diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/endpoints.Rd | 4 | ||||
| -rw-r--r-- | man/intervals.nlmixr.mmkin.Rd | 25 | ||||
| -rw-r--r-- | man/nlmixr.mmkin.Rd | 245 | ||||
| -rw-r--r-- | man/reexports.Rd | 6 | ||||
| -rw-r--r-- | man/summary.nlmixr.mmkin.Rd | 103 | ||||
| -rw-r--r-- | man/tffm0.Rd | 46 |
6 files changed, 3 insertions, 426 deletions
diff --git a/man/endpoints.Rd b/man/endpoints.Rd index a37ff98d..75fa9503 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -8,8 +8,8 @@ with mkinfit} endpoints(fit) } \arguments{ -\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin}, \link{saem.mmkin} or -\link{nlmixr.mmkin}. Or another object that has list components +\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or \link{saem.mmkin}, +or another object that has list components mkinmod containing an \link{mkinmod} degradation model, and two numeric vectors, bparms.optim and bparms.fixed, that contain parameter values for that model.} diff --git a/man/intervals.nlmixr.mmkin.Rd b/man/intervals.nlmixr.mmkin.Rd deleted file mode 100644 index e6da8901..00000000 --- a/man/intervals.nlmixr.mmkin.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/intervals.R -\name{intervals.nlmixr.mmkin} -\alias{intervals.nlmixr.mmkin} -\title{Confidence intervals for parameters in nlmixr.mmkin objects} -\usage{ -\method{intervals}{nlmixr.mmkin}(object, level = 0.95, backtransform = TRUE, ...) -} -\arguments{ -\item{object}{The fitted saem.mmkin object} - -\item{level}{The confidence level.} - -\item{backtransform}{Should we backtransform the parameters where a one to -one correlation between transformed and backtransformed parameters exists?} - -\item{\dots}{For compatibility with the generic method} -} -\value{ -An object with 'intervals.saem.mmkin' and 'intervals.lme' in the -class attribute -} -\description{ -Confidence intervals for parameters in nlmixr.mmkin objects -} diff --git a/man/nlmixr.mmkin.Rd b/man/nlmixr.mmkin.Rd deleted file mode 100644 index c1a203eb..00000000 --- a/man/nlmixr.mmkin.Rd +++ /dev/null @@ -1,245 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/nlmixr.R -\name{nlmixr.mmkin} -\alias{nlmixr.mmkin} -\alias{print.nlmixr.mmkin} -\alias{nlmixr_model} -\alias{nlmixr_data} -\title{Fit nonlinear mixed models using nlmixr} -\usage{ -\method{nlmixr}{mmkin}( - object, - data = NULL, - est = NULL, - control = list(), - table = tableControl(), - error_model = object[[1]]$err_mod, - test_log_parms = TRUE, - conf.level = 0.6, - degparms_start = "auto", - eta_start = "auto", - ..., - save = NULL, - envir = parent.frame() -) - -\method{print}{nlmixr.mmkin}(x, digits = max(3, getOption("digits") - 3), ...) - -nlmixr_model( - object, - est = c("saem", "focei"), - degparms_start = "auto", - eta_start = "auto", - test_log_parms = TRUE, - conf.level = 0.6, - error_model = object[[1]]$err_mod, - add_attributes = FALSE -) - -nlmixr_data(object, ...) -} -\arguments{ -\item{object}{An \link{mmkin} row object containing several fits of the same -\link{mkinmod} model to different datasets} - -\item{data}{Not used, as the data are extracted from the mmkin row object} - -\item{est}{Estimation method passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}} - -\item{control}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}} - -\item{table}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}} - -\item{error_model}{Optional argument to override the error model which is -being set based on the error model used in the mmkin row object.