Rudimentary support for setting up nlmixr models

- All degradation models are specified as ODE models. This appears to be
fast enough
- Error models are being translated to nlmixr as close to the mkin error
model as possible. When using the 'saem' backend, it appears not to be
possible to use the same error model for more than one observed variable
- No support yet for models with parallel formation of metabolites, where
the ilr transformation is used in mkin per default
- There is a bug in nlmixr which appears to be triggered if the data are
not balanced, see nlmixrdevelopment/nlmixr#530
- There is a print and a plot method, the summary method is not finished

1 files changed, 13 insertions, 11 deletions

diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index 67cb3cbb..86938d31 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -1,30 +1,32 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/summary.saem.mmkin.R
-\name{summary.saem.mmkin}
-\alias{summary.saem.mmkin}
+% Please edit documentation in R/summary.nlmixr.mmkin.R, R/summary.saem.mmkin.R
+\name{print.summary.saem.mmkin}
 \alias{print.summary.saem.mmkin}
+\alias{summary.saem.mmkin}
 \title{Summary method for class "saem.mmkin"}
 \usage{
+\method{print}{summary.saem.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
+
 \method{summary}{saem.mmkin}(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
 
 \method{print}{summary.saem.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
 }
 \arguments{
-\item{object}{an object of class \link{saem.mmkin}}
+\item{x}{an object of class \link{summary.saem.mmkin}}
 
-\item{data}{logical, indicating whether the full data should be included in
-the summary.}
+\item{digits}{Number of digits to use for printing}
 
 \item{verbose}{Should the summary be verbose?}
 
-\item{distimes}{logical, indicating whether DT50 and DT90 values should be
-included.}
-
 \item{\dots}{optional arguments passed to methods like \code{print}.}
 
-\item{x}{an object of class \link{summary.saem.mmkin}}
+\item{object}{an object of class \link{saem.mmkin}}
 
-\item{digits}{Number of digits to use for printing}
+\item{data}{logical, indicating whether the full data should be included in
+the summary.}
+
+\item{distimes}{logical, indicating whether DT50 and DT90 values should be
+included.}
 }
 \value{
 The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject}