.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 25be0af6..e4b3e9d0 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -49,19 +49,25 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -96,12 +102,18 @@ mixed-effects model fitting functions.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre><code>mhmkin(objects, backend = "saemix", algorithm = "saem", ...) + <div class="sourceCode"><pre><code>mhmkin(objects, ...) + +# S3 method for mmkin +mhmkin(objects, ...) # S3 method for list mhmkin( objects, backend = "saemix", + algorithm = "saem", + no_random_effect = NULL, + auto_ranef_threshold = 3, ..., cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL @@ -118,7 +130,14 @@ print(x, ...)</code></pre></div> <h2>Arguments</h2> <dl><dt>objects</dt> <dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same -degradation models to the same data, but using different error models.</p></dd> +degradation models to the same data, but using different error models. +Alternatively, a single <a href="mmkin.html">mmkin</a> object containing fits of several +degradation models to the same data</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments that will be passed to the nonlinear mixed-effects +model fitting function.</p></dd> <dt>backend</dt> @@ -130,9 +149,17 @@ supported</p></dd> <dd><p>The algorithm to be used for fitting (currently not used)</p></dd> -<dt>...</dt> -<dd><p>Further arguments that will be passed to the nonlinear mixed-effects -model fitting function.</p></dd> +<dt>no_random_effect</dt> +<dd><p>Default is NULL and will be passed to <a href="saem.html">saem</a>. If +you specify "auto", random effects are only included if the number +of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'. +Beware that while this may make for convenient model reduction or even +numerical stability of the algorithm, it will likely lead to +underparameterised models.</p></dd> + + +<dt>auto_ranef_threshold</dt> +<dd><p>See 'no_random_effect.</p></dd> <dt>cores</dt> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex fe7e6c47..dbba1b03 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index dfc7a731..5b250072 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,73 +93,84 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mixed.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object</p></dd> + + <dt>...</dt> <dd><p>Currently not used</p></dd> + + <dt>method</dt> <dd><p>The method to be used</p></dd> + + <dt>x</dt> <dd><p>A mixed.mmkin object to print</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object of class 'mixed.mmkin' which has the observed data in a + + +<p>An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting</p> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span> -<span class="r-in"><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span> -<span class="r-in"><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span> -<span class="r-in"><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> -<span class="r-in"> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"> <span class="op">}</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span> -<span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span> -<span class="r-in"> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"><span class="op">}</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span></span> +<span class="r-in"><span><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span></span> +<span class="r-in"><span><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic model fitted by nonlinear regression to each dataset</span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -177,12 +194,12 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean fitted parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.762456 -0.004347 -3.348812 -3.986853 </span> +<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.087391 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -197,7 +214,7 @@ single dataframe which is convenient for plotting</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ba00a80a..1008876d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -19,7 +19,7 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,7 +97,7 @@ variable and several dependent variables as columns.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">long_data</span>, time <span class="op">=</span> <span class="st">"time"</span>, outtime <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">long_data</span>, time <span class="op">=</span> <span class="st">"time"</span>, outtime <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -101,14 +107,21 @@ variable and several dependent variables as columns.</p> the time values specified by the <code>time</code> argument, one column called "name" with the grouping of the observed values, and finally one column of observed values called "value".</p></dd> + + <dt>time</dt> <dd><p>The name of the time variable in the long input data.</p></dd> + + <dt>outtime</dt> <dd><p>The name of the time variable in the wide output data.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Dataframe in wide format.</p> + + +<p>Dataframe in wide format.</p> </div> <div id="author"> <h2>Author</h2> @@ -117,8 +130,8 @@ observed values called "value".</p></dd> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time parent m1</span> <span class="r-out co"><span class="r-pr">#></span> 1 0 99.46 0.00</span> <span class="r-out co"><span class="r-pr">#></span> 2 0 102.04 0.00</span> @@ -142,7 +155,7 @@ observed values called "value".</p></dd> <span class="r-out co"><span class="r-pr">#></span> 20 100 NA 33.13</span> <span class="r-out co"><span class="r-pr">#></span> 21 120 NA 25.15</span> <span class="r-out co"><span class="r-pr">#></span> 22 120 NA 33.31</span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -157,7 +170,7 @@ observed values called "value".</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 0cb9ebca..15ead67f 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -19,7 +19,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,7 +97,7 @@ several dependent variable and converts it into the long form as required by </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide_data</span>, time <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide_data</span>, time <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -100,12 +106,17 @@ several dependent variable and converts it into the long form as required by <dd><p>The dataframe must contain one variable with the time values specified by the <code>time</code> argument and usually more than one column of observed values.</p></dd> + + <dt>time</dt> <dd><p>The name of the time variable.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Dataframe in long format as needed for <code><a href="mkinfit.html">mkinfit</a></code>.</p> + + +<p>Dataframe in long format as needed for <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> <div id="author"> <h2>Author</h2> @@ -114,9 +125,9 @@ column of observed values.</p></dd> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">3</span><span class="op">)</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">4</span>,<span class="fl">7</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">3</span><span class="op">)</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">4</span>,<span class="fl">7</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> name time value</span> <span class="r-out co"><span class="r-pr">#></span> 1 x 1 1</span> <span class="r-out co"><span class="r-pr">#></span> 2 x 2 4</span> @@ -124,7 +135,7 @@ column of observed values.</p></dd> <span class="r-out co"><span class="r-pr">#></span> 4 y 1 3</span> <span class="r-out co"><span class="r-pr">#></span> 5 y 2 4</span> <span class="r-out co"><span class="r-pr">#></span> 6 y 3 5</span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -139,7 +150,7 @@ column of observed values.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index f43cfed4..801d2364 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -225,7 +231,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 37ec29bd..c72fe585 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -413,7 +419,7 @@ or covariates like soil pH).</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index b6051ab8..eaed3aa4 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -18,7 +18,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,26 +95,31 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>fit</dt> <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>alpha</dt> <dd><p>The confidence level chosen for the chi-squared test.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A dataframe with the following components:</p> + + +<p>A dataframe with the following components:</p> <dl><dt>err.min</dt> <dd><p>The relative error, expressed as a fraction.</p></dd> -<dt>n.optim</dt> + <dt>n.optim</dt> <dd><p>The number of optimised parameters attributed to the data series.</p></dd> -<dt>df</dt> + <dt>df</dt> <dd><p>The number of remaining degrees of freedom for the chi2 error level calculations. Note that mean values are used for the chi2 statistic and therefore every time @@ -132,28 +143,28 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.0646 2 7</span> <span class="r-out co"><span class="r-pr">#></span> m1 0.0469 2 8</span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.1544 4 13</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.1659 2 7</span> <span class="r-out co"><span class="r-pr">#></span> m1 0.1095 2 6</span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -168,7 +179,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 852da18d..49bb1c0e 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 4b78f6eb..6c640652 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -21,7 +21,7 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,56 +101,81 @@ using the argument <code>show_errplot = TRUE</code>.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinerrplot</span><span class="op">(</span> - <span class="va">object</span>, - obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>, - xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">predicted</span><span class="op">)</span><span class="op">)</span>, - xlab <span class="op">=</span> <span class="st">"Predicted"</span>, - ylab <span class="op">=</span> <span class="st">"Squared residual"</span>, - maxy <span class="op">=</span> <span class="st">"auto"</span>, - legend <span class="op">=</span> <span class="cn">TRUE</span>, - lpos <span class="op">=</span> <span class="st">"topright"</span>, - col_obs <span class="op">=</span> <span class="st">"auto"</span>, - pch_obs <span class="op">=</span> <span class="st">"auto"</span>, - frame <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">predicted</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Predicted"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Squared residual"</span>,</span> +<span> maxy <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + <dt>obs_vars</dt> <dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in the model</p></dd> + + <dt>xlim</dt> <dd><p>plot range in x direction.</p></dd> + + <dt>xlab</dt> <dd><p>Label for the x axis.</p></dd> + + <dt>ylab</dt> <dd><p>Label for the y axis.</p></dd> + + <dt>maxy</dt> <dd><p>Maximum value of the residuals. This is used for the scaling of the y axis and defaults to "auto".</p></dd> + + <dt>legend</dt> <dd><p>Should a legend be plotted?</p></dd> + + <dt>lpos</dt> <dd><p>Where should the legend be placed? Default is "topright". Will be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + + <dt>col_obs</dt> <dd><p>Colors for the observed variables.</p></dd> + + <dt>pch_obs</dt> <dd><p>Symbols to be used for the observed variables.</p></dd> + + <dt>frame</dt> <dd><p>Should a frame be drawn around the plots?</p></dd> + + <dt>...</dt> <dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Nothing is returned by this function, as it is called for its side + + +<p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> <div id="see-also"> @@ -159,16 +190,16 @@ lines of the mkinfit object.</p></div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -183,7 +214,7 @@ lines of the mkinfit object.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3b27ac7f..62e4bd8d 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -52,19 +52,25 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -378,17 +384,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 13:14:25 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 13:14:25 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 13:58:19 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 13:58:19 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.046 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.044 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -528,11 +534,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.540</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.537 0.830</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.687 1.451</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.570</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.682 0.959</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.609 1.487</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -559,10 +564,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 13:14:36 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 13:14:36 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 13:58:30 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 13:58:30 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -571,7 +576,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.488 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.464 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 3a29b39b..7dfa740a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,22 +101,22 @@ components.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinmod</span><span class="op">(</span> - <span class="va">...</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span>, - name <span class="op">=</span> <span class="cn">NULL</span>, - speclist <span class="op">=</span> <span class="cn">NULL</span>, - quiet <span class="op">=</span> <span class="cn">FALSE</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span>, - dll_dir <span class="op">=</span> <span class="cn">NULL</span>, - unload <span class="op">=</span> <span class="cn">FALSE</span>, - overwrite <span class="op">=</span> <span class="cn">FALSE</span> -<span class="op">)</span> - -<span class="co"># S3 method for mkinmod</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span> - -<span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span> +<span> <span class="va">...</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> +<span> name <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> speclist <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> unload <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinmod</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -130,72 +136,108 @@ If the argument <code>use_of_ff</code> is set to "min" additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively fixing the flux to sink to zero. In print.mkinmod, this argument is currently not used.</p></dd> + + <dt>use_of_ff</dt> <dd><p>Specification of the use of formation fractions in the model equations and, if applicable, the coefficient matrix. If "max", formation fractions are always used (default). If "min", a minimum use of formation fractions is made, i.e. each first-order pathway to a metabolite has its own rate constant.</p></dd> + + <dt>name</dt> <dd><p>A name for the model. Should be a valid R object name.</p></dd> + + <dt>speclist</dt> <dd><p>The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL.</p></dd> + + <dt>quiet</dt> <dd><p>Should messages be suppressed?</p></dd> + + <dt>verbose</dt> <dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if applicable to give detailed information about the C function being built.</p></dd> + + <dt>dll_dir</dt> <dd><p>Directory where an DLL object, if generated internally by <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a permanent location for use in future sessions, if 'dll_dir' and 'name' are specified.</p></dd> + + <dt>unload</dt> <dd><p>If a DLL from the target location in 'dll_dir' is already loaded, should that be unloaded first?</p></dd> + + <dt>overwrite</dt> <dd><p>If a file exists at the target DLL location in 'dll_dir', should this be overwritten?</p></dd> + + <dt>x</dt> <dd><p>An <code>mkinmod</code> object.</p></dd> + + <dt>submodel</dt> <dd><p>Character vector of length one to specify the submodel type. See <code>mkinmod</code> for the list of allowed submodel names.</p></dd> + + <dt>to</dt> <dd><p>Vector of the names of the state variable to which a transformation shall be included in the model.</p></dd> + + <dt>sink</dt> <dd><p>Should a pathway to sink be included in the model in addition to the pathways to other state variables?</p></dd> + + <dt>full_name</dt> <dd><p>An optional name to be used e.g. for plotting fits performed with the model. You can use non-ASCII characters here, but then your R code will not be portable, <em>i.e.</em> may produce unintended plot results on other operating systems or system configurations.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, + + +<p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, containing, among others,</p> <dl><dt>diffs</dt> <dd><p>A vector of string representations of differential equations, one for each modelling variable.</p></dd> + <dt>map</dt> <dd><p>A list containing named character vectors for each observed variable, specifying the modelling variables by which it is represented.</p></dd> + <dt>use_of_ff</dt> <dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> + <dt>deg_func</dt> <dd><p>If generated, a function containing the solution of the degradation model.</p></dd> + <dt>coefmat</dt> <dd><p>The coefficient matrix, if the system of differential equations can be represented by one.</p></dd> + <dt>cf</dt> <dd><p>If generated, a compiled function calculating the derivatives as returned by cfunction.</p></dd> + + </dl><p>A list for use with <code>mkinmod</code>.</p> </div> <div id="details"> @@ -233,16 +275,16 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span> -<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> <span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> <span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> @@ -255,32 +297,32 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> Differential equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> -<span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> -<span class="r-in"> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span> -<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> -<span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkcKjUM/file8dd657f864c2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> -<span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span> +<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span> +<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span></span> +<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp6DB2Bl/file3f5b93b53e71f.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Show details of creating the C function</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Program source:</span> <span class="r-out co"><span class="r-pr">#></span> 1: #include <R.h></span> <span class="r-out co"><span class="r-pr">#></span> 2: </span> @@ -302,10 +344,10 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span> <span class="r-out co"><span class="r-pr">#></span> 19: }</span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The symbolic solution which is available in this case is not</span></span> -<span class="r-in"><span class="co"># made for human reading but for speed of computation</span></span> -<span class="r-in"><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span> +<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span></span> <span class="r-out co"><span class="r-pr">#></span> function (observed, odeini, odeparms) </span> <span class="r-out co"><span class="r-pr">#></span> {</span> <span class="r-out co"><span class="r-pr">#></span> predicted <- numeric(0)</span> @@ -321,21 +363,21 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55cc1a5f8ad8></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> -<span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> -<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span> -<span class="r-in"> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55556401ac50></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> +<span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -350,7 +392,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 69d9ac75..fff98391 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index b9eda413..a41456f2 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -18,7 +18,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,17 +95,20 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Nothing is returned by this function, as it is called for its side + + +<p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> <div id="author"> @@ -109,18 +118,20 @@ effect, namely to produce a plot.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> anisole <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> +<span class="r-in"><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -135,7 +146,7 @@ effect, namely to produce a plot.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index cad5b35f..46ffe33e 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -18,7 +18,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,19 +95,24 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinplot</span><span class="op">(</span><span class="va">fit</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinplot</span><span class="op">(</span><span class="va">fit</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>fit</dt> <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>...</dt> <dd><p>further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="author"> <h2>Author</h2> @@ -120,7 +131,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index d888bb25..2aab0b50 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -86,95 +92,125 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> <div class="ref-description"> <p>This function produces a time series for all the observed variables in a -kinetic model as specified by <code><a href="mkinmod.html">mkinmod</a></code>, using a specific set of +kinetic model as specified by <a href="mkinmod.html">mkinmod</a>, using a specific set of kinetic parameters and initial values for the state variables.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mkinmod</span> -<span class="fu">mkinpredict</span><span class="op">(</span> - <span class="va">x</span>, - odeparms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent_sink <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, - odeini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, - outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, - solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, - use_compiled <span class="op">=</span> <span class="st">"auto"</span>, - method.ode <span class="op">=</span> <span class="st">"lsoda"</span>, - atol <span class="op">=</span> <span class="fl">1e-08</span>, - rtol <span class="op">=</span> <span class="fl">1e-10</span>, - map_output <span class="op">=</span> <span class="cn">TRUE</span>, - na_stop <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="co"># S3 method for mkinfit</span> -<span class="fu">mkinpredict</span><span class="op">(</span> - <span class="va">x</span>, - odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>, - odeini <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.state</span>, - outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, - solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, - use_compiled <span class="op">=</span> <span class="st">"auto"</span>, - method.ode <span class="op">=</span> <span class="st">"lsoda"</span>, - atol <span class="op">=</span> <span class="fl">1e-08</span>, - rtol <span class="op">=</span> <span class="fl">1e-10</span>, - map_output <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinmod</span></span> +<span><span class="fu">mkinpredict</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> odeparms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent_sink <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span> odeini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span> outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span> +<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span> +<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span> +<span> maxsteps <span class="op">=</span> <span class="fl">20000</span>,</span> +<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> na_stop <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">mkinpredict</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> odeini <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.state</span>,</span> +<span> outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span> +<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span> +<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span> +<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>x</dt> -<dd><p>A kinetic model as produced by <code><a href="mkinmod.html">mkinmod</a></code>, or a kinetic -fit as fitted by <code><a href="mkinfit.html">mkinfit</a></code>. In the latter case, the fitted -parameters are used for the prediction.</p></dd> +<dd><p>A kinetic model as produced by <a href="mkinmod.html">mkinmod</a>, or a kinetic fit as +fitted by <a href="mkinfit.html">mkinfit</a>. In the latter case, the fitted parameters are used for +the prediction.</p></dd> + + <dt>odeparms</dt> <dd><p>A numeric vector specifying the parameters used in the -kinetic model, which is generally defined as a set of ordinary -differential equations.</p></dd> +kinetic model, which is generally defined as a set of ordinary differential +equations.</p></dd> + + <dt>odeini</dt> <dd><p>A numeric vector containing the initial values of the state variables of the model. Note that the state variables can differ from the observed variables, for example in the case of the SFORB model.</p></dd> + + <dt>outtimes</dt> <dd><p>A numeric vector specifying the time points for which model predictions should be generated.</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to the ode solver in case such a solver is used.</p></dd> + + <dt>solution_type</dt> <dd><p>The method that should be used for producing the predictions. This should generally be "analytical" if there is only one observed variable, and usually "deSolve" in the case of several observed variables. The third possibility "eigen" is faster but not applicable to some models e.g. using FOMC for the parent compound.</p></dd> + + <dt>use_compiled</dt> <dd><p>If set to <code>FALSE</code>, no compiled version of the -<code><a href="mkinmod.html">mkinmod</a></code> model is used, even if is present.</p></dd> +<a href="mkinmod.html">mkinmod</a> model is used, even if is present.</p></dd> + + <dt>method.ode</dt> -<dd><p>The solution method passed via <code>mkinpredict</code> -to <code>ode</code> in case the solution type is "deSolve". The default -"lsoda" is performant, but sometimes fails to converge.</p></dd> +<dd><p>The solution method passed via mkinpredict to ode] in +case the solution type is "deSolve". The default "lsoda" is performant, but +sometimes fails to converge.</p></dd> + + <dt>atol</dt> -<dd><p>Absolute error tolerance, passed to <code>ode</code>. Default -is 1e-8, lower than in <code>lsoda</code>.</p></dd> +<dd><p>Absolute error tolerance, passed to ode. Default is 1e-8, +lower than in lsoda.</p></dd> + + <dt>rtol</dt> -<dd><p>Absolute error tolerance, passed to <code>ode</code>. Default -is 1e-10, much lower than in <code>lsoda</code>.</p></dd> +<dd><p>Absolute error tolerance, passed to ode. Default is 1e-10, +much lower than in lsoda.</p></dd> + + +<dt>maxsteps</dt> +<dd><p>Maximum number of steps, passed to ode.</p></dd> + + <dt>map_output</dt> <dd><p>Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to FALSE). Setting this to FALSE has no effect for analytical solutions, as these always return mapped output.</p></dd> + + <dt>na_stop</dt> -<dd><p>Should it be an error if deSolve::ode returns NaN values</p></dd> +<dd><p>Should it be an error if ode returns NaN values</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A matrix with the numeric solution in wide format</p> + + +<p>A matrix with the numeric solution in wide format</p> </div> <div id="author"> <h2>Author</h2> @@ -183,11 +219,11 @@ as these always return mapped output.