diff options
Diffstat (limited to 'man/saem.Rd')
| -rw-r--r-- | man/saem.Rd | 30 |
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{ |