Finished 'summary.nlmixr.mmkin', checks, docs

6 files changed, 48 insertions, 28 deletions

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 72487717..a37ff98d 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -8,8 +8,8 @@ with mkinfit}
 endpoints(fit)
 }
 \arguments{
-\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or
-\link{saem.mmkin}. Or another object that has list components
+\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin}, \link{saem.mmkin} or
+\link{nlmixr.mmkin}. Or another object that has list components
 mkinmod containing an \link{mkinmod} degradation model, and two numeric vectors,
 bparms.optim and bparms.fixed, that contain parameter values
 for that model.}
diff --git a/man/mean_degparms.Rd b/man/mean_degparms.Rd
index 92ed4c9d..5e2b4b0f 100644
--- a/man/mean_degparms.Rd
+++ b/man/mean_degparms.Rd
@@ -7,6 +7,8 @@
 mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6)
 }
 \arguments{
+\item{object}{An mmkin row object containing several fits of the same model to different datasets}
+
 \item{random}{Should a list with fixed and random effects be returned?}
 
 \item{test_log_parms}{If TRUE, log parameters are only considered in
diff --git a/man/nlmixr.mmkin.Rd b/man/nlmixr.mmkin.Rd
index 86bbdc9f..4ab30272 100644
--- a/man/nlmixr.mmkin.Rd
+++ b/man/nlmixr.mmkin.Rd
@@ -29,7 +29,8 @@ nlmixr_model(
   degparms_start = "auto",
   test_log_parms = FALSE,
   conf.level = 0.6,
-  error_model = object[[1]]$err_mod
+  error_model = object[[1]]$err_mod,
+  add_attributes = FALSE
 )
 
 nlmixr_data(object, ...)
@@ -38,9 +39,16 @@ nlmixr_data(object, ...)
 \item{object}{An \link{mmkin} row object containing several fits of the same
 \link{mkinmod} model to different datasets}
 
+\item{data}{Not used, as the data are extracted from the mmkin row object}
+
 \item{est}{Estimation method passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
 
-\item{control}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}.}
+\item{control}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
+
+\item{table}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
+
+\item{error_model}{Possibility to override the error model which is being
+set based on the error model used in the mmkin row object.}
 
 \item{test_log_parms}{If TRUE, an attempt is made to use more robust starting
 values for population parameters fitted as log parameters in mkin (like
@@ -52,6 +60,10 @@ for parameter that are tested if requested by 'test_log_parms'.}
 
 \item{\dots}{Passed to \link{nlmixr_model}}
 
+\item{save}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
+
+\item{envir}{Passed to \link[nlmixr:nlmixr]{nlmixr::nlmixr}}
+
 \item{x}{An nlmixr.mmkin object to print}
 
 \item{digits}{Number of digits to use for printing}
@@ -59,8 +71,9 @@ 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{solution_type}{Possibility to specify the solution type in case the
-automatic choice is not desired}
+\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?}
 }
 \value{
 An S3 object of class 'nlmixr.mmkin', containing the fitted
@@ -81,9 +94,11 @@ An mmkin row object is essentially a list of mkinfit objects that have been
 obtained by fitting the same model to a list of datasets using \link{mkinfit}.
 }
 \examples{
+\dontrun{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")]))
 names(ds) <- paste("Dataset", 6:10)
+
 f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1)
 f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc",
   cores = 1, quiet = TRUE)
@@ -117,7 +132,6 @@ AIC(nlme(f_mmkin_parent["HS", ]))
 # solution, the two-component error model does not improve it
 plot(f_nlmixr_fomc_saem)
 
-\dontrun{
 sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
   A1 = mkinsub("SFO"))
 fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
diff --git a/man/reexports.Rd b/man/reexports.Rd
index ccba7567..d4fc6b96 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -1,10 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/lrtest.mkinfit.R, R/nlme.mmkin.R
+% Please edit documentation in R/lrtest.mkinfit.R, R/nlme.mmkin.R, R/nlmixr.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
 \alias{lrtest}
 \alias{nlme}
+\alias{nlmixr}
 \title{Objects exported from other packages}
 \keyword{internal}
 \description{
@@ -15,5 +16,7 @@ below to see their documentation.
   \item{lmtest}{\code{\link[lmtest]{lrtest}}}
 
