From 954f7514144a281b73e9b47ac88a6b13e8799f31 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 15 Oct 2020 10:25:48 +0200
Subject: Reintroduce saemix helper functions

---
 man/saemix.Rd | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 man/saemix.Rd

(limited to 'man/saemix.Rd')

diff --git a/man/saemix.Rd b/man/saemix.Rd
new file mode 100644
index 00000000..eedbf537
--- /dev/null
+++ b/man/saemix.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/saemix.R
+\name{saemix_model}
+\alias{saemix_model}
+\alias{saemix_data}
+\title{Create saemix models from mmkin row objects}
+\usage{
+saemix_model(object, cores = parallel::detectCores())
+
+saemix_data(object, ...)
+}
+\arguments{
+\item{object}{An mmkin row object containing several fits of the same model to different datasets}
+
+\item{cores}{The number of cores to be used for multicore processing.
+On Windows machines, cores > 1 is currently not supported.}
+
+\item{\dots}{Further parameters passed to \link[saemix:saemixData]{saemix::saemixData}}
+}
+\value{
+An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object.
+
+An \link[saemix:SaemixData-class]{saemix::SaemixData} object.
+}
+\description{
+This function sets up a nonlinear mixed effects model for an mmkin row
+object for use with the saemix package. 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{
+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
+mmkin. Starting variances of the random effects (argument omega.init) are the
+variances of the deviations of the parameters from these mean values.
+}
+\examples{
+ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) subset(x$data[c("name", "time", "value")]))
+names(ds) <- paste("Dataset", 6:10)
+sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
+  A1 = mkinsub("SFO"))
+\dontrun{
+f_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo), ds, quiet = TRUE)
+library(saemix)
+m_saemix <- saemix_model(f_mmkin)
+d_saemix <- saemix_data(f_mmkin)
+saemix_options <- list(seed = 123456,
+  save = FALSE, save.graphs = FALSE, displayProgress = FALSE,
+  nbiter.saemix = c(200, 80))
+f_saemix <- saemix(m_saemix, d_saemix, saemix_options)
+plot(f_saemix, plot.type = "convergence")
+}
+}
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