</p></dd> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># Compare solution types</span></span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Compare solution types</span></span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol</span> <span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> <span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> @@ -210,8 +246,8 @@ as these always return mapped output.</p></dd> <span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> <span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> <span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol</span> <span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> <span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> @@ -234,8 +270,8 @@ as these always return mapped output.</p></dd> <span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> <span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> <span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol</span> <span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> <span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> @@ -258,8 +294,8 @@ as these always return mapped output.</p></dd> <span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> <span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> <span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol</span> <span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> <span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> @@ -282,77 +318,82 @@ as these always return mapped output.</p></dd> <span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> <span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> <span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Compare integration methods to analytical solution</span></span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Compare integration methods to analytical solution</span></span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> -<span class="r-in"> method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2480043 </span> -<span class="r-in"><span class="co"># rk4 is not as precise here</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The number of output times used to make a lot of difference until the</span></span> -<span class="r-in"><span class="co"># default for atol was adjusted</span></span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span></span> +<span class="r-in"><span><span class="co"># rk4 is not as precise here</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The number of output times used to make a lot of difference until the</span></span></span> +<span class="r-in"><span><span class="co"># default for atol was adjusted</span></span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> -<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">2001</span>,<span class="op">]</span></span> +<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">2001</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Comparison of the performance of solution types</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Comparison of the performance of solution types</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> -<span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> -<span class="r-in"> deSolve_compiled <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> -<span class="r-in"> deSolve <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> -<span class="r-in"> analytical <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="co"># Predict from a fitted model</span></span> -<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> time parent m1</span> -<span class="r-out co"><span class="r-pr">#></span> 0 0.0 82.49216 0.000000</span> -<span class="r-out co"><span class="r-pr">#></span> 0.1 0.1 80.00562 1.236394</span> -<span class="r-out co"><span class="r-pr">#></span> 0.2 0.2 77.59404 2.423201</span> -<span class="r-out co"><span class="r-pr">#></span> 0.3 0.3 75.25514 3.562040</span> -<span class="r-out co"><span class="r-pr">#></span> 0.4 0.4 72.98675 4.654478</span> -<span class="r-out co"><span class="r-pr">#></span> 0.5 0.5 70.78673 5.702033</span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span> +<span class="r-in"><span> deSolve_compiled <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span> +<span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span> +<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 5.5 0.022</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 51.0 0.204</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> DLSODA- At current T (=R1), MXSTEP (=I1) steps </span> +<span class="r-out co"><span class="r-pr">#></span> taken on this call before reaching TOUT </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, I1 = 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 9.99904e-07</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>an excessive amount of work (> maxsteps ) was done, but integration was not successful - increase maxsteps</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Returning early. Results are accurate, as far as they go</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in out[available, var]:</span> (subscript) logical subscript too long</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -367,7 +408,7 @@ as these always return mapped output.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 654b93d8..6966cd90 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -20,7 +20,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -93,60 +99,87 @@ argument <code>show_residuals = TRUE</code>.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinresplot</span><span class="op">(</span> - <span class="va">object</span>, - obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>, - xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>, - standardized <span class="op">=</span> <span class="cn">FALSE</span>, - xlab <span class="op">=</span> <span class="st">"Time"</span>, - ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>, - maxabs <span class="op">=</span> <span class="st">"auto"</span>, - legend <span class="op">=</span> <span class="cn">TRUE</span>, - lpos <span class="op">=</span> <span class="st">"topright"</span>, - col_obs <span class="op">=</span> <span class="st">"auto"</span>, - pch_obs <span class="op">=</span> <span class="st">"auto"</span>, - frame <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,</span> +<span> maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + <dt>obs_vars</dt> <dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in the model</p></dd> + + <dt>xlim</dt> <dd><p>plot range in x direction.</p></dd> + + <dt>standardized</dt> <dd><p>Should the residuals be standardized by dividing by the standard deviation given by the error model of the fit?</p></dd> + + <dt>xlab</dt> <dd><p>Label for the x axis.</p></dd> + + <dt>ylab</dt> <dd><p>Label for the y axis.</p></dd> + + <dt>maxabs</dt> <dd><p>Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".</p></dd> + + <dt>legend</dt> <dd><p>Should a legend be plotted?</p></dd> + + <dt>lpos</dt> <dd><p>Where should the legend be placed? Default is "topright". Will be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + + <dt>col_obs</dt> <dd><p>Colors for the observed variables.</p></dd> + + <dt>pch_obs</dt> <dd><p>Symbols to be used for the observed variables.</p></dd> + + <dt>frame</dt> <dd><p>Should a frame be drawn around the plots?</p></dd> + + <dt>...</dt> <dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Nothing is returned by this function, as it is called for its side + + +<p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> <div id="see-also"> @@ -162,14 +195,14 @@ combining the plot of the fit and the residual plot.</p></div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -184,7 +217,7 @@ combining the plot of the fit and the residual plot.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 75cbc054..8ad9c11d 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 76f42b73..da2a48a8 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex e92d81b2..10d3f35b 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 8d747ffe..132380a8 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex ffd7640d..4bfcc55e 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index cbb46ab0..686c9310 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -20,7 +20,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -92,16 +98,16 @@ datasets specified in its first two arguments.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mmkin</span><span class="op">(</span> - models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, - <span class="va">datasets</span>, - cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>, - cluster <span class="op">=</span> <span class="cn">NULL</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mmkin</span><span class="op">(</span></span> +<span> models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> +<span> <span class="va">datasets</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -110,9 +116,13 @@ datasets specified in its first two arguments.</p> <dd><p>Either a character vector of shorthand names like <code>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</code>, or an optionally named list of <code><a href="mkinmod.html">mkinmod</a></code> objects.</p></dd> + + <dt>datasets</dt> <dd><p>An optionally named list of datasets suitable as observed data for <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>cores</dt> <dd><p>The number of cores to be used for multicore processing. This is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows @@ -120,17 +130,29 @@ machines, cores > 1 is not supported, you need to use the <code>cluster</code argument to use multiple logical processors. Per default, all cores detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where the default is 1.</p></dd> + + <dt>cluster</dt> -<dd><p>A cluster as returned by <code><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeCluster</a></code> to be used +<dd><p>A cluster as returned by <code>makeCluster</code> to be used for parallel execution.</p></dd> + + <dt>...</dt> <dd><p>Not used.</p></dd> + + <dt>x</dt> <dd><p>An mmkin object.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code>objects and/or try-errors that can be indexed using the model names for the + + +<p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code></p> + + +<p>objects and/or try-errors that can be indexed using the model names for the first index (row index) and the dataset names for the second index (column index).</p> </div> @@ -146,33 +168,33 @@ plotting.</p></div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">m_synth_FOMC_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_FOMC_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">models</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span> -<span class="r-in"><span class="va">datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">time_default</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="va">time_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">time_default</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">models</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">time_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 35.152 1.185 8.439 </span> -<span class="r-in"><span class="va">time_1</span></span> +<span class="r-out co"><span class="r-pr">#></span> 5.526 0.809 2.006 </span> +<span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 14.744 0.008 14.768 </span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> 5.403 0.008 5.412 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_M1 parent_sink M1_M2 M1_sink </span> <span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505683 0.2494317 </span> @@ -180,51 +202,44 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> -<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725955</span> -<span class="r-out co"><span class="r-pr">#></span> M2 33.720111 112.015785</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span> -<span class="r-in"><span class="co"># by plot.mkinfit and can be plotted using plot_sep</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span></span> +<span class="r-in"><span><span class="co"># by plot.mkinfit and can be plotted using plot_sep</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span> -<span class="r-in"><span class="co"># allow to plot the observed variables separately</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span></span> +<span class="r-in"><span><span class="co"># allow to plot the observed variables separately</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span> -<span class="r-in"><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span> -<span class="r-in"><span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</span>, B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span> -<span class="r-in"> cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> -<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> dataset</span> -<span class="r-out co"><span class="r-pr">#></span> model A B C D </span> -<span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC C OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> DFOP OK OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> -<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> -<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> -<span class="r-in"><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span> -<span class="r-in"><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span></span> +<span class="r-in"><span><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span></span> +<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in makePSOCKcluster(12):</span> could not find function "makePSOCKcluster"</span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</span>, B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in system.time({ if (is.null(cluster)) { results <- parallel::mclapply(as.list(1:n.fits), fit_function, mc.cores = cores, mc.preschedule = FALSE) } else { results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function) }}):</span> object 'cl' not found</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in print(f):</span> object 'f' not found</span> +<span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span> +<span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span> +<span class="r-in"><span><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in stopCluster(cl):</span> could not find function "stopCluster"</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -239,7 +254,7 @@ plotting.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png Binary files differnew file mode 100644 index 00000000..cd12bac1 --- /dev/null +++ b/docs/reference/multistart-1.png diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png Binary files differnew file mode 100644 index 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crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Perform a hierarchical model fit with multiple starting values — multistart"><meta property="og:description" content="The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Perform a hierarchical model fit with multiple starting values</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/multistart.R" class="external-link"><code>R/multistart.R</code></a></small> + <div class="hidden name"><code>multistart.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021).</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> n <span class="op">=</span> <span class="fl">50</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, cluster <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for default</span></span> +<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for default</span></span> +<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The fit object to work with</p></dd> + + +<dt>n</dt> +<dd><p>How many different combinations of starting parameters should be +used?</p></dd> + + +<dt>cores</dt> +<dd><p>How many fits should be run in parallel (only on posix platforms)?</p></dd> + + +<dt>cluster</dt> +<dd><p>A cluster as returned by <a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">parallel::makeCluster</a> to be used +for parallel execution.</p></dd> + + +<dt>...</dt> +<dd><p>Passed to the update function.</p></dd> + + +<dt>x</dt> +<dd><p>The multistart object to print</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes +'multistart.saem.mmkin' and 'multistart'.</p> + + +<p>The object with the highest likelihood</p> + + +<p>The index of the object with the highest likelihood</p> + </div> + <div id="references"> + <h2>References</h2> + <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical +identifiability in the frame of nonlinear mixed effects models: the example +of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. +doi: 10.1186/s12859-021-04373-4.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="parplot.html">parplot</a>, <a href="llhist.html">llhist</a></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">ds_i</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(log_k2)"</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span> +<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span> +<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 1d22b617..5906db4c 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -21,7 +21,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,10 +101,10 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for nafta</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="source"> @@ -120,22 +126,35 @@ Degradation time values specified by the <code>time</code> argument, one column called "name" with the grouping of the observed values, and finally one column of observed values called "value".</p></dd> + + <dt>title</dt> <dd><p>Optional title of the dataset</p></dd> + + <dt>quiet</dt> <dd><p>Should the evaluation text be shown?</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="mmkin.html">mmkin</a></code> (not for the printing method).</p></dd> + + <dt>x</dt> <dd><p>An <code>nafta</code> object.</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to be used for printing parameters and dissipation times.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An list of class <code>nafta</code>. The list element named "mmkin" is the + + +<p>An list of class <code>nafta</code>. The list element named "mmkin" is the <code><a href="mmkin.html">mmkin</a></code> object containing the fits of the three models. The list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.</p> @@ -147,13 +166,13 @@ list element "data" contains the dataset used in the fits.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> <span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> <span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> <span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> <span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> <span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> @@ -192,9 +211,9 @@ list element "data" contains the dataset used in the fits.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> <span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nafta-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -209,7 +228,7 @@ list element "data" contains the dataset used in the fits.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 0b6cb78d..f4d04e1d 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex ef152270..d9512f41 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index ff8de9f3..83576e56 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -93,20 +99,25 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span> - -<span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A function that can be used with nlme -A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> + + +<p>A function that can be used with nlme</p> + + +<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> </div> <div id="see-also"> <h2>See also</h2> @@ -115,78 +126,78 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># These assignments are necessary for these objects to be</span></span> -<span class="r-in"><span class="co"># visible to nlme and augPred when evaluation is done by</span></span> -<span class="r-in"><span class="co"># pkgdown to generate the html docs.</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span> -<span class="r-in"> data <span class="op">=</span> <span class="va">grouped_data</span>,</span> -<span class="r-in"> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span> -<span class="r-in"> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span> -<span class="r-in"> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># These assignments are necessary for these objects to be</span></span></span> +<span class="r-in"><span><span class="co"># visible to nlme and augPred when evaluation is done by</span></span></span> +<span class="r-in"><span><span class="co"># pkgdown to generate the html docs.</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">grouped_data</span>,</span></span> +<span class="r-in"><span> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> <span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 300.6824 310.2426 -145.3412</span> +<span class="r-out co"><span class="r-pr">#></span> 266.6428 275.8935 -128.3214</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 1.697361 0.6801209 3.666073</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.000368491 0.7058039 3.065183</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> -<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.99378 1.3890416 46 72.70753 0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0</span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> prnt_0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.027 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.031 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> -<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> -<span class="r-out co"><span class="r-pr">#></span> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 </span> +<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> +<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 50</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> <span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># augPred does not work on fits with more than one state</span></span> -<span class="r-in"><span class="co"># variable</span></span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span> -<span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># augPred does not work on fits with more than one state</span></span></span> +<span class="r-in"><span><span class="co"># variable</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span></span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> </code></pre></div> </div> @@ -202,7 +213,7 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index c8bd28e9..1e294eaf 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,78 +97,115 @@ have been obtained by fitting the same model to a list of datasets.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span> - <span class="va">model</span>, - data <span class="op">=</span> <span class="st">"auto"</span>, - fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span> - <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, - random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, - <span class="va">groups</span>, - start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, - correlation <span class="op">=</span> <span class="cn">NULL</span>, - weights <span class="op">=</span> <span class="cn">NULL</span>, - <span class="va">subset</span>, - method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ML"</span>, <span class="st">"REML"</span><span class="op">)</span>, - na.action <span class="op">=</span> <span class="va">na.fail</span>, - <span class="va">naPattern</span>, - control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span> -<span class="op">)</span> - -<span class="co"># S3 method for nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span></span> +<span> <span class="va">model</span>,</span> +<span> data <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,</span> +<span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> +<span> <span class="va">groups</span>,</span> +<span> start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> correlation <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> weights <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">subset</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ML"</span>, <span class="st">"REML"</span><span class="op">)</span>,</span> +<span> na.action <span class="op">=</span> <span class="va">na.fail</span>,</span> +<span> <span class="va">naPattern</span>,</span> +<span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for nlme.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for nlme.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>model</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object.</p></dd> + + <dt>data</dt> <dd><p>Ignored, data are taken from the mmkin model</p></dd> + + <dt>fixed</dt> <dd><p>Ignored, all degradation parameters fitted in the mmkin model are used as fixed parameters</p></dd> + + <dt>random</dt> <dd><p>If not specified, no correlations between random effects are set up for the optimised degradation model parameters. This is achieved by using the <a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">nlme::pdDiag</a> method.</p></dd> + + <dt>groups</dt> <dd><p>See the documentation of nlme</p></dd> + + <dt>start</dt> <dd><p>If not specified, mean values of the fitted degradation parameters taken from the mmkin object are used</p></dd> + + <dt>correlation</dt> <dd><p>See the documentation of nlme</p></dd> + + <dt>weights</dt> <dd><p>passed to nlme</p></dd> + + <dt>subset</dt> <dd><p>passed to nlme</p></dd> + + <dt>method</dt> <dd><p>passed to nlme</p></dd> + + <dt>na.action</dt> <dd><p>passed to nlme</p></dd> + + <dt>naPattern</dt> <dd><p>passed to nlme</p></dd> + + <dt>control</dt> <dd><p>passed to nlme</p></dd> + + <dt>verbose</dt> <dd><p>passed to nlme</p></dd> + + <dt>x</dt> <dd><p>An nlme.mmkin object to print</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> + + <dt>...