mixed.mmkin and test coverage

4 files changed, 94 insertions, 7 deletions

diff --git a/man/mixed.Rd b/man/mixed.Rd
new file mode 100644
index 00000000..8b00382d
--- /dev/null
+++ b/man/mixed.Rd
@@ -0,0 +1,69 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mixed.mmkin.R
+\name{mixed}
+\alias{mixed}
+\alias{mixed.mmkin}
+\alias{print.mixed.mmkin}
+\title{Create a mixed effects model from an mmkin row object}
+\usage{
+mixed(object, ...)
+
+\method{mixed}{mmkin}(object, method = c("none"), ...)
+
+\method{print}{mixed.mmkin}(x, digits = max(3, getOption("digits") - 3), ...)
+}
+\arguments{
+\item{object}{An \link{mmkin} row object}
+
+\item{\dots}{Currently not used}
+
+\item{method}{The method to be used}
+
+\item{x}{A mixed.mmkin object to print}
+
+\item{digits}{Number of digits to use for printing.}
+}
+\description{
+Create a mixed effects model from an mmkin row object
+}
+\examples{
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+n_biphasic <- 8
+err_1 = list(const = 1, prop = 0.07)
+
+DFOP_SFO <- mkinmod(
+  parent = mkinsub("DFOP", "m1"),
+  m1 = mkinsub("SFO"),
+  quiet = TRUE)
+
+set.seed(123456)
+log_sd <- 0.3
+syn_biphasic_parms <- as.matrix(data.frame(
+  k1 = rlnorm(n_biphasic, log(0.05), log_sd),
+  k2 = rlnorm(n_biphasic, log(0.01), log_sd),
+  g = plogis(rnorm(n_biphasic, 0, log_sd)),
+  f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),
+  k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))
+
+ds_biphasic_mean <- lapply(1:n_biphasic,
+  function(i) {
+    mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],
+      c(parent = 100, m1 = 0), sampling_times)
+  }
+)
+
+set.seed(123456L)
+ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
+  add_err(ds,
+    sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
+    n = 1, secondary = "m1")[[1]]
+})
+
+\dontrun{
+f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, error_model = "tc", quiet = TRUE)
+
+f_mixed <- mixed(f_mmkin)
+print(f_mixed)
+plot(f_mixed)
+}
+}
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 95cec09a..bf073634 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -41,8 +41,8 @@ In print.mkinmod, this argument is currently not used.}
 \item{use_of_ff}{Specification of the use of formation fractions in the
 model equations and, if applicable, the coefficient matrix.  If "max",
 formation fractions are always used (default).  If "min", a minimum use of
-formation fractions is made, i.e. each pathway to a metabolite has its
-own rate constant.}
+formation fractions is made, i.e. each first-order pathway to a metabolite
+has its own rate constant.}
 
 \item{name}{A name for the model. Should be a valid R object name.}
 
diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index 66e79f09..b90a4b3a 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -26,7 +26,7 @@
 )
 }
 \arguments{
-\item{x}{An object of class \link{saem.mmkin} or \link{nlme.mmkin}}
+\item{x}{An object of class \link{mixed.mmkin}, \link{saem.mmkin} or \link{nlme.mmkin}}
 
 \item{i}{A numeric index to select datasets for which to plot the individual predictions,
 in case plots get too large}
diff --git a/man/saem.Rd b/man/saem.Rd
index ef5480f1..d8d6ea0f 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -8,10 +8,12 @@
 \alias{saemix_data}
 \title{Fit nonlinear mixed models with SAEM}
 \usage{
-saem(object, control, ...)
+saem(object, ...)
 
 \method{saem}{mmkin}(
   object,
+  transformations = c("mkin", "saemix"),
+  solution_type = "auto",
   control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
     FALSE),
   cores = 1,
@@ -23,7 +25,14 @@ saem(object, control, ...)
 
 \method{print}{saem.mmkin}(x, digits = max(3, getOption("digits") - 3), ...)
 
-saemix_model(object, cores = 1, verbose = FALSE, ...)
+saemix_model(
+  object,
+  solution_type = "auto",
+  transformations = c("mkin", "saemix"),
+  cores = 1,
+  verbose = FALSE,
+  ...
+)
 
 saemix_data(object, verbose = FALSE, ...)
 }
@@ -31,10 +40,19 @@ saemix_data(object, verbose = FALSE, ...)
 \item{object}{An \link{mmkin} row object containing several fits of the same
 \link{mkinmod} model to different datasets}
 
-\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
-
 \item{\dots}{Further parameters passed to \link[saemix:saemixModel]{saemix::saemixModel}.}
 
+\item{transformations}{Per default, all parameter transformations are done
+in mkin. If this argument is set to 'saemix', parameter transformations
+are done in 'saemix' for the supported cases. Currently this is only
+supported in cases where the initial concentration of the parent is not fixed,
+SFO or DFOP is used for the parent and there is either no metabolite or one.}
+
+\item{solution_type}{Possibility to specify the solution type in case the
+automatic choice is not desired}
+
+\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
+
 \item{cores}{The number of cores to be used for multicore processing using
 \code{\link[parallel:mclapply]{parallel::mclapply()}}. Using more than 1 core is experimental and may
 lead to excessive forking, apparently depending on the BLAS version