Let backtransform_odeparms handle nlmixr formation fractions

Also adapt summary.nlmixr.mmkin to correctly handle the way
formation fractions are translated to nlmixr

1 files changed, 42 insertions, 0 deletions

diff --git a/man/tffm0.Rd b/man/tffm0.Rd
new file mode 100644
index 00000000..46978d5e
--- /dev/null
+++ b/man/tffm0.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tffm0.R
+\name{tffm0}
+\alias{tffm0}
+\alias{invtffm0}
+\title{Transform formation fractions as in the first published mkin version}
+\usage{
+tffm0(ff)
+
+invtffm0(ff_trans)
+}
+\arguments{
+\item{ff}{Vector of untransformed formation fractions. The sum
+must be smaller or equal to one}
+
+\item{ff_trans}{Vector of transformed formation fractions that can be
+restricted to the interval from 0 to 1}
+}
+\value{
+A vector of the transformed formation fractions
+
+A vector of backtransformed formation fractions for natural use in degradation models
+}
+\description{
+The transformed fractions can be restricted between 0 and 1 in model
+optimisations. Therefore this transformation was used originally in mkin. It
+was later replaced by the \link{ilr} transformation because the ilr transformed
+fractions can assumed to follow normal distribution. As the ilr
+transformation is not available in \link{RxODE} and can therefore not be used in
+the nlmixr modelling language, this transformation is currently used for
+translating mkin models with formation fractions to more than one target
+compartment for fitting with nlmixr in \link{nlmixr_model}. However,
+this implementation cannot be used there, as it is not accessible
+from RxODE.
+}
+\examples{
+ff_example <- c(
+  0.10983681, 0.09035905, 0.08399383
+)
+ff_example_trans <- tffm0(ff_example)
+invtffm0(ff_example_trans)
+}