diff options
42 files changed, 266 insertions, 217 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 8bef6055..70872c1d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.0.0 -Date: 2021-02-03 +Version: 1.0.1 +Date: 2021-02-04 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", @@ -1,3 +1,11 @@ +# mkin 1.0.1 + +- 'confint.mmkin', 'nlme.mmkin', 'transform_odeparms': Fix example code in dontrun sections that failed with current defaults + +- 'logLik.mkinfit': Improve example code to avoid warnings and show convenient syntax + +- 'mkinresplot': Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago + # mkin 1.0.0 ## General diff --git a/R/confint.mkinfit.R b/R/confint.mkinfit.R index 53eb45ee..6403c349 100644 --- a/R/confint.mkinfit.R +++ b/R/confint.mkinfit.R @@ -57,20 +57,20 @@ #' if (identical(Sys.getenv("NOT_CRAN"), "true")) { #' n_cores <- parallel::detectCores() - 1 #' } else { -#' n_cores <- 1 +#' n_cores <- 1 #' } #' if (Sys.getenv("TRAVIS") != "") n_cores = 1 #' if (Sys.info()["sysname"] == "Windows") n_cores = 1 #' -#' SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), quiet = TRUE) +#' SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), +#' use_of_ff = "min", quiet = TRUE) #' SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), #' use_of_ff = "max", quiet = TRUE) #' f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) #' system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE)) #' # Using more cores does not save much time here, as parent_0 takes up most of the time #' # If we additionally exclude parent_0 (the confidence of which is often of -#' # minor interest), we get a nice performance improvement from about 50 -#' # seconds to about 12 seconds if we use at least four cores +#' # minor interest), we get a nice performance improvement if we use at least 4 cores #' system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", #' c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores)) #' ci_profile diff --git a/R/logLik.mkinfit.R b/R/logLik.mkinfit.R index 1c025893..7cc10234 100644 --- a/R/logLik.mkinfit.R +++ b/R/logLik.mkinfit.R @@ -25,10 +25,10 @@ #' parent = mkinsub("SFO", to = "m1"), #' m1 = mkinsub("SFO") #' ) -#' d_t <- FOCUS_2006_D +#' d_t <- subset(FOCUS_2006_D, value != 0) #' f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity) -#' f_obs <- mkinfit(sfo_sfo, d_t, error_model = "obs", quiet = TRUE) -#' f_tc <- mkinfit(sfo_sfo, d_t, error_model = "tc", quiet = TRUE) +#' f_obs <- update(f_nw, error_model = "obs") +#' f_tc <- update(f_nw, error_model = "tc") #' AIC(f_nw, f_obs, f_tc) #' } #' diff --git a/R/mkinfit.R b/R/mkinfit.R index d7de718b..704e70a9 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -542,6 +542,8 @@ mkinfit <- function(mkinmod, observed, { assign("calls", calls + 1, inherits = TRUE) # Increase the model solution counter + #browser() + # Trace parameter values if requested and if we are actually optimising if(trace_parms & update_data) cat(format(P, width = 10, digits = 6), "\n") diff --git a/R/mkinresplot.R b/R/mkinresplot.R index bad28ae8..be361690 100644 --- a/R/mkinresplot.R +++ b/R/mkinresplot.R @@ -28,7 +28,7 @@ utils::globalVariables(c("variable", "residual")) #' @param \dots further arguments passed to \code{\link{plot}}. #' @return Nothing is returned by this function, as it is called for its side #' effect, namely to produce a plot. -#' @author Johannes Ranke +#' @author Johannes Ranke and Katrin Lindenberger #' @seealso \code{\link{mkinplot}}, for a way to plot the data and the fitted #' lines of the mkinfit object, and \code{\link{plot_res}} for a function #' combining the plot of the fit and the residual plot. @@ -162,6 +162,7 @@ mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, #' #' @param x An [mmkin] object. #' @param \dots Not used. +#' @rdname mmkin #' @export print.mmkin <- function(x, ...) { cat("<mmkin> object\n") diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index 82d5f6de..ff1f2fff 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -24,6 +24,11 @@ get_deg_func <- function() { #' This functions sets up a nonlinear mixed effects model for an mmkin row #' object. An mmkin row object is essentially a list of mkinfit objects that #' have been obtained by fitting the same model to a list of datasets. +#' +#' Note that the convergence of the nlme algorithms depends on the quality +#' of the data. In degradation kinetics, we often only have few datasets +#' (e.g. data for few soils) and complicated degradation models, which may +#' make it impossible to obtain convergence with nlme. #' #' @param model An [mmkin] row object. #' @param data Ignored, data are taken from the mmkin model @@ -88,11 +93,10 @@ get_deg_func <- function() { #' # f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ]) #' #plot(f_nlme_sfo_sfo_ff) #' -#' # With the log-Cholesky parameterization, this converges in 11 -#' # iterations and around 100 seconds, but without tweaking control -#' # parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was -#' # necessary) -#' f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ]) +#' # For the following, we need to increase pnlsMaxIter and the tolerance +#' # to get convergence +#' f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], +#' control = list(pnlsMaxIter = 120, tolerance = 5e-4)) #' #' plot(f_nlme_dfop_sfo) #' @@ -112,22 +116,18 @@ get_deg_func <- function() { #' print(f_nlme_dfop_tc) #' } #' -#' f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo, -#' "DFOP-SFO" = m_dfop_sfo), -#' ds_2, quiet = TRUE, error_model = "obs") +#' f_2_obs <- update(f_2, error_model = "obs") #' f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) #' print(f_nlme_sfo_sfo_obs) -#' f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ]) +#' f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], +#' control = list(pnlsMaxIter = 120, tolerance = 