</dt> <dd><p>Update specifications passed to update.nlme</p></dd> + + <dt>object</dt> <dd><p>An nlme.mmkin object to update</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object + + +<p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> </div> <div id="details"> @@ -185,19 +228,19 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nlme_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nlme_dfop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_dfop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> @@ -222,50 +265,50 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis Residual</span> <span class="r-out co"><span class="r-pr">#></span> StdDev: 2.488 0.8447 1.33 0.4652 2.321</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme.mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34193 4.193938 43.85443</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">m_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">m_sfo_sfo_ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">m_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_2</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_sfo_sfo</span>,</span> -<span class="r-in"> <span class="st">"SFO-SFO-ff"</span> <span class="op">=</span> <span class="va">m_sfo_sfo_ff</span>,</span> -<span class="r-in"> <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">m_dfop_sfo</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">ds_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_nlme_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">m_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">m_sfo_sfo_ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">m_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_2</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_sfo_sfo</span>,</span></span> +<span class="r-in"><span> <span class="st">"SFO-SFO-ff"</span> <span class="op">=</span> <span class="va">m_sfo_sfo_ff</span>,</span></span> +<span class="r-in"><span> <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">m_dfop_sfo</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">ds_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme.mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># With formation fractions this does not coverge with defaults</span></span> -<span class="r-in"> <span class="co"># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span></span> -<span class="r-in"> <span class="co">#plot(f_nlme_sfo_sfo_ff)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># For the following, we need to increase pnlsMaxIter and the tolerance</span></span> -<span class="r-in"> <span class="co"># to get convergence</span></span> -<span class="r-in"> <span class="va">f_nlme_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> -<span class="r-in"> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># With formation fractions this does not coverge with defaults</span></span></span> +<span class="r-in"><span> <span class="co"># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span></span></span> +<span class="r-in"><span> <span class="co">#plot(f_nlme_sfo_sfo_ff)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For the following, we need to increase pnlsMaxIter and the tolerance</span></span></span> +<span class="r-in"><span> <span class="co"># to get convergence</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span> +<span class="r-in"><span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme.mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_sink parent_A1 A1_sink </span> <span class="r-out co"><span class="r-pr">#></span> 0.5912432 0.4087568 1.0000000 </span> @@ -275,27 +318,27 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> parent 19.13518 63.5657</span> <span class="r-out co"><span class="r-pr">#></span> A1 66.02155 219.3189</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> <span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30524 539.1663 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30519 539.1662 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"></span> -<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span> -<span class="r-in"> <span class="co"># Attempts to fit metabolite kinetics with the tc error model are possible,</span></span> -<span class="r-in"> <span class="co"># but need tweeking of control values and sometimes do not converge</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nlme_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nlme_dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_sfo_tc</span>, <span class="va">f_nlme_dfop</span>, <span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span> -<span class="r-in"> <span class="op">}</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span> +<span class="r-in"><span> <span class="co"># Attempts to fit metabolite kinetics with the tc error model are possible,</span></span></span> +<span class="r-in"><span> <span class="co"># but need tweeking of control values and sometimes do not converge</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_sfo_tc</span>, <span class="va">f_nlme_dfop</span>, <span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> @@ -311,7 +354,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04775 -1.82340 -4.16715 0.05685 </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05686 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> @@ -325,11 +368,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223513 0.01262371 </span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_2_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo_obs</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.23223147 0.01262395 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_2_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo_obs</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> @@ -358,24 +401,24 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049985 </span> -<span class="r-in"> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> -<span class="r-in"> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"> <span class="co"># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span></span> -<span class="r-in"> <span class="co"># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span></span> -<span class="r-in"> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049995 </span> +<span class="r-in"><span> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span> +<span class="r-in"><span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="co"># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span></span></span> +<span class="r-in"><span> <span class="co"># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span></span></span> +<span class="r-in"><span> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32092</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span> <span class="r-out co"><span class="r-pr">#></span> p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -390,7 +433,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index e37fff64..edf97142 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,20 +93,25 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/stats/nobs.html" class="external-link">nobs</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/nobs.html" class="external-link">nobs</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mkinfit object</p></dd> + + <dt>...</dt> <dd><p>For compatibility with the generic method</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The number of rows in the data included in the mkinfit object</p> + + +<p>The number of rows in the data included in the mkinfit object</p> </div> </div> @@ -115,7 +126,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 18f3566e..a3d62d1e 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -1,7 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Extract model parameters from mkinfit models — parms • mkin</title><!-- jquery --><script 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returns degradation model parameters as well as error +model parameters per default, in order to avoid working with a fitted model +without considering the error structure that was assumed for the fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body data-spy="scroll" data-target="#toc"> @@ -19,7 +19,7 @@ considering the error structure that was assumed for the fit."><!-- mathjax -->< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ considering the error structure that was assumed for the fit."><!-- mathjax -->< <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -79,69 +85,91 @@ considering the error structure that was assumed for the fit."><!-- mathjax -->< </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Extract model parameters from mkinfit models</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.mkinfit.R" class="external-link"><code>R/parms.mkinfit.R</code></a></small> + <h1>Extract model parameters</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.R" class="external-link"><code>R/parms.R</code></a></small> <div class="hidden name"><code>parms.Rd</code></div> </div> <div class="ref-description"> - <p>This function always returns degradation model parameters as well as error -model parameters, in order to avoid working with a fitted model without -considering the error structure that was assumed for the fit.</p> + <p>This function returns degradation model parameters as well as error +model parameters per default, in order to avoid working with a fitted model +without considering the error structure that was assumed for the fit.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mkinfit</span> -<span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, exclude_failed <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> -<dd><p>A fitted model object. Methods are implemented for -<code><a href="mkinfit.html">mkinfit()</a></code> objects and for <code><a href="mmkin.html">mmkin()</a></code> objects.</p></dd> +<dd><p>A fitted model object.</p></dd> + + <dt>...</dt> <dd><p>Not used</p></dd> + + <dt>transformed</dt> -<dd><p>Should the parameters be returned -as used internally during the optimisation?</p></dd> +<dd><p>Should the parameters be returned as used internally +during the optimisation?</p></dd> + + +<dt>errparms</dt> +<dd><p>Should the error model parameters be returned +in addition to the degradation parameters?</p></dd> + + +<dt>exclude_failed</dt> +<dd><p>For <a href="multistart.html">multistart</a> objects, should rows for failed fits +be removed from the returned parameter matrix?</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>For mkinfit objects, a numeric vector of fitted model parameters. -For mmkin row objects, a matrix with the parameters with a -row for each dataset. If the mmkin object has more than one row, a list of -such matrices is returned.</p> + + +<p>Depending on the object, a numeric vector of fitted model parameters, +a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for +mmkin objects with more than one row).</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># mkinfit objects</span></span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> <span class="r-out co"><span class="r-pr">#></span> 82.4921598 0.3060633 4.6730124 </span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma </span> <span class="r-out co"><span class="r-pr">#></span> 82.492160 -1.183963 4.673012 </span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># mmkin objects</span></span> -<span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># mmkin objects</span></span></span> +<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="fl">2</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="fl">2</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $SFO</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 82.666781678</span> @@ -157,13 +185,13 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971599</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.526942414</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $SFO</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span> @@ -179,13 +207,13 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971599 90.34509493 98.14858821 94.311323732</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $SFO</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span> @@ -207,7 +235,7 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -222,7 +250,7 @@ such matrices is returned.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> 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(2021)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot parameter variability of multistart objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parplot.R" class="external-link"><code>R/parplot.R</code></a></small> + <div class="hidden name"><code>parplot.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Produces a boxplot with all parameters from the multiple runs, scaled +either by the parameters of the run with the highest likelihood, +or by their medians as proposed in the paper by Duchesne et al. (2021).</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parplot</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart.saem.mmkin</span></span> +<span><span class="fu">parplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span> +<span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span> +<span> main <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The <a href="multistart.html">multistart</a> object</p></dd> + + +<dt>...</dt> +<dd><p>Passed to <a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></p></dd> + + +<dt>llmin</dt> +<dd><p>The minimum likelihood of objects to be shown</p></dd> + + +<dt>scale</dt> +<dd><p>By default, scale parameters using the best available fit. +If 'median', parameters are scaled using the median parameters from all fits.</p></dd> + + +<dt>lpos</dt> +<dd><p>Positioning of the legend.</p></dd> + + +<dt>main</dt> +<dd><p>Title of the plot</p></dd> + +</dl></div> + <div id="references"> + <h2>References</h2> + <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical +identifiability in the frame of nonlinear mixed effects models: the example +of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. +doi: 10.1186/s12859-021-04373-4.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div> + </div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex b35f28d6..8678c166 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex c981538f..9bd01852 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex ccbe5861..a849aaee 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 2af2328d..b1083204 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,94 +93,146 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mixed.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> - <span class="va">x</span>, - i <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mmkin</span><span class="op">)</span>, - obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>, - standardized <span class="op">=</span> <span class="cn">TRUE</span>, - xlab <span class="op">=</span> <span class="st">"Time"</span>, - xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>, - resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"predicted"</span>, <span class="st">"time"</span><span class="op">)</span>, - pred_over <span class="op">=</span> <span class="cn">NULL</span>, - test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, - conf.level <span class="op">=</span> <span class="fl">0.6</span>, - default_log_parms <span class="op">=</span> <span class="cn">NA</span>, - ymax <span class="op">=</span> <span class="st">"auto"</span>, - maxabs <span class="op">=</span> <span class="st">"auto"</span>, - ncol.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">8</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span>, - nrow.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling</a></span><span class="op">(</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span><span class="op">)</span><span class="op">/</span><span class="va">ncol.legend</span><span class="op">)</span>, - rel.height.legend <span class="op">=</span> <span class="fl">0.02</span> <span class="op">+</span> <span class="fl">0.07</span> <span class="op">*</span> <span class="va">nrow.legend</span>, - rel.height.bottom <span class="op">=</span> <span class="fl">1.1</span>, - pch_ds <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span>, - col_ds <span class="op">=</span> <span class="va">pch_ds</span> <span class="op">+</span> <span class="fl">1</span>, - lty_ds <span class="op">=</span> <span class="va">col_ds</span>, - frame <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> i <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mmkin</span><span class="op">)</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span> +<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"predicted"</span>, <span class="st">"time"</span><span class="op">)</span>,</span> +<span> pop_curve <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pred_over <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> +<span> default_log_parms <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> ncol.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">8</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span>,</span> +<span> nrow.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling</a></span><span class="op">(</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span><span class="op">)</span><span class="op">/</span><span class="va">ncol.legend</span><span class="op">)</span>,</span> +<span> rel.height.legend <span class="op">=</span> <span class="fl">0.02</span> <span class="op">+</span> <span class="fl">0.07</span> <span class="op">*</span> <span class="va">nrow.legend</span>,</span> +<span> rel.height.bottom <span class="op">=</span> <span class="fl">1.1</span>,</span> +<span> pch_ds <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span>,</span> +<span> col_ds <span class="op">=</span> <span class="va">pch_ds</span> <span class="op">+</span> <span class="fl">1</span>,</span> +<span> lty_ds <span class="op">=</span> <span class="va">col_ds</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>x</dt> <dd><p>An object of class <a href="mixed.html">mixed.mmkin</a>, <a href="saem.html">saem.mmkin</a> or <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> + + <dt>i</dt> <dd><p>A numeric index to select datasets for which to plot the individual predictions, in case plots get too large</p></dd> + + <dt>obs_vars</dt> <dd><p>A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed variables in the model.</p></dd> + + <dt>standardized</dt> <dd><p>Should the residuals be standardized? Only takes effect if <code>resplot = "time"</code>.</p></dd> + + <dt>xlab</dt> <dd><p>Label for the x axis.</p></dd> + + <dt>xlim</dt> <dd><p>Plot range in x direction.</p></dd> + + <dt>resplot</dt> <dd><p>Should the residuals plotted against time or against predicted values?</p></dd> + + +<dt>pop_curve</dt> +<dd><p>Per default, a population curve is drawn in case +population parameters are fitted by the model, e.g. for saem objects. +In case there is a covariate model, no population curve is currently shown.</p></dd> + + <dt>pred_over</dt> <dd><p>Named list of alternative predictions as obtained from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinmod.html">mkinmod</a>.</p></dd> + + <dt>test_log_parms</dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> + + <dt>conf.level</dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> + + <dt>default_log_parms</dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> + + <dt>ymax</dt> <dd><p>Vector of maximum y axis values</p></dd> + + <dt>maxabs</dt> <dd><p>Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".</p></dd> + + <dt>ncol.legend</dt> <dd><p>Number of columns to use in the legend</p></dd> + + <dt>nrow.legend</dt> <dd><p>Number of rows to use in the legend</p></dd> + + <dt>rel.height.legend</dt> <dd><p>The relative height of the legend shown on top</p></dd> + + <dt>rel.height.bottom</dt> <dd><p>The relative height of the bottom plot row</p></dd> + + <dt>pch_ds</dt> <dd><p>Symbols to be used for plotting the data.</p></dd> + + <dt>col_ds</dt> <dd><p>Colors used for plotting the observed data and the corresponding model prediction lines for the different datasets.</p></dd> + + <dt>lty_ds</dt> <dd><p>Line types to be used for the model predictions.</p></dd> + + <dt>frame</dt> <dd><p>Should a frame be drawn around the plots?</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="author"> <h2>Author</h2> @@ -183,41 +241,41 @@ corresponding model prediction lines for the different datasets.</p></dd> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"ds "</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span> -<span class="r-in"><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"ds "</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mixed.mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># For this fit we need to increase pnlsMaxiter, and we increase the</span></span> -<span class="r-in"><span class="co"># tolerance in order to speed up the fit for this example evaluation</span></span> -<span class="r-in"><span class="co"># It still takes 20 seconds to run</span></span> -<span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># For this fit we need to increase pnlsMaxiter, and we increase the</span></span></span> +<span class="r-in"><span><span class="co"># tolerance in order to speed up the fit for this example evaluation</span></span></span> +<span class="r-in"><span><span class="co"># It still takes 20 seconds to run</span></span></span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mixed.mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mixed.mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_nlmix</span> <span class="op"><-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_nlmix</span> <span class="op"><-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmix(f_obs):</span> could not find function "nlmix"</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlmix</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlmix</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_nlmix):</span> object 'f_nlmix' not found</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># We can overlay the two variants if we generate predictions</span></span> -<span class="r-in"><span class="va">pred_nlme</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span> -<span class="r-in"> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, A1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">180</span>, by <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem</span>, pred_over <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>nlme <span class="op">=</span> <span class="va">pred_nlme</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># We can overlay the two variants if we generate predictions</span></span></span> +<span class="r-in"><span><span class="va">pred_nlme</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span> +<span class="r-in"><span> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, A1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">180</span>, by <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem</span>, pred_over <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>nlme <span class="op">=</span> <span class="va">pred_nlme</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mixed.mmkin-4.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -232,7 +290,7 @@ corresponding model prediction lines for the different datasets.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 39098648..cef94cb8 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 3545b8d8..f90b3f54 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex daf43033..3e5d828e 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 23cf27b5..cf96990e 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,50 +97,50 @@ observed data together with the solution of the fitted model.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> - <span class="va">x</span>, - fit <span class="op">=</span> <span class="va">x</span>, - obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>, - xlab <span class="op">=</span> <span class="st">"Time"</span>, - ylab <span class="op">=</span> <span class="st">"Residue"</span>, - xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>, - ylim <span class="op">=</span> <span class="st">"default"</span>, - col_obs <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span>, - pch_obs <span class="op">=</span> <span class="va">col_obs</span>, - lty_obs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span><span class="op">)</span>, - add <span class="op">=</span> <span class="cn">FALSE</span>, - legend <span class="op">=</span> <span class="op">!</span><span class="va">add</span>, - show_residuals <span class="op">=</span> <span class="cn">FALSE</span>, - show_errplot <span class="op">=</span> <span class="cn">FALSE</span>, - maxabs <span class="op">=</span> <span class="st">"auto"</span>, - sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, - rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>, - row_layout <span class="op">=</span> <span class="cn">FALSE</span>, - lpos <span class="op">=</span> <span class="st">"topright"</span>, - inset <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.05</span>, <span class="fl">0.05</span><span class="op">)</span>, - show_errmin <span class="op">=</span> <span class="cn">FALSE</span>, - errmin_digits <span class="op">=</span> <span class="fl">3</span>, - frame <span class="op">=</span> <span class="cn">TRUE</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="fu">plot_sep</span><span class="op">(</span> - <span class="va">fit</span>, - show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, - show_residuals <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">TRUE</span>, <span class="st">"standardized"</span><span class="op">)</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="fu">plot_res</span><span class="op">(</span> - <span class="va">fit</span>, - sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, - show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, - standardized <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> fit <span class="op">=</span> <span class="va">x</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span> +<span> ylim <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="va">col_obs</span>,</span> +<span> lty_obs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span><span class="op">)</span>,</span> +<span> add <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> legend <span class="op">=</span> <span class="op">!</span><span class="va">add</span>,</span> +<span> show_residuals <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errplot <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> sep_obs <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span> +<span> row_layout <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> inset <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.05</span>, <span class="fl">0.05</span><span class="op">)</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">plot_sep</span><span class="op">(</span></span> +<span> <span class="va">fit</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> show_residuals <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">TRUE</span>, <span class="st">"standardized"</span><span class="op">)</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">plot_res</span><span class="op">(</span></span> +<span> <span class="va">fit</span>,</span> +<span> sep_obs <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="va">sep_obs</span>,</span> +<span> standardized <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -142,32 +148,56 @@ observed data together with the solution of the fitted model.</p> <dl><dt>x</dt> <dd><p>Alias for fit introduced for compatibility with the generic S3 method.</p></dd> + + <dt>fit</dt> <dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + <dt>obs_vars</dt> <dd><p>A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed variables in the model.</p></dd> + + <dt>xlab</dt> <dd><p>Label for the x axis.</p></dd> + + <dt>ylab</dt> <dd><p>Label for the y axis.</p></dd> + + <dt>xlim</dt> <dd><p>Plot range in x direction.</p></dd> + + <dt>ylim</dt> <dd><p>Plot range in y direction. If given as a list, plot ranges for the different plot rows can be given for row layout.</p></dd> + + <dt>col_obs</dt> <dd><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></dd> + + <dt>pch_obs</dt> <dd><p>Symbols to be used for plotting the data.</p></dd> + + <dt>lty_obs</dt> <dd><p>Line types to be used for the model predictions.</p></dd> + + <dt>add</dt> <dd><p>Should the plot be added to an existing plot?</p></dd> + + <dt>legend</dt> <dd><p>Should a legend be added to the plot?</p></dd> + + <dt>show_residuals</dt> <dd><p>Should residuals be shown? If only one plot of the fits is shown, the residual plot is in the lower third of the plot. @@ -175,47 +205,74 @@ Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. If this is set to 'standardized', a plot of the residuals divided by the standard deviation given by the fitted error model will be shown.</p></dd> + + <dt>show_errplot</dt> <dd><p>Should squared residuals and the error model be shown? If only one plot of the fits is shown, this plot is in the lower third of the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves.</p></dd> + + <dt>maxabs</dt> <dd><p>Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".</p></dd> + + <dt>sep_obs</dt> <dd><p>Should the observed variables be shown in separate subplots? If yes, residual plots requested by "show_residuals" will be shown next to, not below the plot of the fits.</p></dd> + + <dt>rel.height.middle</dt> <dd><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></dd> + + <dt>row_layout</dt> <dd><p>Should we use a row layout where the residual plot or the error model plot is shown to the right?</p></dd> + + <dt>lpos</dt> <dd><p>Position(s) of the legend(s). Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> as the first argument. If not length one, this should be of the same length as the obs_var argument.</p></dd> + + <dt>inset</dt> <dd><p>Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> if applicable.</p></dd> + + <dt>show_errmin</dt> <dd><p>Should the FOCUS chi2 error value be shown in the upper margin of the plot?</p></dd> + + <dt>errmin_digits</dt> <dd><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></dd> + + <dt>frame</dt> <dd><p>Should a frame be drawn around the plots?</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + + <dt>standardized</dt> <dd><p>When calling 'plot_res', should the residuals be standardized in the residual plot?</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="details"> <h2>Details</h2> @@ -230,41 +287,41 @@ latex is being used for the formatting of the chi2 error level, if <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order, path from</span></span> -<span class="r-in"><span class="co"># parent to sink included</span></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order, path from</span></span></span> +<span class="r-in"><span><span class="co"># parent to sink included</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-4.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Show the observed variables separately, with residuals</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span> -<span class="r-in"> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Show the observed variables separately, with residuals</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-5.