From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Feb 2021 16:41:31 +0100 Subject: Prepare for v1.0.0 - Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest --- man/saem.Rd | 155 ------------------------------------------------------------ 1 file changed, 155 deletions(-) delete mode 100644 man/saem.Rd (limited to 'man/saem.Rd') diff --git a/man/saem.Rd b/man/saem.Rd deleted file mode 100644 index d5a8f17e..00000000 --- a/man/saem.Rd +++ /dev/null @@ -1,155 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/saem.R -\name{saem} -\alias{saem} -\alias{saem.mmkin} -\alias{print.saem.mmkin} -\alias{saemix_model} -\alias{saemix_data} -\title{Fit nonlinear mixed models with SAEM} -\usage{ -saem(object, ...) - -\method{saem}{mmkin}( - object, - transformations = c("mkin", "saemix"), - degparms_start = numeric(), - solution_type = "auto", - control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = - FALSE), - verbose = FALSE, - quiet = FALSE, - ... -) - -\method{print}{saem.mmkin}(x, digits = max(3, getOption("digits") - 3), ...) - -saemix_model( - object, - solution_type = "auto", - transformations = c("mkin", "saemix"), - degparms_start = numeric(), - verbose = FALSE, - ... -) - -saemix_data(object, verbose = FALSE, ...) -} -\arguments{ -\item{object}{An \link{mmkin} row object containing several fits of the same -\link{mkinmod} model to different datasets} - -\item{\dots}{Further parameters passed to \link[saemix:saemixModel]{saemix::saemixModel}.} - -\item{transformations}{Per default, all parameter transformations are done -in mkin. If this argument is set to 'saemix', parameter transformations -are done in 'saemix' for the supported cases. Currently this is only -supported in cases where the initial concentration of the parent is not fixed, -SFO or DFOP is used for the parent and there is either no metabolite or one.} - -\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{solution_type}{Possibility to specify the solution type in case the -automatic choice is not desired} - -\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}} - -\item{verbose}{Should we print information about created objects of -type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?} - -\item{quiet}{Should we suppress the messages saemix prints at the beginning -and the end of the optimisation process?} - -\item{x}{An saem.mmkin object to print} - -\item{digits}{Number of digits to use for printing} -} -\value{ -An S3 object of class 'saem.mmkin', containing the fitted -\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The -object also inherits from 'mixed.mmkin'. - -An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object. - -An \link[saemix:SaemixData-class]{saemix::SaemixData} object. -} -\description{ -This function uses \code{\link[saemix:saemix]{saemix::saemix()}} 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}. - -Starting values for the fixed effects (population mean parameters, argument -psi0 of \code{\link[saemix:saemixModel]{saemix::saemixModel()}} are the mean values of the parameters found -using \link{mmkin}. -} -\examples{ -\dontrun{ -ds <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")])) -names(ds) <- paste("Dataset", 6:10) -f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, - state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) -f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed) - -f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) -f_saem_sfo <- saem(f_mmkin_parent["SFO", ]) -f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) -f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) - -# The returned saem.mmkin object contains an SaemixObject, therefore we can use -# functions from saemix -library(saemix) -compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) -plot(f_saem_fomc$so, plot.type = "convergence") -plot(f_saem_fomc$so, plot.type = "individual.fit") -plot(f_saem_fomc$so, plot.type = "npde") -plot(f_saem_fomc$so, plot.type = "vpc") - -f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") -f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) -compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) - -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")) -# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, -# and compiled ODEs for FOMC that are much slower -f_mmkin <- mmkin(list( - "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), - ds, quiet = TRUE) -# saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds -# each on this system, as we use analytical solutions written for saemix. -# When using the analytical solutions written for mkin this took around -# four minutes -f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ]) -f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) -# We can use print, plot and summary methods to check the results -print(f_saem_dfop_sfo) -plot(f_saem_dfop_sfo) -summary(f_saem_dfop_sfo, data = TRUE) - -# The following takes about 6 minutes -#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", -# control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) - -#saemix::compare.saemix(list( -# f_saem_dfop_sfo$so, -# f_saem_dfop_sfo_deSolve$so)) - -# If the model supports it, we can also use eigenvalue based solutions, which -# take a similar amount of time -#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen", -# control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) -} -} -\seealso{ -\link{summary.saem.mmkin} \link{plot.mixed.mmkin} -} -- cgit v1.2.1