5e-4)) #' -#' f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo, -#' "DFOP-SFO" = m_dfop_sfo), -#' ds_2, quiet = TRUE, error_model = "tc") -#' # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message -#' f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ]) -#' # We get warnings about false convergence in the LME step in several iterations -#' # but as the last such warning occurs in iteration 25 and we have 28 iterations -#' # we can ignore these -#' anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc) +#' f_2_tc <- update(f_2, error_model = "tc") +#' # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations +#' # f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ], +#' # control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm +#' +#' anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs) #' #' } nlme.mmkin <- function(model, data = "auto", diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index f21d31fc..4fe4e5c2 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -42,17 +42,21 @@ #' #' SFO_SFO <- mkinmod( #' parent = list(type = "SFO", to = "m1", sink = TRUE), -#' m1 = list(type = "SFO")) +#' m1 = list(type = "SFO"), use_of_ff = "min") +#' #' # Fit the model to the FOCUS example dataset D using defaults -#' fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +#' FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning +#' fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) #' fit.s <- summary(fit) #' # Transformed and backtransformed parameters #' print(fit.s$par, 3) #' print(fit.s$bpar, 3) #' #' \dontrun{ -#' # Compare to the version without transforming rate parameters -#' fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +#' # Compare to the version without transforming rate parameters (does not work +#' # with analytical solution, we get NA values for m1 in predictions) +#' fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE, +#' solution_type = "deSolve", quiet = TRUE) #' fit.2.s <- summary(fit.2) #' print(fit.2.s$par, 3) #' print(fit.2.s$bpar, 3) @@ -66,13 +70,13 @@ #' backtransform_odeparms(transformed, SFO_SFO) #' #' \dontrun{ -#' # The case of formation fractions +#' # The case of formation fractions (this is now the default) #' SFO_SFO.ff <- mkinmod( #' parent = list(type = "SFO", to = "m1", sink = TRUE), #' m1 = list(type = "SFO"), #' use_of_ff = "max") #' -#' fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) +#' fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) #' fit.ff.s <- summary(fit.ff) #' print(fit.ff.s$par, 3) #' print(fit.ff.s$bpar, 3) @@ -87,7 +91,7 @@ #' use_of_ff = "max") #' #' -#' fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) +#' fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE) #' fit.ff.2.s <- summary(fit.ff.2) #' print(fit.ff.2.s$par, 3) #' print(fit.ff.2.s$bpar, 3) @@ -100,6 +100,8 @@ version is found in the ['dev' subdirectory](https://pkgdown.jrwb.de/mkin/dev/). * Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the [nlme.mmkin](https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html) method. + Note that the convergence of the nlme fits depends on the quality of the data. + Convergence is better for simple models and data for many groups (e.g. soils). ## GUI diff --git a/_pkgdown.yml b/_pkgdown.yml index 7d66f5b0..f632ddb0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -35,7 +35,6 @@ reference: - "`[.mmkin`" - plot.mmkin - AIC.mmkin - - print.mmkin - title: Mixed models desc: Create and work with nonlinear mixed effects models contents: @@ -6,5 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.0.tar.gz’ +* building ‘mkin_1.0.1.tar.gz’ @@ -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 ‘1.0.0’ +* this is package ‘mkin’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ diff --git a/docs/404.html b/docs/404.html index 42423c5d..45a45f3e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> diff --git a/docs/articles/index.html b/docs/articles/index.html index 369b506c..66393487 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> diff --git a/docs/authors.html b/docs/authors.html index f5c6160c..0f68e2ce 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index c7b2e277..bcdaa7e4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> @@ -146,7 +146,7 @@ <li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function.</li> <li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li> <li>A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li> -<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method.</li> +<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).</li> </ul> </div> <div id="gui" class="section level2"> diff --git a/docs/news/index.html b/docs/news/index.html index 88c7c49c..7a307709 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> @@ -141,9 +141,19 @@ <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small> </div> + <div id="mkin-1-0-1" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.1"> +<a href="#mkin-1-0-1" class="anchor"></a>mkin 1.0.1<small> Unreleased </small> +</h1> +<ul> +<li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> +<li><p>‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax</p></li> +<li><p>‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago</p></li> +</ul> +</div> <div id="mkin-1-0-0" class="section level1"> <h1 class="page-header" data-toc-text="1.0.0"> -<a href="#mkin-1-0-0" class="anchor"></a>mkin 1.0.0<small> Unreleased </small> +<a href="#mkin-1-0-0" class="anchor"></a>mkin 1.0.0<small> 2021-02-03 </small> </h1> <div id="general" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 6c5f8bc3..d05f3168 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-03T16:42Z +last_built: 2021-02-04T10:34Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 7f498242..17a35806 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 54c31a3f..bb624e64 