Prepare for v1.0.0v1.0.0

- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest

1 files changed, 0 insertions, 155 deletions

diff --git a/man/saem.Rd b/man/saem.Rd
deleted file mode 100644
index d5a8f17e..00000000
--- a/man/saem.Rd
+++ /dev/null
@@ -1,155 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/saem.R
-\name{saem}
-\alias{saem}
-\alias{saem.mmkin}
-\alias{print.saem.mmkin}
-\alias{saemix_model}
-\alias{saemix_data}
-\title{Fit nonlinear mixed models with SAEM}
-\usage{
-saem(object, ...)
-
-\method{saem}{mmkin}(
-  object,
-  transformations = c("mkin", "saemix"),
-  degparms_start = numeric(),
-  solution_type = "auto",
-  control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
-    FALSE),
-  verbose = FALSE,
-  quiet = FALSE,
-  ...
-)
-
-\method{print}{saem.mmkin}(x, digits = max(3, getOption("digits") - 3), ...)
-
-saemix_model(
-  object,
-  solution_type = "auto",
-  transformations = c("mkin", "saemix"),
-  degparms_start = numeric(),
-  verbose = FALSE,
-  ...
-)
-
-saemix_data(object, verbose = FALSE, ...)
-}
-\arguments{
-\item{object}{An \link{mmkin} row object containing several fits of the same
-\link{mkinmod} model to different datasets}
-
-\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{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{control}{Passed to \link[saemix:saemix]{saemix::saemix}}
-
-\item{verbose}{Should we print information about created objects of
-type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?}
-
-\item{quiet}{Should we suppress the messages saemix prints at the beginning
-and the end of the optimisation process?}
-
-\item{x}{An saem.mmkin object to print}
-
-\item{digits}{Number of digits to use for printing}
-}
-\value{
-An S3 object of class 'saem.mmkin', containing the fitted
-\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The
-object also inherits from 'mixed.mmkin'.
-
-An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object.
-
-An \link[saemix:SaemixData-class]{saemix::SaemixData} object.
-}
-\description{
-This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed
-effects models created from \link{mmkin} row objects using the Stochastic Approximation
-Expectation Maximisation algorithm (SAEM).
-}
-\details{
-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}.
-
-Starting values for the fixed effects (population mean parameters, argument
-psi0 of \code{\link[saemix:saemixModel]{saemix::saemixModel()}} are the mean values of the parameters found
-using \link{mmkin}.
-}
-\examples{
-\dontrun{
-ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) subset(x$data[c("name", "time", "value")]))
-names(ds) <- paste("Dataset", 6:10)
-f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds,
-  state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
-f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
-
-f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
-f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
-f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
-f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
-
-# The returned saem.mmkin object contains an SaemixObject, therefore we can use
-# functions from saemix
-library(saemix)
-compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so))
-plot(f_saem_fomc$so, plot.type = "convergence")
-plot(f_saem_fomc$so, plot.type = "individual.fit")
-plot(f_saem_fomc$so, plot.type = "npde")
-plot(f_saem_fomc$so, plot.type = "vpc")
-
-f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
-f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
-compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
-
-sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"))
-fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
-  A1 = mkinsub("SFO"))
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"))
-# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,
-# and compiled ODEs for FOMC that are much slower
-f_mmkin <- mmkin(list(
-    "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),
-  ds, quiet = TRUE)
-# saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds
-# each on this system, as we use analytical solutions written for saemix.
-# When using the analytical solutions written for mkin this took around
-# four minutes
-f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
-f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
-# We can use print, plot and summary methods to check the results
-print(f_saem_dfop_sfo)
-plot(f_saem_dfop_sfo)
-summary(f_saem_dfop_sfo, data = TRUE)
-
-# The following takes about 6 minutes
-#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",
-#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))
-
-#saemix::compare.saemix(list(
-#  f_saem_dfop_sfo$so,
-#  f_saem_dfop_sfo_deSolve$so))
-
-# If the model supports it, we can also use eigenvalue based solutions, which
-# take a similar amount of time
-#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",
-#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))
-}
-}
-\seealso{
-\link{summary.saem.mmkin} \link{plot.mixed.mmkin}
-}