1 files changed, 100 insertions, 0 deletions
diff --git a/man/saem.Rd b/man/saem.Rd
new file mode 100644
index 00000000..39b66448
--- /dev/null
+++ b/man/saem.Rd
@@ -0,0 +1,100 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/saemix.R
+\name{saem}
+\alias{saem}
+\alias{saem.mmkin}
+\alias{saemix_model}
+\alias{saemix_data}
+\title{Fit nonlinear mixed models with SAEM}
+\usage{
+saem(object, control, ...)
+
+\method{saem}{mmkin}(
+  object,
+  control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
+    FALSE),
+  cores = 1,
+  verbose = FALSE,
+  suppressPlot = TRUE,
+  ...
+)
+
+saemix_model(object, cores = 1, 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{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
+
+\item{\dots}{Further parameters passed to \link[saemix:saemixData]{saemix::saemixData}
+and \link[saemix:saemixModel]{saemix::saemixModel}.}
+
+\item{cores}{The number of cores to be used for multicore processing using
+\code{\link[parallel:mclapply]{parallel::mclapply()}}. Using more than 1 core is experimental and may
+lead to uncontrolled forking, apparently depending on the BLAS version
+used.}
+
+\item{verbose}{Should we print information about created objects?}
+
+\item{suppressPlot}{Should we suppress any plotting that is done
+by the saemix function?}
+}
+\value{
+An \link[saemix:SaemixObject-class]{saemix::SaemixObject}.
+
+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
+to the 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$data[c("name", "time", "value")]))
+names(ds) <- paste("Dataset", 6:10)
+f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, cores = 1,
+  state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
+f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
+
+f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
+f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
+f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+
+# The returned saem.mmkin object contains an SaemixObject, we can use
+# functions from saemix
+library(saemix)
+compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so))
+
+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))
+
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+  A1 = mkinsub("SFO"))
+f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "analytical")
+# This takes about 4 minutes on my system
+f_saem <- saem(f_mmkin)
+
+f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve")
+# Using a single core, the following takes about 6 minutes, using 10 cores
+# it is slower instead of faster
+f_saem_des <- saem(f_mmkin_des, cores = 1)
+compare.saemix(list(f_saemix$so, f_saemix_des$so))
+}
+}