   \item{nlme}{\code{\link[nlme]{nlme}}}
+
+  \item{nlmixr}{\code{\link[nlmixr]{nlmixr}}}
 }}
 
diff --git a/man/summary.nlmixr.mmkin.Rd b/man/summary.nlmixr.mmkin.Rd
index 03f0ffb2..ab8abd5d 100644
--- a/man/summary.nlmixr.mmkin.Rd
+++ b/man/summary.nlmixr.mmkin.Rd
@@ -2,12 +2,15 @@
 % Please edit documentation in R/summary.nlmixr.mmkin.R
 \name{summary.nlmixr.mmkin}
 \alias{summary.nlmixr.mmkin}
+\alias{print.summary.nlmixr.mmkin}
 \title{Summary method for class "nlmixr.mmkin"}
 \usage{
 \method{summary}{nlmixr.mmkin}(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
+
+\method{print}{summary.nlmixr.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
 }
 \arguments{
-\item{object}{an object of class \link{nlmix.mmkin}}
+\item{object}{an object of class \link{nlmixr.mmkin}}
 
 \item{data}{logical, indicating whether the full data should be included in
 the summary.}
@@ -19,7 +22,7 @@ included.}
 
 \item{\dots}{optional arguments passed to methods like \code{print}.}
 
-\item{x}{an object of class \link{summary.nlmix.mmkin}}
+\item{x}{an object of class \link{summary.nlmixr.mmkin}}
 
 \item{digits}{Number of digits to use for printing}
 }
@@ -32,9 +35,7 @@ produced}
 \item{diffs}{The differential equations used in the degradation model}
 \item{use_of_ff}{Was maximum or minimum use made of formation fractions}
 \item{data}{The data}
-\item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}
 \item{confint_back}{Backtransformed parameters, with confidence intervals if available}
-\item{confint_errmod}{Error model parameters with confidence intervals}
 \item{ff}{The estimated formation fractions derived from the fitted
 model.}
 \item{distimes}{The DT50 and DT90 values for each observed variable.}
@@ -85,12 +86,14 @@ ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {
 \dontrun{
 # Evaluate using mmkin and nlmixr
 f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,
-  quiet = TRUE, error_model = "obs", cores = 5)
+  quiet = TRUE, error_model = "tc", cores = 5)
 f_saemix_dfop_sfo <- mkin::saem(f_mmkin_dfop_sfo)
 f_nlme_dfop_sfo <- mkin::nlme(f_mmkin_dfop_sfo)
 f_nlmixr_dfop_sfo_saem <- nlmixr(f_mmkin_dfop_sfo, est = "saem")
-#f_nlmixr_dfop_sfo_focei <- nlmixr(f_mmkin_dfop_sfo, est = "focei")
-summary(f_nlmixr_dfop_sfo, data = TRUE)
+# The following takes a very long time but gives
+f_nlmixr_dfop_sfo_focei <- nlmixr(f_mmkin_dfop_sfo, est = "focei")
+AIC(f_nlmixr_dfop_sfo_saem$nm, f_nlmixr_dfop_sfo_focei$nm)
+summary(f_nlmixr_dfop_sfo_sfo, data = TRUE)
 }
 
 }
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index 86938d31..67cb3cbb 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -1,32 +1,30 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/summary.nlmixr.mmkin.R, R/summary.saem.mmkin.R
-\name{print.summary.saem.mmkin}
-\alias{print.summary.saem.mmkin}
+% Please edit documentation in R/summary.saem.mmkin.R
+\name{summary.saem.mmkin}
 \alias{summary.saem.mmkin}
+\alias{print.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{x}{an object of class \link{summary.saem.mmkin}}
-
-\item{digits}{Number of digits to use for printing}
-
-\item{verbose}{Should the summary be verbose?}
-
-\item{\dots}{optional arguments passed to methods like \code{print}.}
-
 \item{object}{an object of class \link{saem.mmkin}}
 
 \item{data}{logical, indicating whether the full data should be included in
 the summary.}
 
+\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{digits}{Number of digits to use for printing}
 }
 \value{
 The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject}