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

4 files changed, 6 insertions, 270 deletions

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 72487717..0b225e62 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} or \link{nlme.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.}
@@ -32,8 +32,8 @@ Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from
 HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models
 }
 \note{
-The function is used internally by \link{summary.mkinfit},
-\link{summary.nlme.mmkin} and \link{summary.saem.mmkin}.
+The function is used internally by \link{summary.mkinfit}
+and \link{summary.nlme.mmkin}
 }
 \examples{
 
diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index c7b2344f..87a82286 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -17,7 +17,7 @@
   maxabs = "auto",
   ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
   nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
+  rel.height.legend = 0.02 + 0.07 * nrow.legend,
   rel.height.bottom = 1.1,
   pch_ds = 1:length(i),
   col_ds = pch_ds + 1,
@@ -27,7 +27,7 @@
 )
 }
 \arguments{
-\item{x}{An object of class \link{mixed.mmkin}, \link{saem.mmkin} or \link{nlme.mmkin}}
+\item{x}{An object of class \link{mixed.mmkin}, \link{nlme.mmkin}}
 
 \item{i}{A numeric index to select datasets for which to plot the individual predictions,
 in case plots get too large}
@@ -94,15 +94,6 @@ plot(f[, 3:4], standardized = TRUE)
 f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
 plot(f_nlme)
 
-f_saem <- saem(f, transformations = "saemix")
-plot(f_saem)
-
-# We can overlay the two variants if we generate predictions
-pred_nlme <- mkinpredict(dfop_sfo,
-  f_nlme$bparms.optim[-1],
-  c(parent = f_nlme$bparms.optim[[1]], A1 = 0),
-  seq(0, 180, by = 0.2))
-plot(f_saem, pred_over = list(nlme = pred_nlme))
 }
 }
 \author{
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}
-}
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
deleted file mode 100644
index 67cb3cbb..00000000
--- a/man/summary.saem.mmkin.Rd
+++ /dev/null
@@ -1,100 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% 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{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{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}
-obtained in the fit, with at least the following additional components
-\item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used}
-\item{date.fit, date.summary}{The dates where the fit and the summary were
-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.}
-\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}
-The print method is called for its side effect, i.e. printing the summary.
-}
-\description{
-Lists model equations, initial parameter values, optimised parameters
-for fixed effects (population), random effects (deviations from the
-population mean) and residual error model, as well as the resulting
-endpoints such as formation fractions and DT50 values. Optionally
-(default is FALSE), the data are listed in full.
-}
-\examples{
-# Generate five datasets following DFOP-SFO kinetics
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"),
- m1 = mkinsub("SFO"), quiet = TRUE)
-set.seed(1234)
-k1_in <- rlnorm(5, log(0.1), 0.3)
-k2_in <- rlnorm(5, log(0.02), 0.3)
-g_in <- plogis(rnorm(5, qlogis(0.5), 0.3))
-f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3))
-k_m1_in <- rlnorm(5, log(0.02), 0.3)
-
-pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) {
-  mkinpredict(dfop_sfo,
-    c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1),
-    c(parent = 100, m1 = 0),
-    sampling_times)
-}
-
-ds_mean_dfop_sfo <- lapply(1:5, function(i) {
-  mkinpredict(dfop_sfo,
-    c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i],
-      f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]),
-    c(parent = 100, m1 = 0),
-    sampling_times)
-})
-names(ds_mean_dfop_sfo) <- paste("ds", 1:5)
-
-ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {
-  add_err(ds,
-    sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
-    n = 1)[[1]]
-})
-
-\dontrun{
-# Evaluate using mmkin and saem
-f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,
-  quiet = TRUE, error_model = "tc", cores = 5)
-f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
-summary(f_saem_dfop_sfo, data = TRUE)
-}
-
-}
-\author{
-Johannes Ranke for the mkin specific parts
-saemix authors for the parts inherited from saemix.
-}