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 19198739..e96adeb3 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 ead98fba..91058d4b 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 949a9283..91058d4b 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 da52f580..74f43dfa 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 4f7e8872..b71e039a 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -273,68 +273,69 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>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 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'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span> <span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> + <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> <span class='op'>}</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>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 class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>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 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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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>, + 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 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>, 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='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'>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 class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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'>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> </div><div class='output co'>#> user system elapsed -#> 3.796 1.056 3.506 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +#> 4.324 0.980 3.960 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> -<span class='co'># minor interest), we get a nice performance improvement from about 50</span> -<span class='co'># seconds to about 12 seconds if we use at least four cores</span> +<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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'>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 class='fu'><a href='https://rdrr.io/r/base/c.html'>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> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#> <span class='error'>Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0.043 0.246</span></div><div class='input'><span class='va'>ci_profile</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892606 6.702775e-03 -#> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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> +</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed +#> 1.480 0.109 0.905 </div><div class='input'><span class='va'>ci_profile</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.456003640 1.027703e+02 +#> k_parent_sink 0.040762501 5.549764e-02 +#> k_parent_m1 0.046786482 5.500879e-02 +#> k_m1_sink 0.003892605 6.702778e-03 +#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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 class='va'>ci_quadratic_transformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 -#> k_parent 0.090823771 0.10725430 -#> k_m1 0.004012219 0.00689755 -#> f_parent_to_m1 0.469118824 0.55959615 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403841640 1.027931e+02 +#> k_parent_sink 0.041033378 5.596269e-02 +#> k_parent_m1 0.046777902 5.511931e-02 +#> k_m1_sink 0.004012217 6.897547e-03 +#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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 class='va'>ci_quadratic_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 -#> k_parent 0.090491913 1.069035e-01 -#> k_m1 0.003835485 6.685823e-03 -#> f_parent_to_m1 0.469113477 5.598387e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403841645 102.79312449 +#> k_parent_sink 0.040485331 0.05535491 +#> k_parent_m1 0.046611582 0.05494364 +#> k_m1_sink 0.003835483 0.00668582 +#> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> <span class='co'># intervals based on the internal parameter transformation are less</span> <span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> <span class='co'># interval based on the untransformed fit for k_m1_sink</span> <span class='va'>rel_diffs_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>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 class='va'>rel_diffs_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>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 class='va'>rel_diffs_transformed</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent TRUE TRUE -#> k_m1 FALSE FALSE -#> f_parent_to_m1 TRUE FALSE -#> sigma TRUE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent 0.000960 0.000900 -#> k_m1 0.030700 0.029100 -#> f_parent_to_m1 0.004690 0.002780 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent 0.004610 0.002370 -#> k_m1 0.014700 0.002530 -#> f_parent_to_m1 0.004700 0.002350 -#> sigma 0.055000 0.032700</div><div class='input'> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 FALSE FALSE +#> k_parent_sink TRUE FALSE +#> k_parent_m1 TRUE FALSE +#> k_m1_sink FALSE FALSE +#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent_sink 0.006650 0.008380 +#> k_parent_m1 0.000183 0.002010 +#> k_m1_sink 0.030700 0.029100 +#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent_sink 0.006800 0.002570 +#> k_parent_m1 0.003740 0.001180 +#> k_m1_sink 0.014700 0.002530 +#> sigma 0.055000 0.032700</div><div class='input'> <span class='co'># Investigate a case with formation fractions</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'>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> diff --git a/docs/reference/index.html b/docs/reference/index.html index c9f66992..0859a152 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> @@ -175,7 +175,7 @@ </tr><tr> <td> - <p><code><a href="mmkin.html">mmkin()</a></code> </p> + <p><code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> </p> </td> <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> @@ -297,12 +297,6 @@ of an mmkin object</p></td> <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> </td> <td><p>Calculate the AIC for a column of an mmkin object</p></td> - </tr><tr> - - <td> - <p><code><a href="print.mmkin.html">print(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Print method for mmkin objects</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index ac3f570c..8d984e55 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -196,11 +196,11 @@ and the fitted error model parameters.