Make saem using mkinpredict work again

I threw out mclapply as it did not play well with the linear algebra
routines used in the saemix code. Most of the change is actually
indentation in the code creating the model function. But there
is an important fix in mkinpredict which I had broken.

1 files changed, 17 insertions, 13 deletions

diff --git a/man/saem.Rd b/man/saem.Rd
index d8d6ea0f..1fdfb2c4 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -53,11 +53,6 @@ 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
-used.}
-
 \item{verbose}{Should we print information about created objects of
 type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?}
 
@@ -98,7 +93,7 @@ using \link{mmkin}.
 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, cores = 1,
+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)
 
@@ -131,9 +126,10 @@ dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
 f_mmkin <- mmkin(list(
     "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),
   ds, quiet = TRUE)
-# These 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
+# 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
@@ -141,10 +137,18 @@ print(f_saem_dfop_sfo)
 plot(f_saem_dfop_sfo)
 summary(f_saem_dfop_sfo, data = TRUE)
 
-# Using a single core, the following takes about 6 minutes as we do not have an
-# analytical solution. Using 10 cores it is slower instead of faster
-f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
-plot(f_saem_fomc)
+# 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{