Batch processing for hierarchical fits

- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.

- 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects.

- 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects.

tests: Use 2 cores on travis, should work according to docs

1 files changed, 75 insertions, 0 deletions

diff --git a/man/mhmkin.Rd b/man/mhmkin.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mhmkin.R
+\name{mhmkin}
+\alias{mhmkin}
+\alias{mhmkin.list}
+\alias{[.mhmkin}
+\alias{print.mhmkin}
+\title{Fit nonlinear mixed-effects models built from one or more kinetic
+degradation models and one or more error models}
+\usage{
+mhmkin(objects, backend = "saemix", algorithm = "saem", ...)
+
+\method{mhmkin}{list}(
+  objects,
+  backend = "saemix",
+  ...,
+  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
+  cluster = NULL
+)
+
+\method{[}{mhmkin}(x, i, j, ..., drop = FALSE)
+
+\method{print}{mhmkin}(x, ...)
+}
+\arguments{
+\item{objects}{A list of \link{mmkin} objects containing fits of the same
+degradation models to the same data, but using different error models.}
+
+\item{backend}{The backend to be used for fitting. Currently, only saemix is
+supported}
+
+\item{algorithm}{The algorithm to be used for fitting (currently not used)}
+
+\item{\dots}{Further arguments that will be passed to the nonlinear mixed-effects
+model fitting function.}
+
+\item{cores}{The number of cores to be used for multicore processing. This
+is only used when the \code{cluster} argument is \code{NULL}. On Windows
+machines, cores > 1 is not supported, you need to use the \code{cluster}
+argument to use multiple logical processors. Per default, all cores detected
+by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used, except on Windows where the default
+is 1.}
+
+\item{cluster}{A cluster as returned by \link{makeCluster} to be used for
+parallel execution.}
+
+\item{x}{An \link{mhmkin} object.}
+
+\item{i}{Row index selecting the fits for specific models}
+
+\item{j}{Column index selecting the fits to specific datasets}
+
+\item{drop}{If FALSE, the method always returns an mhmkin object, otherwise
+either a list of fit objects or a single fit object.}
+}
+\value{
+A two-dimensional \link{array} of fit objects and/or try-errors that can
+be indexed using the degradation model names for the first index (row index)
+and the error model names for the second index (column index), with class
+attribute 'mhmkin'.
+
+An object of class \code{\link{mhmkin}}.
+}
+\description{
+The name of the methods expresses that (\strong{m}ultiple) \strong{h}ierarchichal
+(also known as multilevel) \strong{m}ulticompartment \strong{kin}etic models are
+fitted. Our kinetic models are nonlinear, so we can use various nonlinear
+mixed-effects model fitting functions.
+}
+\seealso{
+\code{\link{[.mhmkin}} for subsetting \link{mhmkin} objects
+}
+\author{
+Johannes Ranke
+}