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The same can be obtained with less typing, using the convenience function plot_sep</span></span> -<span class="r-in"><span class="fu">plot_sep</span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The same can be obtained with less typing, using the convenience function plot_sep</span></span></span> +<span class="r-in"><span><span class="fu">plot_sep</span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-6.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Show the observed variables separately, with the error model</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_errplot <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span> -<span class="r-in"> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Show the observed variables separately, with the error model</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_errplot <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mkinfit-7.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -279,7 +336,7 @@ latex is being used for the formatting of the chi2 error level, if </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex f5768c40..7af84edf 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex c3f77d3d..56bfac50 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 29439156..5da05f40 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex 89a111b0..3ec224f4 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 3dd0203b..30d0406e 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -94,22 +100,22 @@ the fit of at least one model to the same dataset is shown.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> - <span class="va">x</span>, - main <span class="op">=</span> <span class="st">"auto"</span>, - legends <span class="op">=</span> <span class="fl">1</span>, - resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>, - ylab <span class="op">=</span> <span class="st">"Residue"</span>, - standardized <span class="op">=</span> <span class="cn">FALSE</span>, - show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, - errmin_var <span class="op">=</span> <span class="st">"All data"</span>, - errmin_digits <span class="op">=</span> <span class="fl">3</span>, - cex <span class="op">=</span> <span class="fl">0.7</span>, - rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>, - ymax <span class="op">=</span> <span class="st">"auto"</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legends <span class="op">=</span> <span class="fl">1</span>,</span> +<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span> +<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span> +<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span> +<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -117,43 +123,70 @@ the fit of at least one model to the same dataset is shown.</p> <dl><dt>x</dt> <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one column.</p></dd> + + <dt>main</dt> <dd><p>The main title placed on the outer margin of the plot.</p></dd> + + <dt>legends</dt> <dd><p>An index for the fits for which legends should be shown.</p></dd> + + <dt>resplot</dt> <dd><p>Should the residuals plotted against time, using <code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd> + + <dt>ylab</dt> <dd><p>Label for the y axis.</p></dd> + + <dt>standardized</dt> <dd><p>Should the residuals be standardized? This option is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if <code>resplot = "time"</code>.</p></dd> + + <dt>show_errmin</dt> <dd><p>Should the chi2 error level be shown on top of the plots to the left?</p></dd> + + <dt>errmin_var</dt> <dd><p>The variable for which the FOCUS chi2 error value should be shown.</p></dd> + + <dt>errmin_digits</dt> <dd><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></dd> + + <dt>cex</dt> <dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd> + + <dt>rel.height.middle</dt> <dd><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></dd> + + <dt>ymax</dt> <dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and <code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="details"> <h2>Details</h2> @@ -167,32 +200,32 @@ latex is being used for the formatting of the chi2 error level.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="co"># Only use one core not to offend CRAN checks</span></span> -<span class="r-in"> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span> -<span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span> -<span class="r-in"> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span> -<span class="r-in"> <span class="co"># generated by pkgdown, as far as I know).</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span> +<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span> +<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span> <span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># Show the error models</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Show the error models</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -207,7 +240,7 @@ latex is being used for the formatting of the chi2 error level.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index af65d8eb..a7939f90 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -18,7 +18,7 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,24 +95,33 @@ function (SFO, then IORE, then DFOP).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nafta</span> -<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, legend <span class="op">=</span> <span class="cn">FALSE</span>, main <span class="op">=</span> <span class="st">"auto"</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, legend <span class="op">=</span> <span class="cn">FALSE</span>, main <span class="op">=</span> <span class="st">"auto"</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>x</dt> <dd><p>An object of class <code><a href="nafta.html">nafta</a></code>.</p></dd> + + <dt>legend</dt> <dd><p>Should a legend be added?</p></dd> + + <dt>main</dt> <dd><p>Possibility to override the main title of the plot.</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="details"> <h2>Details</h2> @@ -129,7 +144,7 @@ function (SFO, then IORE, then DFOP).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html new file mode 100644 index 00000000..d2873cee --- /dev/null +++ b/docs/reference/read_spreadsheet.html @@ -0,0 +1,179 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet"><meta property="og:description" content="This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Read datasets and relevant meta information from a spreadsheet file</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/read_spreadsheet.R" class="external-link"><code>R/read_spreadsheet.R</code></a></small> + <div class="hidden name"><code>read_spreadsheet.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_spreadsheet</span><span class="op">(</span></span> +<span> <span class="va">path</span>,</span> +<span> valid_datasets <span class="op">=</span> <span class="st">"all"</span>,</span> +<span> parent_only <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> normalize <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>path</dt> +<dd><p>Absolute or relative path to the spreadsheet file</p></dd> + + +<dt>valid_datasets</dt> +<dd><p>Optional numeric index of the valid datasets, default is +to use all datasets</p></dd> + + +<dt>parent_only</dt> +<dd><p>Should only the parent data be used?</p></dd> + + +<dt>normalize</dt> +<dd><p>Should the time scale be normalized using temperature +and moisture normalisation factors in the sheet 'Datasets'?</p></dd> + +</dl></div> + <div id="details"> + <h2>Details</h2> + <p>There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. +The first row read after the header read in from this sheet is assumed +to contain name and acronym of the parent compound.</p> +<p>The dataset sheets should be named using the dataset numbers read in from +the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, name +of the observed variable (e.g. the acronym of the parent compound or +one of its transformation products) should be in the first column, +the time values should be in the second colum, and the observed value +in the third column.</p> +<p>In case relevant covariate data are available, they should be given +in a sheet 'Covariates', containing one line for each value of the grouping +variable specified in 'Datasets'. These values should be in the first +column and the column must have the same name as the second column in +'Datasets'. Covariates will be read in from columns four and higher. +Their names should preferably not contain special characters like spaces, +so they can be easily used for specifying covariate models.</p> +<p>An similar data structure is defined as the R6 class <a href="mkindsg.html">mkindsg</a>, but +is probably more complicated to use.</p> + </div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 4da7092a..24b9771e 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -55,19 +55,25 @@ intervals, nlme <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -120,7 +126,7 @@ below to see their documentation.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index 7d9e50de..07395436 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -87,28 +93,33 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">object</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">object</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>A <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + <dt>standardized</dt> <dd><p>Should the residuals be standardized by dividing by the standard deviation obtained from the fitted error model?</p></dd> + + <dt>...</dt> <dd><p>Not used</p></dd> + </dl></div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702</span> <span class="r-out co"><span class="r-pr">#></span> [7] -0.03269080 1.45347823 -0.88423697</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208</span> <span class="r-out co"><span class="r-pr">#></span> [7] -0.04695355 2.08761977 -1.27002287</span> </code></pre></div> @@ -125,7 +136,7 @@ standard deviation obtained from the fitted error model?</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/saem-1.png b/docs/reference/saem-1.png Binary files differindex 08939d4f..9e310252 100644 --- a/docs/reference/saem-1.png +++ b/docs/reference/saem-1.png diff --git a/docs/reference/saem-2.png b/docs/reference/saem-2.png Binary files differindex b737db03..de1bcf57 100644 --- a/docs/reference/saem-2.png +++ b/docs/reference/saem-2.png diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png Binary files differindex 08e0f544..de569ce0 100644 --- a/docs/reference/saem-3.png +++ b/docs/reference/saem-3.png diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex bb775c25..0f2ee3e7 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 1bc6308e..5e7e0861 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,14 +103,20 @@ Expectation Maximisation algorithm (SAEM).</p> <span><span class="fu">saem</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> <span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> omega.init <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">0.1</span><span class="op">)</span>,</span> <span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> <span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span> <span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span> fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="va">...</span></span> @@ -117,14 +129,24 @@ Expectation Maximisation algorithm (SAEM).</p> <span> <span class="va">object</span>,</span> <span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> omega.init <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> <span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> <span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -146,6 +168,10 @@ SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP wit one SFO metabolite.</p></dd> +<dt>error_model</dt> +<dd><p>Possibility to override the error model used in the mmkin object</p></dd> + + <dt>degparms_start</dt> <dd><p>Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.</p></dd> @@ -168,6 +194,43 @@ for parameter that are tested if requested by 'test_log_parms'.</p></dd> automatic choice is not desired</p></dd> +<dt>covariance.model</dt> +<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>. Per +default, uncorrelated random effects are specified for all degradation +parameters.</p></dd> + + +<dt>omega.init</dt> +<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>. If using +mkin transformations and the default covariance model with optionally +excluded random effects, the variances of the degradation parameters +are estimated using <a href="mean_degparms.html">mean_degparms</a>, with testing of untransformed +log parameters for significant difference from zero. If not using +mkin transformations or a custom covariance model, the default +initialisation of <a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel</a> is used for omega.init.</p></dd> + + +<dt>covariates</dt> +<dd><p>A data frame with covariate data for use in +'covariate_models', with dataset names as row names.</p></dd> + + +<dt>covariate_models</dt> +<dd><p>A list containing linear model formulas with one explanatory +variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available +in the 'covariates' data frame.</p></dd> + + +<dt>no_random_effect</dt> +<dd><p>Character vector of degradation parameters for +which there should be no variability over the groups. Only used +if the covariance model is not explicitly specified.</p></dd> + + +<dt>error.init</dt> +<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>.</p></dd> + + <dt>nbiter.saemix</dt> <dd><p>Convenience option to increase the number of iterations</p></dd> @@ -177,11 +240,6 @@ iterations</p></dd> <dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix</a>.</p></dd> -<dt>fail_with_errors</dt> -<dd><p>Should a failure to compute standard errors -from the inverse of the Fisher Information Matrix be a failure?</p></dd> - - <dt>verbose</dt> <dd><p>Should we print information about created objects of type <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> and <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a>?</p></dd> @@ -199,6 +257,11 @@ and the end of the optimisation process?</p></dd> <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> + +<dt>ci</dt> +<dd><p>Should a matrix with estimates and confidence interval boundaries +be returned? If FALSE (default), a vector of estimates is returned.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> @@ -241,40 +304,43 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] "sd(g_qlogis)"</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by SAEM</span> -<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.33 622.38 -307.17</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.85 465.11 -226.92</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.76 490.24 -237.88</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_dfop</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 490.6 487.5 -237.3</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.33 622.38 -307.17 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.76 490.24 -237.88 138.57 4 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(g_qlogis)"</span> +<span class="r-in"><span><span class="va">f_saem_dfop_red</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, no_random_effect <span class="op">=</span> <span class="st">"g_qlogis"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, <span class="va">f_saem_dfop_red</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.902 91.3695 96.4339</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.936 -3.9950 -1.8762</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.091 -4.9290 -1.2523</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.366 -0.6484 -0.0836</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 2.385 2.0033 2.7664</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.476 0.3890 4.5623</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.195 0.4381 1.9517</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.092 0.7906 3.3932</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] 493.9811</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_red 8 488.68 485.55 -236.34 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.76 490.24 -237.88 0 1 1</span> <span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.33 622.38 -307.17</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.85 465.11 -226.92</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.76 490.24 -237.88</span> <span class="r-in"><span><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span></span> <span class="r-in"><span><span class="co"># functions from saemix</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: npde</span> -<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.1</span> +<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.2</span> <span class="r-msg co"><span class="r-pr">#></span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘saemix’</span> @@ -284,9 +350,9 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> -<span class="r-out co"><span class="r-pr">#></span> 1 624.2598 622.3070</span> -<span class="r-out co"><span class="r-pr">#></span> 2 467.8664 465.1324</span> -<span class="r-out co"><span class="r-pr">#></span> 3 493.9811 490.4660</span> +<span class="r-out co"><span class="r-pr">#></span> 1 624.3316 622.3788</span> +<span class="r-out co"><span class="r-pr">#></span> 2 467.8472 465.1132</span> +<span class="r-out co"><span class="r-pr">#></span> 3 493.7592 490.2441</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span></span> @@ -300,11 +366,12 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">f_mmkin_parent_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> -<span class="r-out co"><span class="r-pr">#></span> 1 467.8664 465.1324</span> -<span class="r-out co"><span class="r-pr">#></span> 2 469.9096 466.7851</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_fomc</span>, <span class="va">f_saem_fomc_tc</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.85 465.11 -226.92 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc_tc 8 469.83 466.71 -226.92 0.015 1 0.9027</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -341,32 +408,32 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> 170 observations of 2 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 842 836.9 -408</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 839.2 834.1 -406.6</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.70402 91.04104 96.3670</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.83760 -7.66452 -4.0107</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.95718 -1.35955 -0.5548</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.35514 -3.39402 -1.3163</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.79634 -5.64009 -1.9526</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02108 -0.66463 0.6225</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.88191 1.66491 2.0989</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.81628 0.78922 4.8433</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.78751 0.42105 3.1540</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.45016 0.16116 0.7391</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.06923 0.31676 1.8217</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.03768 0.70938 3.3660</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.44024 -0.09262 0.9731</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 13:15:20 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 13:15:20 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 14:03:17 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:03:17 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -381,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.258 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.829 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -398,230 +465,237 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 842 836.9 -408</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 839.2 834.1 -406.6</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.70402 91.04104 96.3670</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.83760 -7.66452 -4.0107</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.95718 -1.35955 -0.5548</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.35514 -3.39402 -1.3163</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.79634 -5.64009 -1.9526</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02108 -0.66463 0.6225</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.88191 1.66491 2.0989</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.81628 0.78922 4.8433</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.78751 0.42105 3.1540</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.45016 0.16116 0.7391</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.06923 0.31676 1.8217</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.03768 0.70938 3.3660</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.44024 -0.09262 0.9731</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_A1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -0.0160 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.0263 0.0612 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.0100 -0.0014 -0.0033 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0131 0.0050 -0.0011 0.0071 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0419 -0.0199 0.0026 -0.0765 -0.0707</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -0.0147 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.0269 0.0573 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.0263 -0.0011 -0.0040 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0020 0.0065 -0.0002 -0.0776 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0248 -0.0180 -0.0004 -0.0903 -0.0603</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.8163 0.78922 4.8433</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7875 0.42105 3.1540</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4502 0.16116 0.7391</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.0692 0.31676 1.8217</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0377 0.70938 3.3660</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4402 -0.09262 0.9731</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 1.886 1.668 2.104</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.882 1.665 2.099</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.770115 9.115e+01 96.39447</span> -<span class="r-out co"><span class="r-pr">#></span> k_A1 0.002993 5.005e-04 0.01789</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_A1 0.276720 2.034e-01 0.36443</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.075467 2.503e-02 0.22753</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.029516 4.867e-03 0.17902</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.474353 2.949e-01 0.66073</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.704015 9.104e+01 96.36699</span> +<span class="r-out co"><span class="r-pr">#></span> k_A1 0.002916 4.692e-04 0.01812</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_A1 0.277443 2.043e-01 0.36475</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.094880 3.357e-02 0.26813</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.022453 3.553e-03 0.14191</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.494731 3.397e-01 0.65078</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_A1 0.2767</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7233</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 0.2774</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7226</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 14.56 58.26 17.54 9.185 23.48</span> -<span class="r-out co"><span class="r-pr">#></span> A1 231.62 769.41 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> +<span class="r-out co"><span class="r-pr">#></span> parent 14.0 72.38 21.79 7.306 30.87</span> +<span class="r-out co"><span class="r-pr">#></span> A1 237.7 789.68 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> <span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 97.2 95.78623 1.41377 1.886 0.749758</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 96.4 95.78623 0.61377 1.886 0.325498</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 71.1 71.34666 -0.24666 1.886 -0.130812</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 69.2 71.34666 -2.14666 1.886 -1.138429</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 58.1 56.49768 1.60232 1.886 0.849749</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 56.6 56.49768 0.10232 1.886 0.054262</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 44.4 44.53511 -0.13511 1.886 -0.071650</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 43.4 44.53511 -1.13511 1.886 -0.601974</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 33.3 29.77451 3.52549 1.886 1.869656</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 29.2 29.77451 -0.57451 1.886 -0.304675</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 17.6 19.32540 -1.72540 1.886 -0.915023</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 18.0 19.32540 -1.32540 1.886 -0.702894</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 10.5 10.42781 0.07219 1.886 0.038282</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 9.3 10.42781 -1.12781 1.886 -0.598107</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.5 3.74190 0.75810 1.886 0.402037</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.7 3.74190 0.95810 1.886 0.508102</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.0 1.96485 1.03515 1.886 0.548966</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.4 1.96485 1.43515 1.886 0.761096</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.3 1.09395 1.20605 1.886 0.639596</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.7 1.09395 1.60605 1.886 0.851726</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.3 4.72702 -0.42702 1.886 -0.226458</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.6 4.72702 -0.12702 1.886 -0.067361</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.0 7.51314 -0.51314 1.886 -0.272128</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.2 7.51314 -0.31314 1.886 -0.166063</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.2 9.63719 -1.43719 1.886 -0.762179</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.0 9.63719 -1.63719 1.886 -0.868244</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 11.0 11.84931 -0.84931 1.886 -0.450409</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 13.7 11.84931 1.85069 1.886 0.981468</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 11.5 12.82336 -1.32336 1.886 -0.701808</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 12.7 12.82336 -0.12336 1.886 -0.065418</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.9 12.89456 2.00544 1.886 1.063533</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.5 12.89456 1.60544 1.886 0.851403</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.1 11.55919 0.54081 1.886 0.286806</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.3 11.55919 0.74081 1.886 0.392871</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 9.9 10.42334 -0.52334 1.886 -0.277539</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 10.2 10.42334 -0.22334 1.886 -0.118442</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 8.8 9.37987 -0.57987 1.886 -0.307519</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 7.8 9.37987 -1.57987 1.886 -0.837844</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 93.6 90.95702 2.64298 1.886 1.401639</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 92.3 90.95702 1.34298 1.886 0.712217</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 87.0 84.77506 2.22494 1.886 1.179942</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 82.2 84.77506 -2.57506 1.886 -1.365616</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 74.0 77.60962 -3.60962 1.886 -1.914268</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 73.9 77.60962 -3.70962 1.886 -1.967301</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 64.2 67.50646 -3.30646 1.886 -1.753499</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 69.5 67.50646 1.99354 1.886 1.057221</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.0 52.48909 1.51091 1.886 0.801271</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.6 52.48909 2.11091 1.886 1.119465</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 41.1 39.54372 1.55628 1.886 0.825335</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 38.4 39.54372 -1.14372 1.886 -0.606542</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 32.5 33.87968 -1.37968 1.886 -0.731676</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 35.5 33.87968 1.62032 1.886 0.859298</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 28.1 30.41071 -2.31071 1.886 -1.225427</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 29.0 30.41071 -1.41071 1.886 -0.748135</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 26.5 25.36386 1.13614 1.886 0.602524</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 27.6 25.36386 2.23614 1.886 1.185881</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.9 2.74863 1.15137 1.886 0.610600</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.1 2.74863 0.35137 1.886 0.186341</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.9 5.92686 0.97314 1.886 0.516081</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.6 5.92686 0.67314 1.886 0.356983</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 10.4 10.38800 0.01200 1.886 0.006362</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 8.3 10.38800 -2.08800 1.886 -1.107320</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 14.4 16.93529 -2.53529 1.886 -1.344524</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 13.7 16.93529 -3.23529 1.886 -1.715751</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.1 22.33044 -0.23044 1.886 -0.122209</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.3 22.33044 -0.03044 1.886 -0.016144</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 27.5 24.42300 3.07700 1.886 1.631809</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 25.4 24.42300 0.97700 1.886 0.518127</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 28.0 25.51140 2.48860 1.886 1.319768</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 26.6 25.51140 1.08860 1.886 0.577313</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.8 26.80282 -1.00282 1.886 -0.531818</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.3 26.80282 -1.50282 1.886 -0.796981</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 91.9 91.08733 0.81267 1.886 0.430980</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 90.8 91.08733 -0.28733 1.886 -0.152377</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 64.9 67.55332 -2.65332 1.886 -1.407123</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 66.2 67.55332 -1.35332 1.886 -0.717701</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 43.5 41.65811 1.84189 1.886 0.976800</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 44.1 41.65811 2.44189 1.886 1.294994</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.3 19.65773 -1.35773 1.886 -0.720038</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.1 19.65773 -1.55773 1.886 -0.826103</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.2 10.65118 -0.45118 1.886 -0.239269</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.8 10.65118 0.14882 1.886 0.078925</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 4.9 3.11694 1.78306 1.886 0.945601</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 3.3 3.11694 0.18306 1.886 0.097082</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.6 0.43165 1.16835 1.886 0.619603</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.5 0.43165 1.06835 1.886 0.566570</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 1.1 0.05441 1.04559 1.886 0.554503</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 0.9 0.05441 0.84559 1.886 0.448438</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 9.6 7.66431 1.93569 1.886 1.026546</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 7.7 7.66431 0.03569 1.886 0.018930</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.0 15.57948 -0.57948 1.886 -0.307311</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.1 15.57948 -0.47948 1.886 -0.254279</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.2 20.38988 0.81012 1.886 0.429625</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.1 20.38988 0.71012 1.886 0.376593</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 19.7 20.16439 -0.46439 1.886 -0.246276</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 18.9 20.16439 -1.26439 1.886 -0.670535</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 17.5 16.40918 1.09082 1.886 0.578489</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 15.9 16.40918 -0.50918 1.886 -0.270030</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.5 10.12011 -0.62011 1.886 -0.328861</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.8 10.12011 -0.32011 1.886 -0.169764</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.2 5.79080 0.40920 1.886 0.217011</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.1 5.79080 0.30920 1.886 0.163979</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 99.8 97.38786 2.41214 1.886 1.279218</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 98.3 97.38786 0.91214 1.886 0.483731</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.1 79.25431 -2.15431 1.886 -1.142481</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.2 79.25431 -2.05431 1.886 -1.089449</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 59.0 55.69866 3.30134 1.886 1.750781</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 58.1 55.69866 2.40134 1.886 1.273489</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 27.4 31.64893 -4.24893 1.886 -2.253314</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 29.2 31.64893 -2.44893 1.886 -1.298729</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 19.1 22.57316 -3.47316 1.886 -1.841901</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 29.6 22.57316 7.02684 1.886 3.726507</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 10.1 14.11345 -4.01345 1.886 -2.128430</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 18.2 14.11345 4.08655 1.886 2.167199</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 4.5 6.95586 -2.45586 1.886 -1.302400</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 9.1 6.95586 2.14414 1.886 1.137093</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.3 3.31753 -1.01753 1.886 -0.539619</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.9 3.31753 -0.41753 1.886 -0.221424</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 2.0 1.63642 0.36358 1.886 0.192816</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 1.8 1.63642 0.16358 1.886 0.086751</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.0 0.61667 1.38333 1.886 0.733614</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.2 0.61667 1.58333 1.886 0.839679</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 4.2 3.67247 0.52753 1.886 0.279763</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 3.9 3.67247 0.22753 1.886 0.120666</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.4 8.36240 -0.96240 1.886 -0.510385</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.9 8.36240 -0.46240 1.886 -0.245223</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 14.5 12.80590 1.69410 1.886 0.898422</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 13.7 12.80590 0.89410 1.886 0.474162</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 14.2 13.99625 0.20375 1.886 0.108053</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 12.2 13.99625 -1.79625 1.886 -0.952596</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.7 14.22730 -0.52730 1.886 -0.279641</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.2 14.22730 -1.02730 1.886 -0.544803</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 13.6 13.33713 0.26287 1.886 0.139406</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 15.4 13.33713 2.06287 1.886 1.093991</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 10.4 11.84008 -1.44008 1.886 -0.763708</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 11.6 11.84008 -0.24008 1.886 -0.127318</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 10.0 10.30732 -0.30732 1.886 -0.162980</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 9.5 10.30732 -0.80732 1.886 -0.428142</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.1 8.33981 0.76019 1.886 0.403149</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.0 8.33981 0.66019 1.886 0.350117</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 96.1 93.70349 2.39651 1.886 1.270926</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 94.3 93.70349 0.59651 1.886 0.316342</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 69.4 70.18665 -0.78665 1.886 -0.417182</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 73.1 70.18665 2.91335 1.886 1.545019</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.6 64.03245 1.56755 1.886 0.831308</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.3 64.03245 1.26755 1.886 0.672210</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 55.9 54.71491 1.18509 1.886 0.628480</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 54.4 54.71491 -0.31491 1.886 -0.167007</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 47.0 49.63436 -2.63436 1.886 -1.397065</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 49.3 49.63436 -0.33436 1.886 -0.177319</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 44.7 45.08853 -0.38853 1.886 -0.206049</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 46.7 45.08853 1.61147 1.886 0.854600</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 42.1 41.07653 1.02347 1.886 0.542772</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 41.3 41.07653 0.22347 1.886 0.118513</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.3 4.08295 -0.78295 1.886 -0.415218</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.4 4.08295 -0.68295 1.886 -0.362186</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 3.9 6.04367 -2.14367 1.886 -1.136841</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 2.9 6.04367 -3.14367 1.886 -1.667165</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59693 -1.19693 1.886 -0.634761</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59693 -0.39693 1.886 -0.210502</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.86436 -0.76436 1.886 -0.405361</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723555</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.99397 0.70603 1.886 0.374425</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.99397 1.00603 1.886 0.533522</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.91274 1.38726 1.886 0.735696</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.2 11.91274 1.28726 1.886 0.682663</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 14.3 12.66519 1.63481 1.886 0.866981</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.66519 -0.56519 1.886 -0.299733</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 97.2 95.70025 1.49975 1.882 0.79693</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 96.4 95.70025 0.69975 1.882 0.37183</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 71.1 71.44670 -0.34670 1.882 -0.18423</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 69.2 71.44670 -2.24670 1.882 -1.19384</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 58.1 56.59283 1.50717 1.882 0.80087</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 56.6 56.59283 0.00717 1.882 0.00381</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 44.4 44.56648 -0.16648 1.882 -0.08847</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 43.4 44.56648 -1.16648 1.882 -0.61984</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 33.3 29.76020 3.53980 1.882 1.88096</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 29.2 29.76020 -0.56020 1.882 -0.29767</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 17.6 19.39208 -1.79208 1.882 -0.95226</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 18.0 19.39208 -1.39208 1.882 -0.73971</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 10.5 10.55761 -0.05761 1.882 -0.03061</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 9.3 10.55761 -1.25761 1.882 -0.66826</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.5 3.84742 0.65258 1.882 0.34676</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.7 3.84742 0.85258 1.882 0.45304</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.0 2.03997 0.96003 1.882 0.51013</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.4 2.03997 1.36003 1.882 0.72268</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.3 1.14585 1.15415 1.882 0.61328</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.7 1.14585 1.55415 1.882 0.82583</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.3 4.86054 -0.56054 1.882 -0.29786</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.6 4.86054 -0.26054 1.882 -0.13844</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.0 7.74179 -0.74179 1.882 -0.39417</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.2 7.74179 -0.54179 1.882 -0.28789</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.2 9.94048 -1.74048 1.882 -0.92485</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.0 9.94048 -1.94048 1.882 -1.03112</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 11.0 12.19109 -1.19109 1.882 -0.63291</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 13.7 12.19109 1.50891 1.882 0.80180</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 11.5 13.10706 -1.60706 1.882 -0.85395</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 12.7 13.10706 -0.40706 1.882 -0.21630</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.9 13.06131 1.83869 1.882 0.97703</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.5 13.06131 1.43869 1.882 0.76448</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.1 11.54495 0.55505 1.882 0.29494</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.3 11.54495 0.75505 1.882 0.40122</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 9.9 10.31533 -0.41533 1.882 -0.22070</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 10.2 10.31533 -0.11533 1.882 -0.06128</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 8.8 9.20222 -0.40222 1.882 -0.21373</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 7.8 9.20222 -1.40222 1.882 -0.74510</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 93.6 90.82357 2.77643 1.882 1.47532</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 92.3 90.82357 1.47643 1.882 0.78453</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 87.0 84.73448 2.26552 1.882 1.20384</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 82.2 84.73448 -2.53448 1.882 -1.34675</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 74.0 77.65013 -3.65013 1.882 -1.93958</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 73.9 77.65013 -3.75013 1.882 -1.99272</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 64.2 67.60639 -3.40639 1.882 -1.81007</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 69.5 67.60639 1.89361 1.882 1.00621</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.0 52.53663 1.46337 1.882 0.77760</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.6 52.53663 2.06337 1.882 1.09642</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 41.1 39.42728 1.67272 1.882 0.88884</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 38.4 39.42728 -1.02728 1.882 -0.54587</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 32.5 33.76360 -1.26360 1.882 -0.67144</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 35.5 33.76360 1.73640 1.882 0.92268</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 28.1 30.39975 -2.29975 1.882 -1.22203</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 29.0 30.39975 -1.39975 1.882 -0.74379</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 26.5 25.62379 0.87621 1.882 0.46559</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 27.6 25.62379 1.97621 1.882 1.05010</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.9 2.70005 1.19995 1.882 0.63762</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.1 2.70005 0.39995 1.882 0.21252</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.9 5.83475 1.06525 1.882 0.56605</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.6 5.83475 0.76525 1.882 0.40663</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 10.4 10.26142 0.13858 1.882 0.07364</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 8.3 10.26142 -1.96142 1.882 -1.04225</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 14.4 16.82999 -2.42999 1.882 -1.29123</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 13.7 16.82999 -3.12999 1.882 -1.66319</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.1 22.32486 -0.22486 1.882 -0.11949</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.3 22.32486 -0.02486 1.882 -0.01321</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 27.5 24.45927 3.04073 1.882 1.61576</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 25.4 24.45927 0.94073 1.882 0.49988</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 28.0 25.54862 2.45138 1.882 1.30260</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 26.6 25.54862 1.05138 1.882 0.55868</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.8 26.82277 -1.02277 1.882 -0.54347</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.3 26.82277 -1.52277 1.882 -0.80916</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 91.9 91.16791 0.73209 1.882 0.38901</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 90.8 91.16791 -0.36791 1.882 -0.19550</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 64.9 67.58358 -2.68358 1.882 -1.42598</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 66.2 67.58358 -1.38358 1.882 -0.73520</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 43.5 41.62086 1.87914 1.882 0.99853</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 44.1 41.62086 2.47914 1.882 1.31735</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.3 19.60116 -1.30116 1.882 -0.69140</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.1 19.60116 -1.50116 1.882 -0.79768</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.2 10.63101 -0.43101 1.882 -0.22903</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.8 10.63101 0.16899 1.882 0.08980</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 4.9 3.12435 1.77565 1.882 0.94354</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 3.3 3.12435 0.17565 1.882 0.09334</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.6 0.43578 1.16422 1.882 0.61864</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.5 0.43578 1.06422 1.882 0.56550</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 1.1 0.05534 1.04466 1.882 0.55510</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 0.9 0.05534 0.84466 1.882 0.44883</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 9.6 7.63450 1.96550 1.882 1.04442</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 7.7 7.63450 0.06550 1.882 0.03481</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.0 15.52593 -0.52593 1.882 -0.27947</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.1 15.52593 -0.42593 1.882 -0.22633</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.2 20.32192 0.87808 1.882 0.46659</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.1 20.32192 0.77808 1.882 0.41345</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 19.7 20.09721 -0.39721 1.882 -0.21107</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 18.9 20.09721 -1.19721 1.882 -0.63617</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 17.5 16.37477 1.12523 1.882 0.59792</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 15.9 16.37477 -0.47477 1.882 -0.25228</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.5 10.13141 -0.63141 1.882 -0.33551</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.8 10.13141 -0.33141 1.882 -0.17610</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.2 5.81827 0.38173 1.882 0.20284</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.1 5.81827 0.28173 1.882 0.14970</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 99.8 97.48728 2.31272 1.882 1.22892</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 98.3 97.48728 0.81272 1.882 0.43186</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.1 79.29476 -2.19476 1.882 -1.16624</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.2 79.29476 -2.09476 1.882 -1.11310</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 59.0 55.67060 3.32940 1.882 1.76915</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 58.1 55.67060 2.42940 1.882 1.29092</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 27.4 31.57871 -4.17871 1.882 -2.22046</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 29.2 31.57871 -2.37871 1.882 -1.26398</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 19.1 22.51546 -3.41546 1.882 -1.81489</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 29.6 22.51546 7.08454 1.882 3.76454</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 10.1 14.09074 -3.99074 1.882 -2.12057</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 18.2 14.09074 4.10926 1.882 2.18355</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 4.5 6.95747 -2.45747 1.882 -1.30584</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 9.1 6.95747 2.14253 1.882 1.13848</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.3 3.32472 -1.02472 1.882 -0.54451</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.9 3.32472 -0.42472 1.882 -0.22569</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 2.0 1.64300 0.35700 1.882 0.18970</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 1.8 1.64300 0.15700 1.882 0.08343</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.0 0.62073 1.37927 1.882 0.73291</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.2 0.62073 1.57927 1.882 0.83918</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 4.2 3.64568 0.55432 1.882 0.29455</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 3.9 3.64568 0.25432 1.882 0.13514</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.4 8.30173 -0.90173 1.882 -0.47916</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.9 8.30173 -0.40173 1.882 -0.21347</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 14.5 12.71589 1.78411 1.882 0.94803</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 13.7 12.71589 0.98411 1.882 0.52293</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 14.2 13.90452 0.29548 1.882 0.15701</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 12.2 13.90452 -1.70452 1.882 -0.90574</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.7 14.15523 -0.45523 1.882 -0.24190</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.2 14.15523 -0.95523 1.882 -0.50759</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 13.6 13.31038 0.28962 1.882 0.15389</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 15.4 13.31038 2.08962 1.882 1.11037</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 10.4 11.85965 -1.45965 1.882 -0.77562</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 11.6 11.85965 -0.25965 1.882 -0.13797</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 10.0 10.36294 -0.36294 1.882 -0.19286</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 9.5 10.36294 -0.86294 1.882 -0.45855</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.1 8.43003 0.66997 1.882 0.35601</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.0 8.43003 0.56997 1.882 0.30287</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 96.1 93.95603 2.14397 1.882 1.13925</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 94.3 93.95603 0.34397 1.882 0.18278</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.70592 -3.80592 1.882 -2.02237</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.70592 -3.80592 1.882 -2.02237</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 69.4 70.04570 -0.64570 1.882 -0.34311</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 73.1 70.04570 3.05430 1.882 1.62298</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.6 64.01710 1.58290 1.882 0.84111</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.3 64.01710 1.28290 1.882 0.68170</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 55.9 54.98434 0.91566 1.882 0.48656</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 54.4 54.98434 -0.58434 1.882 -0.31050</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 47.0 49.87137 -2.87137 1.882 -1.52577</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 49.3 49.87137 -0.57137 1.882 -0.30361</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 44.7 45.06727 -0.36727 1.882 -0.19516</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 46.7 45.06727 1.63273 1.882 0.86759</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 42.1 40.76402 1.33598 1.882 0.70991</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 41.3 40.76402 0.53598 1.882 0.28481</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.3 4.14599 -0.84599 1.882 -0.44954</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.4 4.14599 -0.74599 1.882 -0.39640</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 3.9 6.08478 -2.18478 1.882 -1.16093</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 2.9 6.08478 -3.18478 1.882 -1.69231</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59411 -1.19411 1.882 -0.63452</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59411 -0.39411 1.882 -0.20942</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.78292 -0.68292 1.882 -0.36289</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.78292 -1.28292 1.882 -0.68171</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.93274 0.76726 1.882 0.40770</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.93274 1.06726 1.882 0.56711</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.93986 1.36014 1.882 0.72274</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.2 11.93986 1.26014 1.882 0.66961</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 14.3 12.79238 1.50762 1.882 0.80111</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.79238 -0.69238 1.882 -0.36791</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span> <span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index e1032453..365f2e4c 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -19,7 +19,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -46,19 +46,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -91,7 +97,7 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">schaefer07_complex_case</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div> </div> <div id="format"> @@ -127,19 +133,19 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span> -<span class="r-in"> B1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> C1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> A2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> B1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> C1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="schaefer07_complex_case-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span> <span class="r-out co"><span class="r-pr">#></span> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 </span> @@ -152,9 +158,9 @@ <span class="r-out co"><span class="r-pr">#></span> C1 11.23131 37.30961</span> <span class="r-out co"><span class="r-pr">#></span> A2 28.50624 94.69567</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"> <span class="co"># Compare with the results obtained in the original publication</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">schaefer07_complex_results</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span> <span class="co"># Compare with the results obtained in the original publication</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">schaefer07_complex_results</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> compound parameter KinGUI ModelMaker deviation</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent degradation rate 0.0496 0.0506 2.0</span> <span class="r-out co"><span class="r-pr">#></span> 2 parent DT50 13.9900 13.6900 2.2</span> @@ -184,7 +190,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html new file mode 100644 index 00000000..a16c02d7 --- /dev/null +++ b/docs/reference/set_nd_nq.html @@ -0,0 +1,261 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • mkin</title><!-- jquery 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set_nd_nq"><meta property="og:description" content="This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Set non-detects and unquantified values in residue series without replicates</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/set_nd_nq.R" class="external-link"><code>R/set_nd_nq.R</code></a></small> + <div class="hidden name"><code>set_nd_nq.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015).