</p> 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>, 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> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='va'>FOCUS_2006_D</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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='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> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_obs</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>, error_model <span class='op'>=</span> <span class='st'>"obs"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_tc</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>, 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> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>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 class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>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 class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>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 class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>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> </div><div class='output co'>#> df AIC #> f_nw 5 204.4486 #> f_obs 6 205.8727 diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index a9638c93..69517f36 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -242,7 +242,7 @@ lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a>< combining the plot of the fit and the residual plot.</p></div> <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> + <p>Johannes Ranke and Katrin Lindenberger</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 20134030..77f815da 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -158,7 +158,10 @@ datasets specified in its first two arguments.</p> 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'>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></pre> +<span class='op'>)</span> + +<span class='co'># S3 method for mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -189,7 +192,11 @@ for parallel execution.</p></td> </tr> <tr> <th>...</th> - <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + <td><p>Not used.</p></td> + </tr> + <tr> + <th>x</th> + <td><p>An mmkin object.</p></td> </tr> </table> @@ -227,9 +234,9 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.869 0.357 1.415 </div><div class='input'><span class='va'>time_1</span> +#> 4.634 0.317 1.280 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.502 0.002 5.507 </div><div class='input'> +#> 5.249 0.016 5.267 </div><div class='input'> <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> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 0b7ce0f6..7c04df4b 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index dd1670fe..2e4f6337 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.</p> 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'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='nlme_function.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'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>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'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, + random <span class='op'>=</span> <span class='fu'>pdDiag</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='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, correlation <span class='op'>=</span> <span class='cn'>NULL</span>, @@ -262,6 +262,12 @@ parameters taken from the mmkin object are used</p></td> <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>Note that the convergence of the nlme algorithms depends on the quality +of the data. In degradation kinetics, we often only have few datasets +(e.g. data for few soils) and complicated degradation models, which may +make it impossible to obtain convergence with nlme.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of @@ -335,16 +341,17 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='co'># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span> <span class='co'>#plot(f_nlme_sfo_sfo_ff)</span> - <span class='co'># With the log-Cholesky parameterization, this converges in 11</span> - <span class='co'># iterations and around 100 seconds, but without tweaking control</span> - <span class='co'># parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was</span> - <span class='co'># necessary)</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'>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 class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.8101519326534, log_k_A1 = -9.76474551635931, f_parent_qlogis = -0.971114801595408, log_k1 = -1.87993711571859, log_k2 = -4.27081421366622, g_qlogis = 0.135644115277507 ), random = list(ds = structure(c(2.56569977430371, -3.49441920289139, -3.32614443321494, 4.35347873814922, -0.0986148763466161, 4.65850590018027, 1.8618544764481, 6.12693257601545, 4.91792724701579, -17.5652201996596, -0.466203822618637, 0.746660653597927, 0.282193987271096, -0.42053488943072, -0.142115928819667, 0.369240076779088, -1.38985563501659, 1.02592753494098, 0.73090914081534, -0.736221117518819, 0.768170629350299, -1.89347658079869, 1.72168783460352, 0.844607177798114, -1.44098906095325, -0.377731855445672, 