} - -\item{test_log_parms}{If TRUE, an attempt is made to use more robust starting -values for population parameters fitted as log parameters in mkin (like -rate constants) by only considering rate constants that pass the t-test -when calculating mean degradation parameters using \link{mean_degparms}.} - -\item{conf.level}{Possibility to adjust the required confidence level -for parameter that are tested if requested by 'test_log_parms'.} - -\item{degparms_start}{Parameter values given as a named numeric vector will -be used to override the starting values obtained from the 'mmkin' object.} - -\item{eta_start}{Standard deviations on the transformed scale given as a -named numeric vector will be used to override the starting values obtained -from the 'mmkin' object.} - -\item{\dots}{Passed to \link{nlmixr_model}} - -\item{save}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}} - -\item{envir}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}} - -\item{x}{An nlmixr.mmkin object to print} - -\item{digits}{Number of digits to use for printing} - -\item{add_attributes}{Should the starting values used for degradation model -parameters and their distribution and for the error model parameters -be returned as attributes?} -} -\value{ -An S3 object of class 'nlmixr.mmkin', containing the fitted -\link[nlmixr:nlmixr]{nlmixr::nlmixr} object as a list component named 'nm'. The -object also inherits from 'mixed.mmkin'. - -An function defining a model suitable for fitting with \link[nlmixr:nlmixr]{nlmixr::nlmixr}. - -An dataframe suitable for use with \link[nlmixr:nlmixr]{nlmixr::nlmixr} -} -\description{ -This function uses \code{\link[nlmixr:nlmixr]{nlmixr::nlmixr()}} as a backend for fitting nonlinear mixed -effects models created from \link{mmkin} row objects using the Stochastic Approximation -Expectation Maximisation algorithm (SAEM) or First Order Conditional -Estimation with Interaction (FOCEI). -} -\details{ -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 using \link{mkinfit}. -} -\examples{ -\dontrun{ -ds <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")])) -names(ds) <- paste("Dataset", 6:10) - -f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1) -f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc", - cores = 1, quiet = TRUE) - -library(nlmixr) -f_nlmixr_sfo_saem <- nlmixr(f_mmkin_parent["SFO", ], est = "saem", - control = saemControl(print = 0)) -f_nlmixr_sfo_focei <- nlmixr(f_mmkin_parent["SFO", ], est = "focei", - control = foceiControl(print = 0)) - -f_nlmixr_fomc_saem <- nlmixr(f_mmkin_parent["FOMC", ], est = "saem", - control = saemControl(print = 0)) -f_nlmixr_fomc_focei <- nlmixr(f_mmkin_parent["FOMC", ], est = "focei", - control = foceiControl(print = 0)) - -f_nlmixr_dfop_saem <- nlmixr(f_mmkin_parent["DFOP", ], est = "saem", - control = saemControl(print = 0)) -f_nlmixr_dfop_focei <- nlmixr(f_mmkin_parent["DFOP", ], est = "focei", - control = foceiControl(print = 0)) - -f_nlmixr_hs_saem <- nlmixr(f_mmkin_parent["HS", ], est = "saem", - control = saemControl(print = 0)) -f_nlmixr_hs_focei <- nlmixr(f_mmkin_parent["HS", ], est = "focei", - control = foceiControl(print = 0)) - -f_nlmixr_fomc_saem_tc <- nlmixr(f_mmkin_parent_tc["FOMC", ], est = "saem", - control = saemControl(print = 0)) -f_nlmixr_fomc_focei_tc <- nlmixr(f_mmkin_parent_tc["FOMC", ], est = "focei", - control = foceiControl(print = 0)) - -AIC( - f_nlmixr_sfo_saem$nm, f_nlmixr_sfo_focei$nm, - f_nlmixr_fomc_saem$nm, f_nlmixr_fomc_focei$nm, - f_nlmixr_dfop_saem$nm, f_nlmixr_dfop_focei$nm, - f_nlmixr_hs_saem$nm, f_nlmixr_hs_focei$nm, - f_nlmixr_fomc_saem_tc$nm, f_nlmixr_fomc_focei_tc$nm) - -AIC(nlme(f_mmkin_parent["FOMC", ])) -AIC(nlme(f_mmkin_parent["HS", ])) - -# The FOCEI fit of FOMC with constant variance or the tc error model is best -plot(f_nlmixr_fomc_saem_tc) - -sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), - A1 = mkinsub("SFO"), quiet = TRUE) -fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), - A1 = mkinsub("SFO"), quiet = TRUE) -dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), - A1 = mkinsub("SFO"), quiet = TRUE) - -f_mmkin_const <- mmkin(list( - "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), - ds, quiet = TRUE, error_model = "const") -f_mmkin_obs <- mmkin(list( - "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), - ds, quiet = TRUE, error_model = "obs") -f_mmkin_tc <- mmkin(list( - "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), - ds, quiet = TRUE, error_model = "tc") - -nlmixr_model(f_mmkin_const["SFO-SFO", ]) - -# A single constant variance is currently only possible with est = 'focei' in nlmixr -f_nlmixr_sfo_sfo_focei_const <- nlmixr(f_mmkin_const["SFO-SFO", ], est = "focei") -f_nlmixr_fomc_sfo_focei_const <- nlmixr(f_mmkin_const["FOMC-SFO", ], est = "focei") -f_nlmixr_dfop_sfo_focei_const <- nlmixr(f_mmkin_const["DFOP-SFO", ], est = "focei") - -# Variance by variable is supported by 'saem' and 'focei' -f_nlmixr_fomc_sfo_saem_obs <- nlmixr(f_mmkin_obs["FOMC-SFO", ], est = "saem") -f_nlmixr_fomc_sfo_focei_obs <- nlmixr(f_mmkin_obs["FOMC-SFO", ], est = "focei") -f_nlmixr_dfop_sfo_saem_obs <- nlmixr(f_mmkin_obs["DFOP-SFO", ], est = "saem") -f_nlmixr_dfop_sfo_focei_obs <- nlmixr(f_mmkin_obs["DFOP-SFO", ], est = "focei") - -# Identical two-component error for all variables is only possible with -# est = 'focei' in nlmixr -f_nlmixr_fomc_sfo_focei_tc <- nlmixr(f_mmkin_tc["FOMC-SFO", ], est = "focei") -f_nlmixr_dfop_sfo_focei_tc <- nlmixr(f_mmkin_tc["DFOP-SFO", ], est = "focei") - -# Two-component error by variable is possible with both estimation methods -# Variance by variable is supported by 'saem' and 'focei' -f_nlmixr_fomc_sfo_saem_obs_tc <- nlmixr(f_mmkin_tc["FOMC-SFO", ], est = "saem", - error_model = "obs_tc") -f_nlmixr_fomc_sfo_focei_obs_tc <- nlmixr(f_mmkin_tc["FOMC-SFO", ], est = "focei", - error_model = "obs_tc") -f_nlmixr_dfop_sfo_saem_obs_tc <- nlmixr(f_mmkin_tc["DFOP-SFO", ], est = "saem", - error_model = "obs_tc") -f_nlmixr_dfop_sfo_focei_obs_tc <- nlmixr(f_mmkin_tc["DFOP-SFO", ], est = "focei", - error_model = "obs_tc") - -AIC( - f_nlmixr_sfo_sfo_focei_const$nm, - f_nlmixr_fomc_sfo_focei_const$nm, - f_nlmixr_dfop_sfo_focei_const$nm, - f_nlmixr_fomc_sfo_saem_obs$nm, - f_nlmixr_fomc_sfo_focei_obs$nm, - f_nlmixr_dfop_sfo_saem_obs$nm, - f_nlmixr_dfop_sfo_focei_obs$nm, - f_nlmixr_fomc_sfo_focei_tc$nm, - f_nlmixr_dfop_sfo_focei_tc$nm, - f_nlmixr_fomc_sfo_saem_obs_tc$nm, - f_nlmixr_fomc_sfo_focei_obs_tc$nm, - f_nlmixr_dfop_sfo_saem_obs_tc$nm, - f_nlmixr_dfop_sfo_focei_obs_tc$nm -) -# Currently, FOMC-SFO with two-component error by variable fitted by focei gives the -# lowest AIC -plot(f_nlmixr_fomc_sfo_focei_obs_tc) -summary(f_nlmixr_fomc_sfo_focei_obs_tc) - -# Two parallel metabolites -dmta_ds <- lapply(1:7, function(i) { - ds_i <- dimethenamid_2018$ds[[i]]$data - ds_i[ds_i$name == "DMTAP", "name"] <- "DMTA" - ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] - ds_i -}) -names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) -dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]]) -dmta_ds[["Elliot 1"]] <- NULL -dmta_ds[["Elliot 2"]] <- NULL -sfo_sfo2 <- mkinmod( - DMTA = mkinsub("SFO", c("M23", "M27")), - M23 = mkinsub("SFO"), - M27 = mkinsub("SFO"), - quiet = TRUE -) -f_dmta_sfo_sfo2 <- mmkin( - list("SFO-SFO2" = sfo_sfo2), - dmta_ds, quiet = TRUE, error_model = "obs") -nlmixr_model(f_dmta_sfo_sfo2) -nlmixr_focei_dmta_sfo_sfo2 <- nlmixr(f_dmta_sfo_sfo2, est = "focei") -} -} -\seealso{ -\link{summary.nlmixr.mmkin} \link{plot.mixed.mmkin} -} diff --git a/man/reexports.Rd b/man/reexports.Rd index dfbb76a7..43d27ac1 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -1,13 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R, -% R/nlme.mmkin.R, R/nlmixr.R +% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R, R/nlme.mmkin.R \docType{import} \name{reexports} \alias{reexports} \alias{intervals} \alias{lrtest} \alias{nlme} -\alias{nlmixr} \title{Objects exported from other packages} \keyword{internal} \description{ @@ -18,7 +16,5 @@ below to see their documentation. \item{lmtest}{\code{\link[lmtest]{lrtest}}} \item{nlme}{\code{\link[nlme]{intervals}}, \code{\link[nlme]{nlme}}} - - \item{nlmixr}{\code{\link[nlmixr]{nlmixr}}} }} diff --git a/man/summary.nlmixr.mmkin.Rd b/man/summary.nlmixr.mmkin.Rd deleted file mode 100644 index ab8abd5d..00000000 --- a/man/summary.nlmixr.mmkin.Rd +++ /dev/null @@ -1,103 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/summary.nlmixr.mmkin.R -\name{summary.nlmixr.mmkin} -\alias{summary.nlmixr.mmkin} -\alias{print.summary.nlmixr.mmkin} -\title{Summary method for class "nlmixr.mmkin"} -\usage{ -\method{summary}{nlmixr.mmkin}(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) - -\method{print}{summary.nlmixr.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) -} -\arguments{ -\item{object}{an object of class \link{nlmixr.mmkin}} - -\item{data}{logical, indicating whether the full data should be included in -the summary.} - -\item{verbose}{Should the summary be verbose?} - -\item{distimes}{logical, indicating whether DT50 and DT90 values should be -included.} - -\item{\dots}{optional arguments passed to methods like \code{print}.} - -\item{x}{an object of class \link{summary.nlmixr.mmkin}} - -\item{digits}{Number of digits to use for printing} -} -\value{ -The summary function returns a list obtained in the fit, with at -least the following additional components -\item{nlmixrversion, mkinversion, Rversion}{The nlmixr, mkin and R versions used} -\item{date.fit, date.summary}{The dates where the fit and the summary were -produced} -\item{diffs}{The differential equations used in the degradation model} -\item{use_of_ff}{Was maximum or minimum use made of formation fractions} -\item{data}{The data} -\item{confint_back}{Backtransformed parameters, with confidence intervals if available} -\item{ff}{The estimated formation fractions derived from the fitted -model.} -\item{distimes}{The DT50 and DT90 values for each observed variable.