</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">res_raw</span>, <span class="va">lod</span>, loq <span class="op">=</span> <span class="cn">NA</span>, time_zero_presence <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">set_nd_nq_focus</span><span class="op">(</span></span> +<span> <span class="va">res_raw</span>,</span> +<span> <span class="va">lod</span>,</span> +<span> loq <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> set_first_sample_nd <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> first_sample_nd_value <span class="op">=</span> <span class="fl">0</span>,</span> +<span> ignore_below_loq_after_first_nd <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>res_raw</dt> +<dd><p>Character vector of a residue time series, or matrix of +residue values with rows representing depth profiles for a specific sampling +time, and columns representing time series of residues at the same depth. +Values below the limit of detection (lod) have to be coded as "nd", values +between the limit of detection and the limit of quantification, if any, have +to be coded as "nq". Samples not analysed have to be coded as "na". All +values that are not "na", "nd" or "nq" have to be coercible to numeric</p></dd> + + +<dt>lod</dt> +<dd><p>Limit of detection (numeric)</p></dd> + + +<dt>loq</dt> +<dd><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to +stop after the first non-detection is to be applied</p></dd> + + +<dt>time_zero_presence</dt> +<dd><p>Do we assume that residues occur at time zero? +This only affects samples from the first sampling time that have been +reported as "nd" (not detected).</p></dd> + + +<dt>set_first_sample_nd</dt> +<dd><p>Should the first sample be set to "first_sample_nd_value" +in case it is a non-detection?</p></dd> + + +<dt>first_sample_nd_value</dt> +<dd><p>Value to be used for the first sample if it is a non-detection</p></dd> + + +<dt>ignore_below_loq_after_first_nd</dt> +<dd><p>Should we ignore values below the LOQ after the first +non-detection that occurs after the quantified values?</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> + </div> + <div id="functions"> + <h2>Functions</h2> + +<ul><li><p><code>set_nd_nq_focus()</code>: Set non-detects in residue time series according to FOCUS rules</p></li> +</ul></div> + <div id="references"> + <h2>References</h2> + <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. +J. and Pol, J. W. (2015). Leaching of plant protection products and their +transformation products; Proposals for improving the assessment of leaching +to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra +Wageningen UR (University & Research centre)</p> +<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, +18 December 2014, p. 251</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># FOCUS (2014) p. 75/76 and 131/132</span></span></span> +<span class="r-in"><span><span class="va">parent_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_1</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">parent_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">parent_3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.06</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span> +<span class="r-in"><span><span class="va">metabolite</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">0.03</span>, <span class="fl">0.06</span>, <span class="fl">0.10</span>, <span class="fl">0.11</span>, <span class="fl">0.10</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span>, <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># Boesten et al. (2015), p. 57/58</span></span></span> +<span class="r-in"><span><span class="va">table_8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nq"</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>,</span></span> +<span class="r-in"><span> <span class="st">"nq"</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="st">"nd"</span>, <span class="st">"nq"</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_8</span>, <span class="fl">0.5</span>, <span class="fl">1.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 1.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 1.00 10.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] 0.25 1.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA 0.25 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">table_10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="st">"nd"</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_10</span>, <span class="fl">0.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 0.25 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] NA 0.25 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 23102f17..c1db0d30 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,23 +95,30 @@ dependence of the measured value \(y\):</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>y</dt> <dd><p>The magnitude of the observed value</p></dd> + + <dt>sigma_low</dt> <dd><p>The asymptotic minimum of the standard deviation for low observed values</p></dd> + + <dt>rsd_high</dt> <dd><p>The coefficient describing the increase of the standard deviation with the magnitude of the observed value</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The standard deviation of the response variable.</p> + + +<p>The standard deviation of the response variable.</p> </div> <div id="details"> <h2>Details</h2> @@ -131,26 +144,26 @@ Degradation Data. <em>Environments</em> 6(12) 124 <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">times</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_pred</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_syn</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span> -<span class="r-in"> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"><span class="va">f_nls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span> -<span class="r-in"> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_gnls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span> -<span class="r-in"> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span> -<span class="r-in"> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="va">f_gnls_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">f_gnls_tc_sf</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-in"><span class="va">f_mkin</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">times</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_pred</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_syn</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="va">f_nls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_gnls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc_sf</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="va">f_mkin</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="sigma_twocomp-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> f_nls 3 114.4817</span> <span class="r-out co"><span class="r-pr">#></span> f_gnls 3 114.4817</span> @@ -172,7 +185,7 @@ Degradation Data. 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--><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span 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class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for status.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mhmkin</span></span> +<span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for status.mhmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The object to investigate</p></dd> + + +<dt>...</dt> +<dd><p>For potential future extensions</p></dd> + + +<dt>x</dt> +<dd><p>The object to be printed</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object with the same dimensions as the fit array +suitable printing method.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> +<span class="r-in"><span> <span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">status</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model FOCUS A FOCUS B</span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK OK </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 17ecdfe4..0bb7f424 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -96,7 +102,7 @@ values.</p> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -105,7 +111,7 @@ values.</p> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> -<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> +<dd><p>an object of class <a href="mkinfit.html">mkinfit</a>.</p></dd> <dt>data</dt> @@ -186,7 +192,8 @@ model.</p></dd> <dd><p>The DT50 and DT90 values for each observed variable.</p></dd> <dt>SFORB</dt> -<dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> +<dd><p>If applicable, eigenvalues and fractional eigenvector component +g of SFORB systems in the model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> @@ -206,11 +213,11 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div id="ref-examples"> <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Jul 22 11:39:29 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Jul 22 11:39:29 2022 </span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 14:03:23 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:03:23 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -296,7 +303,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index dfbd766e..9edf10c0 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "mmkin" — summary.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc 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crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summary method for class " mmkin summary.mmkin><meta property="og:description" content="Shows status information on the mkinfit objects contained in the object and gives an overview of ill-defined parameters calculated by illparms."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -84,13 +90,13 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma </div> <div class="ref-description"> - <p>Shows convergence information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object + <p>Shows status information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object and gives an overview of ill-defined parameters calculated by <a href="illparms.html">illparms</a>.</p> </div> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -127,11 +133,11 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> <span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.607 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.835 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Convergence:</span> +<span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model FOCUS A FOCUS C</span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK </span> @@ -159,7 +165,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index ff014cc1..eb01ef7a 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -95,68 +101,95 @@ endpoints such as formation fractions and DT50 values. Optionally </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span> - <span class="va">object</span>, - data <span class="op">=</span> <span class="cn">FALSE</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span>, - distimes <span class="op">=</span> <span class="cn">TRUE</span>, - alpha <span class="op">=</span> <span class="fl">0.05</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="co"># S3 method for summary.nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nlme.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> data <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> distimes <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> alpha <span class="op">=</span> <span class="fl">0.05</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for summary.nlme.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>an object of class <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> + + <dt>data</dt> <dd><p>logical, indicating whether the full data should be included in the summary.</p></dd> + + <dt>verbose</dt> <dd><p>Should the summary be verbose?</p></dd> + + <dt>distimes</dt> <dd><p>logical, indicating whether DT50 and DT90 values should be included.</p></dd> + + <dt>alpha</dt> <dd><p>error level for confidence interval estimation from the t distribution</p></dd> + + <dt>...</dt> <dd><p>optional arguments passed to methods like <code>print</code>.</p></dd> + + <dt>x</dt> <dd><p>an object of class summary.nlme.mmkin</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a> object + + +<p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a> object obtained in the fit, with at least the following additional components</p> <dl><dt>nlmeversion, mkinversion, Rversion</dt> <dd><p>The nlme, mkin and R versions used</p></dd> + <dt>date.fit, date.summary</dt> <dd><p>The dates where the fit and the summary were produced</p></dd> + <dt>diffs</dt> <dd><p>The differential equations used in the degradation model</p></dd> + <dt>use_of_ff</dt> <dd><p>Was maximum or minimum use made of formation fractions</p></dd> + <dt>data</dt> <dd><p>The data</p></dd> + <dt>confint_trans</dt> <dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd> + <dt>confint_back</dt> <dd><p>Backtransformed parameters, with confidence intervals if available</p></dd> + <dt>ff</dt> <dd><p>The estimated formation fractions derived from the fitted model.</p></dd> + <dt>distimes</dt> <dd><p>The DT50 and DT90 values for each observed variable.</p></dd> + <dt>SFORB</dt> <dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> + </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> <div id="author"> @@ -167,44 +200,46 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># Generate five datasets following SFO kinetics</span></span> -<span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">dt50_sfo_in_pop</span> <span class="op"><-</span> <span class="fl">50</span></span> -<span class="r-in"><span class="va">k_in_pop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span> <span class="op">/</span> <span class="va">dt50_sfo_in_pop</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span> -<span class="r-in"><span class="va">k_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">k_in_pop</span><span class="op">)</span>, <span class="fl">0.5</span><span class="op">)</span></span> -<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">pred_sfo</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="va">k</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">ds_sfo_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">k_in</span>, <span class="va">pred_sfo</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12345</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds_sfo_syn</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span> -<span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span> -<span class="r-in"> n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"><span class="op">}</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="co"># Evaluate using mmkin and nlme</span></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Generate five datasets following SFO kinetics</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dt50_sfo_in_pop</span> <span class="op"><-</span> <span class="fl">50</span></span></span> +<span class="r-in"><span><span class="va">k_in_pop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span> <span class="op">/</span> <span class="va">dt50_sfo_in_pop</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">k_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">k_in_pop</span><span class="op">)</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">pred_sfo</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="va">k</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">ds_sfo_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">k_in</span>, <span class="va">pred_sfo</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12345</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds_sfo_syn</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># Evaluate using mmkin and nlme</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.155 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Jun 30 10:23:57 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Jun 30 10:23:57 2022 </span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.160 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 14:03:27 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:03:27 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -220,7 +255,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent </span> -<span class="r-out co"><span class="r-pr">#></span> 101.612 -4.454 </span> +<span class="r-out co"><span class="r-pr">#></span> 101.569 -4.454 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> @@ -244,18 +279,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.904e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.924e-05 0.5863 1</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance function:</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> -<span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 0.000121099 0.078996777 </span> +<span class="r-out co"><span class="r-pr">#></span> const prop </span> +<span class="r-out co"><span class="r-pr">#></span> 0.0001208853 0.0789968036 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370886 101.59243 103.81398</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370882 101.59243 103.81398</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.006923 0.01168 0.01972</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> @@ -266,48 +301,48 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389080</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958481</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063244</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585875</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007681</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249487</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964200</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572173</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901593</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669544</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485010</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68195 7.8379 1.362858</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41805 7.8379 -0.180921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305361</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145814</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618620</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842</span> @@ -315,47 +350,47 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206778</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323283</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535204</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26191 7.7703 -0.033706</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56191 7.7703 -1.359271</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66589 7.5232 0.354356</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56589 7.5232 1.271521</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27373 7.0523 -0.606002</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07373 7.0523 -1.712019</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18659 6.0838 0.852523</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08659 6.0838 1.493568</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44690 5.2970 0.650729</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35310 5.2970 -1.010595</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61902 4.6119 0.351052</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98098 4.6119 -0.429535</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024412</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90062 2.9544 0.304836</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30062 2.9544 1.117176</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19164 1.7926 -0.106910</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89164 1.7926 -1.055271</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36789 1.0876 -0.338255</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03211 1.0876 0.029520</span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -370,7 +405,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 0ab239cb..dfa0b776 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -96,7 +102,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -240,57 +246,56 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 828.1 822.7 -400.1</span> +<span class="r-out co"><span class="r-pr">#></span> 810.8 805.4 -391.4</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.74378 97.81291 103.67465</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.17104 -3.95231</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.31273 -0.53894</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.60206 -2.03623</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.32672 -2.95161</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.15247 1.09394</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.86164 0.67928 1.04400</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.73313 -7.46512 8.93137</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.19017</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.68705</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.34361</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.22590</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.39786</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.86947 97.81542 103.92353</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06947 -4.16944 -3.96950</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.93256 -1.34200 -0.52312</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.37017 -2.72660 -2.01375</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.06264 -4.21344 -3.91184</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02174 -0.45898 0.41549</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87598 0.67275 1.07922</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07949 0.06389 0.09509</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.19170 -30.36286 30.74626</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01883 -0.28736 0.32502</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44300 0.16391 0.72209</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35320 0.09661 0.60978</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.13707 0.02359 0.25056</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.37478 0.04490 0.70467</span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)" "sd(g_qlogis)"</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)"</span> <span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> character(0)</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 97.54844979 100.46239264 103.37633550</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01575805 0.01729111 0.01897331</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.21014925 0.28626877 0.37680664</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.02651112 0.05601399 0.11834908</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01326524 0.02649799 0.05293107</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.31467778 0.51297098 0.70726363</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 97.57609542 100.73343868 103.89078195</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01549292 0.01714893 0.01898194</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20720315 0.28358738 0.37481744</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.06149334 0.08733164 0.12402670</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01448390 0.01699942 0.01995184</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.45084762 0.51075839 0.57036168</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.1658367 0.4471180 0.7283993</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.2768757 0.7929203 1.3089649</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.2693629 0.7566116 1.2438602</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16606767 0.4479731 0.7298784</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.12284609 0.3588446 0.5948430</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.05379723 0.1548780 0.2559588</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.70273100 0.88750764 1.07228428</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06781347 0.08328016 0.09874685</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 14:31:01 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 14:31:01 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.6811490 0.88503409 1.08891921</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.0676515 0.08336272 0.09907394</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 14:04:08 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:04:08 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -305,7 +310,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 26.786 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 26.014 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -323,228 +328,233 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 825.6 821.3 -401.8</span> +<span class="r-out co"><span class="r-pr">#></span> 809.5 805.2 -393.7</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.4624 97.5484 103.3763</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.0576 -4.1504 -3.9647</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9136 -1.3240 -0.5031</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.8822 -3.6302 -2.1341</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.6307 -4.3226 -2.9388</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.0519 -0.7783 0.8821</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06582 -4.16737 -3.96427</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92674 -1.34187 -0.51160</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.43804 -2.78883 -2.08726</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.07458 -4.23472 -3.91443</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.04304 -0.19725 0.28333</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44797 0.16607 0.72988</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35884 0.12285 0.59484</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.15488 0.05380 0.25596</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4102 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2113 0.2439 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1308 -0.1305 -0.0504 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0383 0.0592 0.0151 0.0001 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0029 -0.0118 0.0131 -0.2547 -0.1942</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4698 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2461 0.2709 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1572 -0.1517 -0.0648 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0023 0.0835 0.0125 0.1420 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.2314 -0.2337 -0.0755 -0.2762 -0.4797</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4471 0.1658 0.7284</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.7929 0.2769 1.3090</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.7566 0.2694 1.2439</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4480 0.1661 0.7299</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3588 0.1228 0.5948</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1549 0.0538 0.2560</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01729 0.01576 0.01897</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28627 0.21015 0.37681</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05601 0.02651 0.11835</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02650 0.01327 0.05293</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.51297 0.31468 0.70726</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01715 0.01549 0.01898</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28359 0.20720 0.37482</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.08733 0.06149 0.12403</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01700 0.01448 0.01995</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.51076 0.45085 0.57036</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2863</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7137</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2836</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7164</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 17.44 65.15 19.61 12.37 26.16</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.09 133.17 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 15.94 93.48 28.14 7.937 40.77</span> +<span class="r-out co"><span class="r-pr">#></span> m1 40.42 134.27 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.005e+02 -10.662393 8.4135 -1.267301</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.637607 8.4135 0.432355</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.576e+01 -7.063498 8.0244 -0.880249</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.576e+01 -0.263498 8.0244 -0.032837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.717e+01 -5.369491 7.3135 -0.734185</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.717e+01 