Let backtransform_odeparms handle nlmixr formation fractions

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

3 files changed, 89 insertions, 4 deletions

diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd
index b6f761e8..93fcad26 100644
--- a/man/dimethenamid_2018.Rd
+++ b/man/dimethenamid_2018.Rd
@@ -31,5 +31,41 @@ specific pieces of information in the comments.
 }
 \examples{
 print(dimethenamid_2018)
+dmta_ds <- lapply(1:8, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Borstel"]] <- rbind(dmta_ds[["Borstel 1"]], dmta_ds[["Borstel 2"]])
+dmta_ds[["Borstel 1"]] <- NULL
+dmta_ds[["Borstel 2"]] <- NULL
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- NULL
+dmta_ds[["Elliot 2"]] <- NULL
+\dontrun{
+dfop_sfo3_plus <- mkinmod(
+  DMTA = mkinsub("DFOP", c("M23", "M27", "M31")),
+  M23 = mkinsub("SFO"),
+  M27 = mkinsub("SFO"),
+  M31 = mkinsub("SFO", "M27", sink = FALSE),
+  quiet = TRUE
+)
+f_dmta_mkin_tc <- mmkin(
+  list("DFOP-SFO3+" = dfop_sfo3_plus),
+  dmta_ds, quiet = TRUE, error_model = "tc")
+nlmixr_model(f_dmta_mkin_tc)
+f_dmta_nlmixr_focei <- nlmixr(f_dmta_mkin_tc, est = "focei",
+  control = nlmixr::foceiControl(print = 500))
+summary(f_dmta_nlmixr_focei)
+plot(f_dmta_nlmixr_focei)
+# saem has a problem with this model/data combination, maybe because of the
+# overparameterised error model, to be investigated
+#f_dmta_nlmixr_saem <- nlmixr(f_dmta_mkin_tc, est = "saem",
+#  control = saemControl(print = 500))
+#summary(f_dmta_nlmixr_saem)
+#plot(f_dmta_nlmixr_saem)
+}
 }
 \keyword{datasets}
diff --git a/man/nlmixr.mmkin.Rd b/man/nlmixr.mmkin.Rd
index 4ab30272..0f4f41a2 100644
--- a/man/nlmixr.mmkin.Rd
+++ b/man/nlmixr.mmkin.Rd
@@ -16,6 +16,8 @@
   error_model = object[[1]]$err_mod,
   test_log_parms = TRUE,
   conf.level = 0.6,
+  degparms_start = "auto",
+  eta_start = "auto",
   ...,
   save = NULL,
   envir = parent.frame()
@@ -27,7 +29,8 @@ nlmixr_model(
   object,
   est = c("saem", "focei"),
   degparms_start = "auto",
-  test_log_parms = FALSE,
+  eta_start = "auto",
+  test_log_parms = TRUE,
   conf.level = 0.6,
   error_model = object[[1]]$err_mod,
   add_attributes = FALSE
@@ -58,6 +61,13 @@ when calculating mean degradation parameters using \link{mean_degparms}.}
 \item{conf.level}{Possibility to adjust the required confidence level
 for parameter that are tested if requested by 'test_log_parms'.}
 
+\item{degparms_start}{Parameter values given as a named numeric vector will
+be used to override the starting values obtained from the 'mmkin' object.}
+
+\item{eta_start}{Standard deviations on the transformed scale given as a
+named numeric vector will be used to override the starting values obtained
+from the 'mmkin' object.}
+
 \item{\dots}{Passed to \link{nlmixr_model}}
 
 \item{save}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
@@ -68,9 +78,6 @@ for parameter that are tested if requested by 'test_log_parms'.}
 
 \item{digits}{Number of digits to use for printing}
 
-\item{degparms_start}{Parameter values given as a named numeric vector will
-be used to override the starting values obtained from the 'mmkin' object.}
-
 \item{add_attributes}{Should the starting values used for degradation model
 parameters and their distribution and for the error model parameters
 be returned as attributes?}
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)
+}