0.168180098477565, 0.469683412912104, 0.500717664434525, -0.760849320378522), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 48.39 16.98 43</span></div><div class='input'> + <span class='co'># For the following, we need to increase pnlsMaxIter and the tolerance</span> + <span class='co'># to get convergence</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'>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>, + control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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 class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in plot(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>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> -</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> <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> </div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink @@ -355,7 +362,15 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> parent 19.13518 63.5657 #> A1 66.02155 219.3189 #> </div><div class='input'> <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> -</div><div class='output co'>#> <span class='error'>Error in endpoints(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='output co'>#> $ff +#> parent_A1 parent_sink +#> 0.2768574 0.7231426 +#> +#> $distimes +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 +#> A1 162.30523 539.1663 NA NA NA +#> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>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 class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> <span class='co'># but need tweeking of control values and sometimes do not converge</span> @@ -396,9 +411,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Parameter estimates: #> const prop #> 2.23224114 0.01262341 </div><div class='input'> - <span class='va'>f_2_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'>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='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, - <span class='va'>ds_2</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 class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>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 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'>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 class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood @@ -429,18 +442,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003 </div><div class='input'> <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'>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 class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.4272167134207, log_k_A1 = -9.71590717106959, f_parent_qlogis = -0.953712099744438, log_k1 = -1.95256957646888, log_k2 = -4.42919226610318, g_qlogis = 0.193023137298073 ), random = list(ds = structure(c(2.85557330683041, -3.87630303729395, -2.78062140212751, 4.82042042600536, -1.01906929341432, 4.613992019697, 2.05871276943309, 6.0766404049189, 4.86471337131288, -17.6140585653619, -0.480721175257541, 0.773079218835614, 0.260464433006093, -0.440615012802434, -0.112207463781733, 0.445812953745225, -1.49588630006094, 1.13602040717272, 0.801850880762046, -0.887797941619048, 0.936480292463262, -2.43093808171905, 1.91256225793793, 0.984827519864443, -1.40293198854659, -0.455176326336681, 0.376355651864385, 0.343919720700401, 0.46329187713133, -0.728390923359434 ), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL)), weights = structure(numeric(0), formula = ~1 | name, class = c("varIdent", "varFunc"))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 58.24 16.62 52.48</span></div><div class='input'> - <span class='va'>f_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'>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='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, - <span class='va'>ds_2</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 class='co'># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message</span> - <span class='va'>f_nlme_dfop_sfo_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='error'>Error in X[, fmap[[nm]]] <- gradnm: number of items to replace is not a multiple of replacement length</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 6.327 2.686 5.428</span></div><div class='input'> <span class='co'># We get warnings about false convergence in the LME step in several iterations</span> - <span class='co'># but as the last such warning occurs in iteration 25 and we have 28 iterations</span> - <span class='co'># we can ignore these</span> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>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='va'>f_nlme_dfop_sfo_tc</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +#> 1.0000000 0.2050003 </div><div class='input'> <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'>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>, + control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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 class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>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 class='co'># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span> + <span class='co'># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span> + <span class='co'># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span> + + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>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> +</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32089 +#> p-value +#> f_nlme_dfop_sfo +#> f_nlme_dfop_sfo_obs <.0001</div><div class='input'> <span class='co'># }</span> </div></pre> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index efaf7b46..e2cb876b 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> </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">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> </span> </div> @@ -231,50 +231,64 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ <pre class="examples"><div class='input'> <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'>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>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</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> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> +<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='va'>FOCUS_D</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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 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 class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> <span class='co'># Transformed and backtransformed parameters</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>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> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.60 1.5702 96.40 102.79 +#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 +#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 +#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 +#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> <span class='co'># \dontrun{</span> -<span class='co'># Compare to the version without transforming rate parameters</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_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.003 0 0.003</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$par, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> +<span class='co'># Compare to the version without transforming rate parameters (does not work</span> +<span class='co'># with analytical solution, we get NA values for m1 in predictions)</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>, + 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 class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.59849 1.57022 96.40385 1.03e+02 +#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59849 1.57022 63.43 2.30e-36 96.40385 1.03e+02 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</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 class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> <span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> <span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent log_k_m1 f_parent_qlogis -#> 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><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> -</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 -#> 100.7500 0.1000 0.1001 0.5000 </div><div class='input'> +</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><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> +</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> <span class='co'># \dontrun{</span> -<span class='co'># The case of formation fractions</span> +<span class='co'># The case of formation fractions (this is now the default)</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='https://rdrr.io/r/base/list.html'>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>, m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<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_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</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 class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper #> parent_0 99.5985 1.5702 96.404 102.79 @@ -299,8 +313,8 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> +<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 7e3d8a53..601a4464 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -175,9 +175,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc> </url> <url> diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd index fd2890ff..b19e78c2 100644 --- a/man/confint.mkinfit.Rd +++ b/man/confint.mkinfit.Rd @@ -82,20 +82,20 @@ confint(f, method = "profile") if (identical(Sys.getenv("NOT_CRAN"), "true")) { n_cores <- parallel::detectCores() - 1 } else { - n_cores <- 1 + n_cores <- 1 } if (Sys.getenv("TRAVIS") != "") n_cores = 1 if (Sys.info()["sysname"] == "Windows") n_cores = 1 -SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), quiet = TRUE) +SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), + use_of_ff = "min", quiet = TRUE) SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE) f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE)) # Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of -# minor interest), we get a nice performance improvement from about 50 -# seconds to about 12 seconds if we use at least four cores +# minor interest), we get a nice performance improvement if we use at least 4 cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores)) ci_profile diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index 637570e4..6b40305e 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -35,10 +35,10 @@ and the fitted error model parameters. parent = mkinsub("SFO", to = "m1"), m1 = mkinsub("SFO") ) - d_t <- FOCUS_2006_D + d_t <- subset(FOCUS_2006_D, value != 0) f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity) - f_obs <- mkinfit(sfo_sfo, d_t, error_model = "obs", quiet = TRUE) - f_tc <- mkinfit(sfo_sfo, d_t, error_model = "tc", quiet = TRUE) + f_obs <- update(f_nw, error_model = "obs") + f_tc <- update(f_nw, error_model = "tc") AIC(f_nw, f_obs, f_tc) } diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index 498d914d..9658ddb5 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -75,5 +75,5 @@ lines of the mkinfit object, and \code{\link{plot_res}} for a function combining the plot of the fit and the residual plot. } \author{ -Johannes Ranke +Johannes Ranke and Katrin Lindenberger } diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 9b836242..170ce8df 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/mmkin.R \name{mmkin} \alias{mmkin} +\alias{print.mmkin} \title{Fit one or more kinetic models with one or more state variables to one or more datasets} \usage{ @@ -12,6 +13,8 @@ mmkin( cluster = NULL, ... ) + +\method{print}{mmkin}(x, ...) } \arguments{ \item{models}{Either a character vector of shorthand names like @@ -30,7 +33,9 @@ detected by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used \item{cluster}{A cluster as returned by \code{\link{makeCluster}} to be used for parallel execution.