diff options
Diffstat (limited to 'man/nlmixr.mmkin.Rd')
| -rw-r--r-- | man/nlmixr.mmkin.Rd | 209 |
1 files changed, 209 insertions, 0 deletions
diff --git a/man/nlmixr.mmkin.Rd b/man/nlmixr.mmkin.Rd new file mode 100644 index 00000000..0f4f41a2 --- /dev/null +++ b/man/nlmixr.mmkin.Rd @@ -0,0 +1,209 @@ +% 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}{Possibility 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). +} +\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$data[c("name", "time", "value")])) +names(ds) <- paste("Dataset", 6:10) + +f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1) +f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc", + cores = 1, quiet = TRUE) + +f_nlmixr_sfo_saem <- nlmixr(f_mmkin_parent["SFO", ], est = "saem") +f_nlmixr_sfo_focei <- nlmixr(f_mmkin_parent["SFO", ], est = "focei") + +f_nlmixr_fomc_saem <- nlmixr(f_mmkin_parent["FOMC", ], est = "saem") +f_nlmixr_fomc_focei <- nlmixr(f_mmkin_parent["FOMC", ], est = "focei") + +f_nlmixr_dfop_saem <- nlmixr(f_mmkin_parent["DFOP", ], est = "saem") +f_nlmixr_dfop_focei <- nlmixr(f_mmkin_parent["DFOP", ], est = "focei") + +f_nlmixr_hs_saem <- nlmixr(f_mmkin_parent["HS", ], est = "saem") +f_nlmixr_hs_focei <- nlmixr(f_mmkin_parent["HS", ], est = "focei") + +f_nlmixr_fomc_saem_tc <- nlmixr(f_mmkin_parent_tc["FOMC", ], est = "saem") +f_nlmixr_fomc_focei_tc <- nlmixr(f_mmkin_parent_tc["FOMC", ], est = "focei") + +AIC( + f_nlmixr_sfo_saem$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", ])) + +# nlme is comparable to nlmixr with focei, saem finds a better +# solution, the two-component error model does not improve it +plot(f_nlmixr_fomc_saem) + +sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), + A1 = mkinsub("SFO")) +fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), + A1 = mkinsub("SFO")) +dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO")) + +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") + +# 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) +} +} +\seealso{ +\link{summary.nlmixr.mmkin} \link{plot.mixed.mmkin} +} |