7.330509 7.3135 1.002320</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.274e+01 -1.238672 6.1224 -0.202319</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.274e+01 -2.438672 6.1224 -0.398322</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 0.022691 4.5984 0.004935</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.577309 4.5984 -0.995423</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.241e+01 -0.914545 2.8416 -0.321837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.241e+01 -3.614545 2.8416 -1.271993</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.283e+01 -0.730904 1.3891 -0.526186</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.283e+01 0.769096 1.3891 0.553681</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.128e+00 0.071981 1.0238 0.070309</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.128e+00 2.171981 1.0238 2.121538</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.022e+00 -0.822164 0.9225 -0.891230</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.022e+00 -0.622164 0.9225 -0.674429</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.163e+00 -0.863423 0.8928 -0.967116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.163e+00 -0.963423 0.8928 -1.079126</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.233e+00 -1.032930 0.9274 -1.113734</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.233e+00 -0.232930 0.9274 -0.251152</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.495e+00 0.005314 1.0393 0.005113</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.495e+00 -1.494686 1.0393 -1.438116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.010e+01 0.096372 1.2230 0.078801</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.010e+01 -0.603628 1.2230 -0.493572</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.269e+01 -0.492073 1.3802 -0.356526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.269e+01 0.707927 1.3802 0.512922</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.086e+01 0.944360 1.2669 0.745420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.086e+01 2.344360 1.2669 1.850494</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.723e+00 -1.123088 1.0961 -1.024658</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.723e+00 1.576912 1.0961 1.438708</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.184e+00 -1.683936 0.9869 -1.706219</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.184e+00 0.216064 0.9869 0.218923</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.005e+02 17.537607 8.4135 2.084469</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.005e+02 -0.662393 8.4135 -0.078730</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.566e+01 -5.456414 8.0156 -0.680727</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.566e+01 -1.056414 8.0156 -0.131795</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.702e+01 9.082833 7.3009 1.244062</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.702e+01 -8.617167 7.3009 -1.180281</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.298e+01 4.919834 6.1423 0.800981</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.298e+01 4.719834 6.1423 0.768420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.588e+01 0.124003 4.7372 0.026176</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.588e+01 -1.175997 4.7372 -0.248245</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.719e+01 -0.587869 3.2217 -0.182474</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.719e+01 -0.387869 3.2217 -0.120394</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.013e+01 1.973728 1.8966 1.040673</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.013e+01 4.573728 1.8966 2.411556</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.259e+01 -0.185933 1.3734 -0.135379</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.259e+01 -1.785933 1.3734 -1.300347</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.981e+00 -1.180542 1.1088 -1.064723</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.981e+00 -0.080542 1.1088 -0.072640</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.306e+00 -0.006246 0.8941 -0.006986</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.589e+00 0.110879 0.9365 0.118399</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.589e+00 1.110879 0.9365 1.186217</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.062e+00 1.038045 1.0647 0.974978</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.062e+00 0.838045 1.0647 0.787129</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.065e+01 -0.553713 1.2549 -0.441227</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.065e+01 -0.353713 1.2549 -0.281857</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.284e+01 -2.144854 1.3900 -1.543111</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.284e+01 -0.644854 1.3900 -0.463939</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.082e+01 -0.115278 1.2645 -0.091165</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.082e+01 1.684722 1.2645 1.332337</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.014e+00 1.085607 1.1105 0.977610</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.014e+00 -0.614393 1.1105 -0.553272</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.736e+00 0.363593 1.0079 0.360737</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.736e+00 -1.236407 1.0079 -1.226697</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.005e+02 5.737607 8.4135 0.681955</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.005e+02 6.437607 8.4135 0.765155</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.343e+01 13.972212 7.8311 1.784188</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.343e+01 2.672212 7.8311 0.341229</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.160e+01 -2.196297 6.8531 -0.320484</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.160e+01 1.003703 6.8531 0.146460</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.464e+01 -0.737220 5.4557 -0.135129</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.464e+01 -2.237220 5.4557 -0.410072</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.772e+01 3.278433 4.0722 0.805086</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.772e+01 -0.621567 4.0722 -0.152638</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.303e+01 3.070676 2.8903 1.062400</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.303e+01 3.570676 2.8903 1.235391</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.929e+01 0.808039 1.8355 0.440235</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.929e+01 0.508039 1.8355 0.276789</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.209e+01 -0.794443 1.3425 -0.591785</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.209e+01 -1.394443 1.3425 -1.038728</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.590e+00 0.610002 1.0896 0.559843</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.590e+00 -0.289998 1.0896 -0.266152</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -4.263e-14 0.800000 0.8875 0.901401</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.692e+00 0.107665 0.8986 0.119811</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.692e+00 0.607665 0.8986 0.676214</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.455e+00 -0.255347 0.9619 -0.265449</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.455e+00 -0.355347 0.9619 -0.369404</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.124e+00 -1.324338 1.1160 -1.186685</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.124e+00 1.975662 1.1160 1.770309</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.104e+01 0.361860 1.2778 0.283196</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.104e+01 1.761860 1.2778 1.378852</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.177e+01 -0.272554 1.3225 -0.206097</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.177e+01 -1.172554 1.3225 -0.886648</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.242e+00 -1.741667 1.1747 -1.482591</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.242e+00 -0.641667 1.1747 -0.546218</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.837e+00 0.463318 1.0544 0.439398</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.837e+00 1.263318 1.0544 1.198095</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.906e+00 0.394322 0.9770 0.403595</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.906e+00 -1.105678 0.9770 -1.131677</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.005e+02 4.237607 8.4135 0.503670</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.005e+02 -12.162393 8.4135 -1.445587</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.723e+01 -3.029220 8.1458 -0.371877</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.723e+01 -2.629220 8.1458 -0.322772</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.114e+01 -13.041804 7.6420 -1.706592</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.114e+01 5.358196 7.6420 0.701150</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.033e+01 -4.133084 6.7488 -0.612421</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.033e+01 -2.533084 6.7488 -0.375340</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.504e+01 5.757987 5.4889 1.049017</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.504e+01 2.257987 5.4889 0.411371</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.418e+01 -1.080806 3.7849 -0.285557</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.418e+01 0.919194 3.7849 0.242858</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.110e+01 0.200596 1.9686 0.101899</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.110e+01 2.400596 1.9686 1.219459</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.183e+01 -0.034206 1.3263 -0.025791</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.183e+01 0.265794 1.3263 0.200408</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.985e+00 0.014647 1.0612 0.013803</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.985e+00 -0.785353 1.0612 -0.740078</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 -1.705e-13 1.600000 0.8875 1.802801</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.803e-01 0.219655 0.8893 0.246994</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.927e+00 1.773027 0.9019 1.965880</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.927e+00 0.073027 0.9019 0.080970</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.013e+00 -0.412926 0.9483 -0.435417</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.013e+00 -0.212926 0.9483 -0.224523</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.604e+00 0.495843 1.0441 0.474896</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.604e+00 -0.004157 1.0441 -0.003981</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.077e+00 0.422700 1.1658 0.362576</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.077e+00 0.222700 1.1658 0.191024</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.818e+00 -0.518498 1.1520 -0.450099</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.818e+00 0.181502 1.1520 0.157559</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.738e+00 -0.137785 1.0500 -0.131222</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.738e+00 0.962215 1.0500 0.916383</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.794e+00 -1.093754 0.9732 -1.123914</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.794e+00 -1.293754 0.9732 -1.329429</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.005e+02 9.937607 8.4135 1.181155</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.005e+02 11.637607 8.4135 1.383212</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.372e+01 -0.215694 7.8550 -0.027460</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.372e+01 -2.715694 7.8550 -0.345730</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.226e+01 -11.257156 6.9076 -1.629667</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.226e+01 7.442844 6.9076 1.077480</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.553e+01 -5.128464 5.5289 -0.927571</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.553e+01 -6.428464 5.5289 -1.162699</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.835e+01 8.146351 4.1235 1.975572</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.835e+01 -1.353649 4.1235 -0.328273</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.300e+01 -2.803303 2.8883 -0.970586</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.300e+01 -9.103303 2.8883 -3.151832</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.891e+01 -1.905909 1.8074 -1.054506</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.891e+01 -0.205909 1.8074 -0.113926</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.172e+01 -0.423434 1.3194 -0.320923</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.172e+01 0.176566 1.3194 0.133820</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.281e+00 1.719138 1.0749 1.599402</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.281e+00 0.819138 1.0749 0.762086</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 -2.842e-13 0.700000 0.8875 0.788726</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.252e+00 -0.252227 0.9279 -0.271821</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.252e+00 -0.652227 0.9279 -0.702895</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.615e+00 -3.515326 1.1413 -3.080237</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.615e+00 -1.115326 1.1413 -0.977283</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.588e+01 0.619041 1.5928 0.388661</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.588e+01 3.119041 1.5928 1.958272</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.189e+01 1.014705 2.0272 0.500543</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.189e+01 1.314705 2.0272 0.648529</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.369e+01 -1.487604 2.1632 -0.687701</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.369e+01 0.712396 2.1632 0.329332</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.869e+01 -3.193942 1.7920 -1.782295</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.869e+01 1.106058 1.7920 0.617206</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.380e+01 1.103454 1.4518 0.760041</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.380e+01 0.403454 1.4518 0.277892</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.864e+00 1.035963 1.2093 0.856637</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.864e+00 0.535963 1.2093 0.443187</span> +<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.007e+02 -10.93344 8.4439 -1.29483</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.007e+02 3.36656 8.4439 0.39870</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.591e+01 -7.20789 8.0440 -0.89606</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.591e+01 -0.40789 8.0440 -0.05071</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.712e+01 -5.31561 7.3159 -0.72658</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.712e+01 7.38439 7.3159 1.00936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.246e+01 -0.95675 6.1047 -0.15672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.246e+01 -2.15675 6.1047 -0.35329</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.382e+01 0.38143 4.5729 0.08341</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.382e+01 -4.21857 4.5729 -0.92251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.230e+01 -0.80120 2.8344 -0.28267</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.230e+01 -3.50120 2.8344 -1.23524</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.307e+01 -0.97165 1.4038 -0.69215</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.307e+01 0.52835 1.4038 0.37637</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.353e+00 -0.15285 1.0314 -0.14820</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.353e+00 1.94715 1.0314 1.88790</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.175e+00 -0.97462 0.9238 -1.05506</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.175e+00 -0.77462 0.9238 -0.83855</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.183e+00 -0.88350 0.8905 -0.99212</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.183e+00 -0.98350 0.8905 -1.10441</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.281e+00 -1.08106 0.9263 -1.16703</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.281e+00 -0.28106 0.9263 -0.30341</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.564e+00 -0.06353 1.0405 -0.06106</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.564e+00 -1.56353 1.0405 -1.50266</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.015e+01 0.05147 1.2243 0.04204</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.015e+01 -0.64853 1.2243 -0.52970</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -0.44824 1.3766 -0.32561</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 0.75176 1.3766 0.54610</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.02355 1.2611 0.81165</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.42355 1.2611 1.92181</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.698e+00 -1.09840 1.0932 -1.00474</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.698e+00 1.60160 1.0932 1.46502</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.199e+00 -1.69853 0.9854 -1.72363</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.199e+00 0.20147 0.9854 0.20445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.007e+02 17.26656 8.4439 2.04485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.007e+02 -0.93344 8.4439 -0.11055</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.584e+01 -5.63852 8.0382 -0.70146</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.584e+01 -1.23852 8.0382 -0.15408</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.706e+01 9.04068 7.3113 1.23654</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.706e+01 -8.65932 7.3113 -1.18438</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.286e+01 5.04438 6.1376 0.82188</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.286e+01 4.84438 6.1376 0.78930</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.567e+01 0.33336 4.7242 0.07057</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.567e+01 -0.96664 4.7242 -0.20462</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.705e+01 -0.44800 3.2127 -0.13944</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.705e+01 -0.24800 3.2127 -0.07719</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.008e+01 2.01984 1.8935 1.06672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.008e+01 4.61984 1.8935 2.43984</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.253e+01 -0.12814 1.3689 -0.09360</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.253e+01 -1.72814 1.3689 -1.26238</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.916e+00 -1.11595 1.1040 -1.01085</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.916e+00 -0.01595 1.1040 -0.01445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.317e+00 -0.01669 0.8918 -0.01871</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.613e+00 0.08699 0.9349 0.09305</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.613e+00 1.08699 0.9349 1.16270</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.092e+00 1.00781 1.0643 0.94688</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.092e+00 0.80781 1.0643 0.75897</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.066e+01 -0.56458 1.2545 -0.45006</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.066e+01 -0.36458 1.2545 -0.29063</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.281e+01 -2.11106 1.3870 -1.52201</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.281e+01 -0.61106 1.3870 -0.44055</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.078e+01 -0.08464 1.2616 -0.06709</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.078e+01 1.71536 1.2616 1.35970</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.013e+00 1.08684 1.1088 0.98016</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.013e+00 -0.61316 1.1088 -0.55298</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.749e+00 0.35063 1.0065 0.34838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.749e+00 -1.24937 1.0065 -1.24133</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.007e+02 5.46656 8.4439 0.64740</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.007e+02 6.16656 8.4439 0.73030</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.369e+01 13.70530 7.8606 1.74354</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.369e+01 2.40530 7.8606 0.30599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.185e+01 -2.45363 6.8807 -0.35660</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.185e+01 0.74637 6.8807 0.10847</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.487e+01 -0.97153 5.4798 -0.17729</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.487e+01 -2.47153 5.4798 -0.45103</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.791e+01 3.09024 4.0908 0.75542</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.791e+01 -0.80976 4.0908 -0.19795</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.313e+01 2.97112 2.9001 1.02450</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.313e+01 3.47112 2.9001 1.19691</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.927e+01 0.83265 1.8339 0.45404</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.927e+01 0.53265 1.8339 0.29045</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.203e+01 -0.72783 1.3374 -0.54421</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.203e+01 -1.32783 1.3374 -0.99284</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.516e+00 0.68382 1.0844 0.63061</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.516e+00 -0.21618 1.0844 -0.19936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -9.948e-14 0.80000 0.8850 0.90392</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.682e+00 0.11759 0.8961 0.13123</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.682e+00 0.61759 0.8961 0.68921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.431e+00 -0.23052 0.9590 -0.24037</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.431e+00 -0.33052 0.9590 -0.34465</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.084e+00 -1.28422 1.1124 -1.15445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.084e+00 2.01578 1.1124 1.81208</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.100e+01 0.40274 1.2743 0.31606</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.100e+01 1.80274 1.2743 1.41474</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.176e+01 -0.25977 1.3207 -0.19669</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.176e+01 -1.15977 1.3207 -0.87813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.277e+00 -1.77696 1.1753 -1.51190</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.277e+00 -0.67696 1.1753 -0.57598</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.883e+00 0.41708 1.0548 0.39542</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.883e+00 1.21708 1.0548 1.15389</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.948e+00 0.35179 0.9764 0.36028</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.948e+00 -1.14821 0.9764 -1.17591</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.007e+02 3.96656 8.4439 0.46975</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.007e+02 -12.43344 8.4439 -1.47247</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.738e+01 -3.18358 8.1663 -0.38985</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.738e+01 -2.78358 8.1663 -0.34086</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.110e+01 -12.99595 7.6454 -1.69984</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.110e+01 5.40405 7.6454 0.70684</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.000e+01 -3.79797 6.7273 -0.56456</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.000e+01 -2.19797 6.7273 -0.32672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.446e+01 6.34396 5.4456 1.16496</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.446e+01 2.84396 5.4456 0.52225</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.359e+01 -0.48960 3.7400 -0.13091</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.359e+01 1.51040 3.7400 0.40385</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.095e+01 0.35282 1.9577 0.18022</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.095e+01 2.55282 1.9577 1.30400</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.188e+01 -0.07874 1.3281 -0.05929</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.188e+01 0.22126 1.3281 0.16660</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 7.072e+00 -0.07245 1.0634 -0.06813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 7.072e+00 -0.87245 1.0634 -0.82041</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 5.684e-14 1.60000 0.8850 1.80784</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.960e-01 0.20399 0.8869 0.23000</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.968e+00 1.73240 0.9001 1.92466</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.968e+00 0.03240 0.9001 0.03599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.083e+00 -0.48287 0.9482 -0.50924</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.083e+00 -0.28287 0.9482 -0.29832</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.682e+00 0.41836 1.0457 0.40007</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.682e+00 -0.08164 1.0457 -0.07807</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.103e+00 0.39733 1.1658 0.34082</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.103e+00 0.19733 1.1658 0.16926</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.750e+00 -0.44979 1.1469 -0.39218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.750e+00 0.25021 1.1469 0.21817</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.673e+00 -0.07285 1.0453 -0.06969</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.673e+00 1.02715 1.0453 0.98261</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.757e+00 -1.05747 0.9698 -1.09036</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.757e+00 -1.25747 0.9698 -1.29658</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.007e+02 9.66656 8.4439 1.14480</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.007e+02 11.36656 8.4439 1.34612</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.395e+01 -0.45394 7.8821 -0.05759</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.395e+01 -2.95394 7.8821 -0.37477</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.245e+01 -11.44783 6.9298 -1.65197</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.245e+01 7.25217 6.9298 1.04652</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.567e+01 -5.27002 5.5455 -0.95032</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.567e+01 -6.57002 5.5455 -1.18475</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.847e+01 8.03029 4.1364 1.94139</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.847e+01 -1.46971 4.1364 -0.35532</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.309e+01 -2.89206 2.8971 -0.99825</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.309e+01 -9.19206 2.8971 -3.17281</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.891e+01 -1.90623 1.8076 -1.05458</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.891e+01 -0.20623 1.8076 -0.11409</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.168e+01 -0.38263 1.3160 -0.29076</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.168e+01 0.21737 1.3160 0.16518</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.230e+00 1.77031 1.0708 1.65333</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.230e+00 0.87031 1.0708 0.81280</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 -5.116e-13 0.70000 0.8850 0.79093</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.244e+00 -0.24430 0.9254 -0.26398</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.244e+00 -0.64430 0.9254 -0.69621</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.592e+00 -3.49175 1.1385 -3.06686</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.592e+00 -1.09175 1.1385 -0.95890</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.583e+01 0.66887 1.5890 0.42093</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.583e+01 3.16887 1.5890 1.99424</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.181e+01 1.08658 2.0224 0.53728</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.181e+01 1.38658 2.0224 0.68562</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.364e+01 -1.43659 2.1600 -0.66508</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.364e+01 0.76341 2.1600 0.35342</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.873e+01 -3.23377 1.7950 -1.80150</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.873e+01 1.06623 1.7950 0.59398</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.387e+01 1.03117 1.4560 0.70822</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.387e+01 0.33117 1.4560 0.22745</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.937e+00 0.96270 1.2122 0.79415</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.937e+00 0.46270 1.2122 0.38169</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 8d747ffe..132380a8 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index e9251de3..c00d1b55 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -32,7 +32,7 @@ Compare also the code in the example section to see the degradation models."