Reintroduce interface to saemix

Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.

4 files changed, 269 insertions, 5 deletions

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 0b225e62..72487717 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} or \link{nlme.mmkin}
-or another object that has list components
+\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or
+\link{saem.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}
-and \link{summary.nlme.mmkin}
+The function is used internally by \link{summary.mkinfit},
+\link{summary.nlme.mmkin} and \link{summary.saem.mmkin}.
 }
 \examples{
 
diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd
index 87a82286..b1200729 100644
--- a/man/plot.mixed.mmkin.Rd
+++ b/man/plot.mixed.mmkin.Rd
@@ -27,7 +27,7 @@
 )
 }
 \arguments{
-\item{x}{An object of class \link{mixed.mmkin}, \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}
@@ -94,6 +94,15 @@ 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
new file mode 100644
index 00000000..d5a8f17e
--- /dev/null
+++ b/man/saem.Rd
@@ -0,0 +1,155 @@
+% 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
new file mode 100644
index 00000000..67cb3cbb
--- /dev/null
+++ b/man/summary.saem.mmkin.Rd
@@ -0,0 +1,100 @@
+% 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.
+}