} -\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} -The print method is called for its side effect, i.e. printing the summary. -} -\description{ -Lists model equations, initial parameter values, optimised parameters -for fixed effects (population), random effects (deviations from the -population mean) and residual error model, as well as the resulting -endpoints such as formation fractions and DT50 values. Optionally -(default is FALSE), the data are listed in full. -} -\examples{ -# Generate five datasets following DFOP-SFO kinetics -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"), - m1 = mkinsub("SFO"), quiet = TRUE) -set.seed(1234) -k1_in <- rlnorm(5, log(0.1), 0.3) -k2_in <- rlnorm(5, log(0.02), 0.3) -g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) -f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) -k_m1_in <- rlnorm(5, log(0.02), 0.3) - -pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { - mkinpredict(dfop_sfo, - c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), - c(parent = 100, m1 = 0), - sampling_times) -} - -ds_mean_dfop_sfo <- lapply(1:5, function(i) { - mkinpredict(dfop_sfo, - c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], - f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), - c(parent = 100, m1 = 0), - sampling_times) -}) -names(ds_mean_dfop_sfo) <- paste("ds", 1:5) - -ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { - add_err(ds, - sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), - n = 1)[[1]] -}) - -\dontrun{ -# Evaluate using mmkin and nlmixr -f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, - quiet = TRUE, error_model = "tc", cores = 5) -f_saemix_dfop_sfo <- mkin::saem(f_mmkin_dfop_sfo) -f_nlme_dfop_sfo <- mkin::nlme(f_mmkin_dfop_sfo) -f_nlmixr_dfop_sfo_saem <- nlmixr(f_mmkin_dfop_sfo, est = "saem") -# The following takes a very long time but gives -f_nlmixr_dfop_sfo_focei <- nlmixr(f_mmkin_dfop_sfo, est = "focei") -AIC(f_nlmixr_dfop_sfo_saem$nm, f_nlmixr_dfop_sfo_focei$nm) -summary(f_nlmixr_dfop_sfo_sfo, data = TRUE) -} - -} -\author{ -Johannes Ranke for the mkin specific parts -nlmixr authors for the parts inherited from nlmixr. -} diff --git a/man/tffm0.Rd b/man/tffm0.Rd deleted file mode 100644 index 89bee7d9..00000000 --- a/man/tffm0.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/tffm0.R -\name{tffm0} -\alias{tffm0} -\alias{invtffm0} -\title{Transform formation fractions as in the first published mkin version} -\usage{ -tffm0(ff) - -invtffm0(ff_trans) -} -\arguments{ -\item{ff}{Vector of untransformed formation fractions. The sum -must be smaller or equal to one} - -\item{ff_trans}{Vector of transformed formation fractions that can be -restricted to the interval from 0 to 1} -} -\value{ -A vector of the transformed formation fractions - -A vector of backtransformed formation fractions for natural use in degradation models -} -\description{ -This transformation was used originally in mkin, in order to implement a -constraint for the sum of formation fractions to be smaller than 1. It was -later replaced by the \link{ilr} transformation because the ilr transformed -fractions can assumed to follow normal distribution. As the ilr -transformation is not available in \link{RxODE} and can therefore not be used in -the nlmixr modelling language, the original transformation is currently used -for translating mkin models with formation fractions to more than one target -compartment for fitting with nlmixr in \link{nlmixr_model}. However, this -implementation cannot be used there, as it is not accessible from RxODE. -} -\details{ -If the transformed formation fractions are restricted to the interval -between 0 and 1, the sum of backtransformed values is restricted -to this interval. -} -\examples{ -ff_example <- c( - 0.10983681, 0.09035905, 0.08399383 -) -ff_example_trans <- tffm0(ff_example) -invtffm0(ff_example_trans) -} |