><!- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -59,19 +59,25 @@ Compare also the code in the example section to see the degradation models."><!- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -117,7 +123,7 @@ Compare also the code in the example section to see the degradation models."><!- </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">synthetic_data_for_UBA_2014</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">synthetic_data_for_UBA_2014</span></span></code></pre></div> </div> <div id="format"> @@ -141,115 +147,115 @@ Compare also the code in the example section to see the degradation models."><!- <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="co"># The data have been generated using the following kinetic models</span></span> -<span class="r-in"><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The data have been generated using the following kinetic models</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">m_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> -<span class="r-in"> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The model predictions without intentional error were generated as follows</span></span> -<span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.7</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>,</span> -<span class="r-in"> k_M1 <span class="op">=</span> <span class="fl">0.3</span>, f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>,</span> -<span class="r-in"> k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_lin</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.5</span>,</span> -<span class="r-in"> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fl">0.3</span>,</span> -<span class="r-in"> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.2</span>,</span> -<span class="r-in"> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>, k_M1 <span class="op">=</span> <span class="fl">0.01</span>,</span> -<span class="r-in"> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.2</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.3</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span>,</span> -<span class="r-in"> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.6</span>, k_M1 <span class="op">=</span> <span class="fl">0.04</span>,</span> -<span class="r-in"> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.4</span>, k_M2 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Construct names for datasets with errors</span></span> -<span class="r-in"><span class="va">d_synth_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"d_synth_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO_lin"</span>, <span class="st">"SFO_par"</span>,</span> -<span class="r-in"> <span class="st">"DFOP_lin"</span>, <span class="st">"DFOP_par"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Original function used or adding errors. The add_err function now published</span></span> -<span class="r-in"><span class="co"># with this package is a slightly generalised version where the names of</span></span> -<span class="r-in"><span class="co"># secondary compartments that should have an initial value of zero (M1 and M2</span></span> -<span class="r-in"><span class="co"># in this case) are not hardcoded any more.</span></span> -<span class="r-in"><span class="co"># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span></span> -<span class="r-in"><span class="co"># {</span></span> -<span class="r-in"><span class="co"># set.seed(seed)</span></span> -<span class="r-in"><span class="co"># d_long = mkin_wide_to_long(d, time = "time")</span></span> -<span class="r-in"><span class="co"># d_rep = data.frame(lapply(d_long, rep, each = 2))</span></span> -<span class="r-in"><span class="co"># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span></span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span></span> -<span class="r-in"><span class="co"># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span></span> -<span class="r-in"><span class="co"># d_NA$value <- round(d_NA$value, 1)</span></span> -<span class="r-in"><span class="co"># return(d_NA)</span></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The following is the simplified version of the two-component model of Rocke</span></span> -<span class="r-in"><span class="co"># and Lorenzato (1995)</span></span> -<span class="r-in"><span class="va">sdfunc_twocomp</span> <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span>, <span class="va">sd_low</span>, <span class="va">rsd_high</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">sd_low</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">rsd_high</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Add the errors.</span></span> -<span class="r-in"><span class="kw">for</span> <span class="op">(</span><span class="va">d_synth_name</span> <span class="kw">in</span> <span class="va">d_synth_names</span><span class="op">)</span></span> -<span class="r-in"><span class="op">{</span></span> -<span class="r-in"> <span class="va">d_synth</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/get.html" class="external-link">get</a></span><span class="op">(</span><span class="va">d_synth_name</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_a"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_b"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_c"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu">sdfunc_twocomp</span><span class="op">(</span><span class="va">value</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="op">}</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d_synth_err_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">d_synth_names</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># This is just one example of an evaluation using the kinetic model used for</span></span> -<span class="r-in"><span class="co"># the generation of the data</span></span> -<span class="r-in"> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The model predictions without intentional error were generated as follows</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.7</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fl">0.3</span>, f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fl">0.3</span>,</span></span> +<span class="r-in"><span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.2</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>, k_M1 <span class="op">=</span> <span class="fl">0.01</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.2</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.3</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.6</span>, k_M1 <span class="op">=</span> <span class="fl">0.04</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.4</span>, k_M2 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Construct names for datasets with errors</span></span></span> +<span class="r-in"><span><span class="va">d_synth_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"d_synth_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO_lin"</span>, <span class="st">"SFO_par"</span>,</span></span> +<span class="r-in"><span> <span class="st">"DFOP_lin"</span>, <span class="st">"DFOP_par"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Original function used or adding errors. The add_err function now published</span></span></span> +<span class="r-in"><span><span class="co"># with this package is a slightly generalised version where the names of</span></span></span> +<span class="r-in"><span><span class="co"># secondary compartments that should have an initial value of zero (M1 and M2</span></span></span> +<span class="r-in"><span><span class="co"># in this case) are not hardcoded any more.</span></span></span> +<span class="r-in"><span><span class="co"># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span></span></span> +<span class="r-in"><span><span class="co"># {</span></span></span> +<span class="r-in"><span><span class="co"># set.seed(seed)</span></span></span> +<span class="r-in"><span><span class="co"># d_long = mkin_wide_to_long(d, time = "time")</span></span></span> +<span class="r-in"><span><span class="co"># d_rep = data.frame(lapply(d_long, rep, each = 2))</span></span></span> +<span class="r-in"><span><span class="co"># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span></span></span> +<span class="r-in"><span><span class="co"># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span></span></span> +<span class="r-in"><span><span class="co"># d_NA$value <- round(d_NA$value, 1)</span></span></span> +<span class="r-in"><span><span class="co"># return(d_NA)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is the simplified version of the two-component model of Rocke</span></span></span> +<span class="r-in"><span><span class="co"># and Lorenzato (1995)</span></span></span> +<span class="r-in"><span><span class="va">sdfunc_twocomp</span> <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span>, <span class="va">sd_low</span>, <span class="va">rsd_high</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">sd_low</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">rsd_high</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add the errors.</span></span></span> +<span class="r-in"><span><span class="kw">for</span> <span class="op">(</span><span class="va">d_synth_name</span> <span class="kw">in</span> <span class="va">d_synth_names</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">d_synth</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/get.html" class="external-link">get</a></span><span class="op">(</span><span class="va">d_synth_name</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_a"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_b"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_c"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu">sdfunc_twocomp</span><span class="op">(</span><span class="va">value</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_err_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">d_synth_names</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is just one example of an evaluation using the kinetic model used for</span></span></span> +<span class="r-in"><span><span class="co"># the generation of the data</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:21 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:21 2022 </span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 17 14:04:10 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:04:11 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -258,7 +264,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 830 model solutions performed in 1.716 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.574 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -310,15 +316,15 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.063e-07 -1.980e-07 1.088e-07 1.041e-07 7.820e-09</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 2.063e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -1.980e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 1.088e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 1.041e-07</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 7.820e-09</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 -6.495e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma -6.495e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -355,8 +361,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> <span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56249</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86249</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56248</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86248</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 53.9 4.873e+01 5.17118</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 47.5 4.873e+01 -1.22882</span> <span class="r-out co"><span class="r-pr">#></span> 3 parent 10.4 1.111e+01 -0.70773</span> @@ -365,8 +371,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> <span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> <span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.534e-10 0.60000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.941e-10 3.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> <span class="r-out co"><span class="r-pr">#></span> 3 M1 34.3 3.937e+01 -5.07027</span> @@ -376,9 +382,9 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> <span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> <span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.675e-10 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.671e-10 1.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.671e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 20.9 2.153e+01 -0.62527</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 19.3 2.153e+01 -2.22527</span> @@ -394,7 +400,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 90 M2 10.8 1.013e+01 0.67130</span> <span class="r-out co"><span class="r-pr">#></span> 120 M2 9.8 5.521e+00 4.27893</span> <span class="r-out co"><span class="r-pr">#></span> 120 M2 3.3 5.521e+00 -2.22107</span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -409,7 +415,7 @@ Compare also the code in the example section to see the degradation models."><!- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 327e8ae9..a76f23ab 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -45,19 +45,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -89,7 +95,7 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">test_data_from_UBA_2014</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div> </div> <div id="format"> @@ -111,21 +117,23 @@ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span> -<span class="r-in"> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span> -<span class="r-in"> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span> -<span class="r-in"> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span> -<span class="r-in"> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span> -<span class="r-in"> <span class="co"># model).</span></span> -<span class="r-in"> <span class="va">m_ws</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span> -<span class="r-in"> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span> +<span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span> +<span class="r-in"><span> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span> +<span class="r-in"><span> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span> +<span class="r-in"><span> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span> +<span class="r-in"><span> <span class="co"># model).</span></span></span> +<span class="r-in"><span> <span class="va">m_ws</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="va">f_river</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="va">f_river</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_w_0 95.91998118 NA NA NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_w 0.41145375 NA NA NA NA NA</span> @@ -133,25 +141,26 @@ <span class="r-out co"><span class="r-pr">#></span> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.13612618 NA NA NA NA NA</span> -<span class="r-in"> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.1090929 5 6</span> <span class="r-out co"><span class="r-pr">#></span> parent_w 0.0817436 3 3</span> <span class="r-out co"><span class="r-pr">#></span> parent_s 0.1619965 2 3</span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># This is the evaluation used for the validation of software packages</span></span> -<span class="r-in"> <span class="co"># in the expertise from 2014</span></span> -<span class="r-in"> <span class="va">m_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span> -<span class="r-in"> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># This is the evaluation used for the validation of software packages</span></span></span> +<span class="r-in"><span> <span class="co"># in the expertise from 2014</span></span></span> +<span class="r-in"><span> <span class="va">m_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"> <span class="va">f_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span> @@ -174,14 +183,14 @@ <span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450775</span> <span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.99489895</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.45337221</span> -<span class="r-in"> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.09649963 9 20</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.04721283 2 6</span> <span class="r-out co"><span class="r-pr">#></span> M1 0.26551208 2 5</span> <span class="r-out co"><span class="r-pr">#></span> M2 0.20327575 2 5</span> <span class="r-out co"><span class="r-pr">#></span> M3 0.05196550 3 4</span> -<span class="r-in"> <span class="co"># }</span></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -196,7 +205,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/tex_listing.html b/docs/reference/tex_listing.html new file mode 100644 index 00000000..4b8736c3 --- /dev/null +++ b/docs/reference/tex_listing.html @@ -0,0 +1,143 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Wrap the output of a summary function in tex listing environment — tex_listing • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link 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src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Wrap the output of a summary function in tex listing environment</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/tex_listing.R" class="external-link"><code>R/tex_listing.R</code></a></small> + <div class="hidden name"><code>tex_listing.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function can be used in a R markdown code chunk with the chunk +option <code>results = "asis"</code>.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tex_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span>, label <span class="op">=</span> <span class="cn">NULL</span>, clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The object for which the summary is to be listed</p></dd> + + +<dt>caption</dt> +<dd><p>An optional caption</p></dd> + + +<dt>label</dt> +<dd><p>An optional label</p></dd> + + +<dt>clearpage</dt> +<dd><p>Should a new page be started after the listing?</p></dd> + +</dl></div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2da09efe..66e94941 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,7 +22,7 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -49,19 +49,25 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,19 +103,19 @@ the <a href="ilr.html">ilr</a> transformation is used.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">transform_odeparms</span><span class="op">(</span> - <span class="va">parms</span>, - <span class="va">mkinmod</span>, - transform_rates <span class="op">=</span> <span class="cn">TRUE</span>, - transform_fractions <span class="op">=</span> <span class="cn">TRUE</span> -<span class="op">)</span> - -<span class="fu">backtransform_odeparms</span><span class="op">(</span> - <span class="va">transparms</span>, - <span class="va">mkinmod</span>, - transform_rates <span class="op">=</span> <span class="cn">TRUE</span>, - transform_fractions <span class="op">=</span> <span class="cn">TRUE</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">parms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">backtransform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">transparms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -117,11 +123,15 @@ the <a href="ilr.html">ilr</a> transformation is used.</p> <dl><dt>parms</dt> <dd><p>Parameters of kinetic models as used in the differential equations.</p></dd> + + <dt>mkinmod</dt> <dd><p>The kinetic model of class <a href="mkinmod.html">mkinmod</a>, containing the names of the model variables that are needed for grouping the formation fractions before <a href="ilr.html">ilr</a> transformation, the parameter names and the information if the pathway to sink is included in the model.</p></dd> + + <dt>transform_rates</dt> <dd><p>Boolean specifying if kinetic rate constants should be transformed in the model specification used in the fitting for better @@ -129,6 +139,8 @@ compliance with the assumption of normal distribution of the estimator. If TRUE, also alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS models and the break point tb of the HS model.</p></dd> + + <dt>transform_fractions</dt> <dd><p>Boolean specifying if formation fractions constants should be transformed in the model specification used in the @@ -140,13 +152,18 @@ target variable e.g. a single metabolite plus a pathway to sink), a logistic transformation is used <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">stats::qlogis()</a></code>. In other cases, i.e. if two or more formation fractions need to be transformed whose sum cannot exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd> + + <dt>transparms</dt> <dd><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A vector of transformed or backtransformed parameters</p> + + +<p>A vector of transformed or backtransformed parameters</p> </div> <div id="details"> <h2>Details</h2> @@ -161,119 +178,119 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span> -<span class="r-in"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># Transformed and backtransformed parameters</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Transformed and backtransformed parameters</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.60 1.5702 96.40 102.79</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.04 0.0763 -3.19 -2.88</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1_sink -5.25 0.1332 -5.52 -4.98</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.13 0.3585 2.40 3.85</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span> -<span class="r-in"><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span> -<span class="r-in"><span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span> -<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span></span> +<span class="r-in"><span><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span></span> +<span class="r-in"><span><span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 96.40384 1.03e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 2.39609 3.85e+00</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">initials</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span> -<span class="r-in"><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink </span> <span class="r-out co"><span class="r-pr">#></span> 100.750000 -2.302585 -2.301586 -2.300587 </span> -<span class="r-in"><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent_sink k_parent_m1 k_m1_sink </span> <span class="r-out co"><span class="r-pr">#></span> 100.7500 0.1000 0.1001 0.1002 </span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="co"># The case of formation fractions (this is now the default)</span></span> -<span class="r-in"><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The case of formation fractions (this is now the default)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">fit.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit.ff.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.5985 1.5702 96.404 102.79</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.3157 0.0409 -2.399 -2.23</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.2475 0.1332 -5.518 -4.98</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.0579 0.0893 -0.124 0.24</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.1255 0.3585 2.396 3.85</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> -<span class="r-in"><span class="va">initials</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span> -<span class="r-in"><span class="va">transformed</span> <span class="op"><-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 </span> <span class="r-out co"><span class="r-pr">#></span> 0.5 </span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># And without sink</span></span> -<span class="r-in"><span class="va">SFO_SFO.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And without sink</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">fit.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit.ff.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 84.79 3.012 78.67 90.91</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.76 0.082 -2.92 -2.59</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.21 0.123 -4.46 -3.96</span> <span class="r-out co"><span class="r-pr">#></span> sigma 8.22 0.943 6.31 10.14</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019</span> <span class="r-out co"><span class="r-pr">#></span> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -288,7 +305,7 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index 48bf1d7f..d5b4f6f3 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -20,7 +20,7 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -47,19 +47,25 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -93,38 +99,43 @@ override these starting values.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> -<span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, evaluate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, evaluate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mkinfit object to be updated</p></dd> + + <dt>...</dt> <dd><p>Arguments to <code><a href="mkinfit.html">mkinfit</a></code> that should replace the arguments from the original call. Arguments set to NULL will remove arguments given in the original call</p></dd> + + <dt>evaluate</dt> <dd><p>Should the call be evaluated or returned as a call</p></dd> + </dl></div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.44423886 0.09793574 3.39632469 </span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> 99.44423885 0.09793574 3.39632469 </span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="update.mkinfit-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma_low rsd_high </span> <span class="r-out co"><span class="r-pr">#></span> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </span> -<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="update.mkinfit-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -139,7 +150,7 @@ remove arguments given in the original call</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index b30d21a1..320fe932 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -34,6 +34,12 @@ <loc>https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/articles/web_only/multistart.html</loc> + </url> + <url> + <loc>https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/authors.html</loc> </url> <url> @@ -97,6 +103,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/aw.html</loc> </url> <url> @@ -142,12 +151,18 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/intervals.saem.mmkin.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/llhist.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/loftest.html</loc> </url> <url> <loc>https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/logLik.saem.mmkin.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html</loc> </url> <url> @@ -211,6 +226,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/mmkin.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/multistart.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc> </url> <url> @@ -229,6 +247,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/parplot.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html</loc> </url> <url> @@ -253,6 +274,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc> </url> <url> @@ -265,9 +289,15 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/status.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html</loc> </url> <url> @@ -289,6 +319,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/tex_listing.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/tffm0.html</loc> </url> <url> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 2d3deb26..629b70bd 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda Binary files differindex 55fabf1d..509b1008 100644 --- a/vignettes/web_only/saem_benchmarks.rda +++ b/vignettes/web_only/saem_benchmarks.rda |
