diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinpredict.Rd | 3 | ||||
| -rw-r--r-- | man/saemix.Rd | 50 |
2 files changed, 29 insertions, 24 deletions
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 17916356..f2799bf4 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -30,6 +30,7 @@ mkinpredict( method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + na_stop = TRUE, map_output = TRUE, ... ) @@ -90,6 +91,8 @@ as these always return mapped output.} \item{\dots}{Further arguments passed to the ode solver in case such a solver is used.} + +\item{na_stop}{Should it be an error if deSolve::ode returns NaN values} } \value{ A matrix with the numeric solution in wide format diff --git a/man/saemix.Rd b/man/saemix.Rd index 1959817a..a664b0cc 100644 --- a/man/saemix.Rd +++ b/man/saemix.Rd @@ -14,7 +14,9 @@ saemix(model, data, control, ...) data, control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE), + cores = 1, verbose = FALSE, + suppressPlot = TRUE, ... ) @@ -30,15 +32,15 @@ internally from the \link{mmkin} object.} \item{\dots}{Further parameters passed to \link[saemix:saemixData]{saemix::saemixData} and \link[saemix:saemixModel]{saemix::saemixModel}.} -\item{verbose}{Should we print information about created objects?} - -\item{object}{An \link{mmkin} row object containing several fits of the same -\link{mkinmod} model to different datasets} - \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 uncontrolled forking, apparently depending on the BLAS version used.} + +\item{verbose}{Should we print information about created objects?} + +\item{object}{An \link{mmkin} row object containing several fits of the same +\link{mkinmod} model to different datasets} } \value{ An \link[saemix:SaemixObject-class]{saemix::SaemixObject}. @@ -63,39 +65,39 @@ Starting values for the fixed effects (population mean parameters, argument psi0 } \examples{ \dontrun{ -library(saemix) +# We can load saemix, but should exclude the saemix function +# as it would mask our generic version of it +library(saemix, exclude = "saemix") 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, state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) f_saemix_p0_fixed <- saemix(f_mmkin_parent_p0_fixed) -m_saemix_p0_fixed <- saemix_model(f_mmkin_parent_p0_fixed["FOMC", ]) -d_saemix_parent <- saemix_data(f_mmkin_parent_p0_fixed) -saemix_options <- list(seed = 123456, displayProgress = FALSE, - save = FALSE, save.graphs = FALSE, nbiter.saemix = c(200, 80)) -f_saemix_p0_fixed <- saemix(m_saemix_p0_fixed, d_saemix_parent, saemix_options) f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) -m_saemix_sfo <- saemix_model(f_mmkin_parent["SFO", ]) -m_saemix_fomc <- saemix_model(f_mmkin_parent["FOMC", ]) -m_saemix_dfop <- saemix_model(f_mmkin_parent["DFOP", ]) -d_saemix_parent <- saemix_data(f_mmkin_parent["SFO", ]) -f_saemix_sfo <- saemix(m_saemix_sfo, d_saemix_parent, saemix_options) -f_saemix_fomc <- saemix(m_saemix_fomc, d_saemix_parent, saemix_options) -f_saemix_dfop <- saemix(m_saemix_dfop, d_saemix_parent, saemix_options) +f_saemix_sfo <- saemix(f_mmkin_parent["SFO", ]) +f_saemix_fomc <- saemix(f_mmkin_parent["FOMC", ]) +f_saemix_dfop <- saemix(f_mmkin_parent["DFOP", ]) + +# As this returns an SaemixObject, we can use functions from saemix compare.saemix(list(f_saemix_sfo, f_saemix_fomc, f_saemix_dfop)) + f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") -m_saemix_fomc_tc <- saemix_model(f_mmkin_parent_tc["FOMC", ]) -f_saemix_fomc_tc <- saemix(m_saemix_fomc_tc, d_saemix_parent, saemix_options) +f_saemix_fomc_tc <- saemix(f_mmkin_parent_tc["FOMC", ]) compare.saemix(list(f_saemix_fomc, f_saemix_fomc_tc)) dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO")) -f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) -m_saemix <- saemix_model(f_mmkin) -d_saemix <- saemix_data(f_mmkin) -f_saemix <- saemix(m_saemix, d_saemix, saemix_options) +f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "analytical") +# This takes about 4 minutes on my system +f_saemix <- saemix(f_mmkin) + +# Using a single core, it takes about 6 minutes, using 10 cores it is slower +# instead of faster +f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve") +f_saemix_des <- saemix(f_mmkin_des, cores = 1) +compare.saemix(list(f_saemix, f_saemix_des)) } } |