} -\item{\dots}{Further arguments that will be passed to \code{\link{mkinfit}}.} +\item{\dots}{Not used.} + +\item{x}{An \link{mmkin} object.} } \value{ A two-dimensional \code{\link{array}} of \code{\link{mkinfit}} diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index f78256ac..2fb0488a 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -79,6 +79,12 @@ This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets. } +\details{ +Note that the convergence of the nlme algorithms depends on the quality +of the data. In degradation kinetics, we often only have few datasets +(e.g. data for few soils) and complicated degradation models, which may +make it impossible to obtain convergence with nlme. +} \note{ As the object inherits from \link[nlme:nlme]{nlme::nlme}, there is a wealth of methods that will automatically work on 'nlme.mmkin' objects, such as @@ -120,11 +126,10 @@ f_nlme_sfo <- nlme(f["SFO", ]) # f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ]) #plot(f_nlme_sfo_sfo_ff) - # With the log-Cholesky parameterization, this converges in 11 - # iterations and around 100 seconds, but without tweaking control - # parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was - # necessary) - f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ]) + # For the following, we need to increase pnlsMaxIter and the tolerance + # to get convergence + f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], + control = list(pnlsMaxIter = 120, tolerance = 5e-4)) plot(f_nlme_dfop_sfo) @@ -144,22 +149,18 @@ f_nlme_sfo <- nlme(f["SFO", ]) print(f_nlme_dfop_tc) } - f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo, - "DFOP-SFO" = m_dfop_sfo), - ds_2, quiet = TRUE, error_model = "obs") + f_2_obs <- update(f_2, error_model = "obs") f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) print(f_nlme_sfo_sfo_obs) - f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ]) + f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], + control = list(pnlsMaxIter = 120, tolerance = 5e-4)) - f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo, - "DFOP-SFO" = m_dfop_sfo), - ds_2, quiet = TRUE, error_model = "tc") - # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message - f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ]) - # We get warnings about false convergence in the LME step in several iterations - # but as the last such warning occurs in iteration 25 and we have 28 iterations - # we can ignore these - anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc) + f_2_tc <- update(f_2, error_model = "tc") + # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations + # f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ], + # control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm + + anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs) } } diff --git a/man/print.mmkin.Rd b/man/print.mmkin.Rd deleted file mode 100644 index 29abe143..00000000 --- a/man/print.mmkin.Rd +++ /dev/null @@ -1,16 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mmkin.R -\name{print.mmkin} -\alias{print.mmkin} -\title{Print method for mmkin objects} -\usage{ -\method{print}{mmkin}(x, ...) -} -\arguments{ -\item{x}{An \link{mmkin} object.} - -\item{\dots}{Not used.} -} -\description{ -Print method for mmkin objects -} diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index f38bb051..3a97ff8d 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -69,17 +69,21 @@ This is no problem for the internal use in \link{mkinfit}. SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) + m1 = list(type = "SFO"), use_of_ff = "min") + # Fit the model to the FOCUS example dataset D using defaults -fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning +fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) fit.s <- summary(fit) # Transformed and backtransformed parameters print(fit.s$par, 3) print(fit.s$bpar, 3) \dontrun{ -# Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +# Compare to the version without transforming rate parameters (does not work +# with analytical solution, we get NA values for m1 in predictions) +fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE, + solution_type = "deSolve", quiet = TRUE) fit.2.s <- summary(fit.2) print(fit.2.s$par, 3) print(fit.2.s$bpar, 3) @@ -93,13 +97,13 @@ transform_odeparms(initials, SFO_SFO) backtransform_odeparms(transformed, SFO_SFO) \dontrun{ -# The case of formation fractions +# The case of formation fractions (this is now the default) SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), use_of_ff = "max") -fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) +fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) fit.ff.s <- summary(fit.ff) print(fit.ff.s$par, 3) print(fit.ff.s$bpar, 3) @@ -114,7 +118,7 @@ SFO_SFO.ff.2 <- mkinmod( use_of_ff = "max") -fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) +fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE) fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3) print(fit.ff.2.s$bpar, 3) @@ -21,7 +21,7 @@ Testing mkin ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] -✔ | 9 | Nonlinear mixed-effects models [7.7 s] +✔ | 9 | Nonlinear mixed-effects models [7.8 s] ✔ | 14 | Plotting [1.7 s] ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] @@ -32,6 +32,6 @@ Testing mkin ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 40.4 s +Duration: 40.6 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 176 ] |
