diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinpredict.R | 10 | ||||
| -rw-r--r-- | R/saemix.R | 85 |
2 files changed, 48 insertions, 47 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index a6e7ca1c..7222e247 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -103,12 +103,7 @@ #' } #' #' @export -mkinpredict <- function(x, odeparms, odeini, - outtimes = seq(0, 120, by = 0.1), - solution_type = "deSolve", - use_compiled = "auto", - method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, - map_output = TRUE, ...) +mkinpredict <- function(x, odeparms, odeini, outtimes, ...) { UseMethod("mkinpredict", x) } @@ -122,8 +117,9 @@ mkinpredict.mkinmod <- function(x, solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, + map_output = TRUE, na_stop = TRUE, - map_output = TRUE, ...) + ...) { # Names of state variables and observed variables @@ -1,20 +1,16 @@ -#' Create saemix models +#' Fit nonlinear mixed models with SAEM #' -#' The saemix function defined in this package is an S3 generic function -#' using [saemix::saemix()] as its method for [saemix::SaemixModel] objects. +#' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed +#' effects models created from [mmkin] row objects using the stochastic approximation +#' to the expectation maximisation algorithm (SAEM). #' -#' The method for mmkin row objects sets up a nonlinear mixed effects model for -#' use with the saemix package. 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. +#' 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 [mkinfit]. #' -#' Starting values for the fixed effects (population mean parameters, argument psi0 of -#' [saemix::saemixModel()] are the mean values of the parameters found using -#' [mmkin]. +#' Starting values for the fixed effects (population mean parameters, argument +#' psi0 of [saemix::saemixModel()] are the mean values of the parameters found +#' using [mmkin]. #' -#' @param model For the default method, this is an [saemix::saemixModel] object. -#' If this is an [mmkin] row object, the [saemix::saemixModel] is created -#' internally from the [mmkin] object. #' @param object An [mmkin] row object containing several fits of the same #' [mkinmod] model to different datasets #' @param verbose Should we print information about created objects? @@ -22,75 +18,84 @@ #' [parallel::mclapply()]. Using more than 1 core is experimental and may #' lead to uncontrolled forking, apparently depending on the BLAS version #' used. +#' @param suppressPlot Should we suppress any plotting that is done +#' by the saemix function? +#' @param control Passed to [saemix::saemix] #' @param \dots Further parameters passed to [saemix::saemixData] #' and [saemix::saemixModel]. #' @return An [saemix::SaemixObject]. #' @examples #' \dontrun{ -#' # 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$data[c("name", "time", "value")])) #' names(ds) <- paste("Dataset", 6:10) #' f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, cores = 1, #' state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) -#' f_saemix_p0_fixed <- saemix(f_mmkin_parent_p0_fixed) +#' f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed) #' #' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) -#' f_saemix_sfo <- saemix(f_mmkin_parent["SFO", ]) -#' f_saemix_fomc <- saemix(f_mmkin_parent["FOMC", ]) -#' f_saemix_dfop <- saemix(f_mmkin_parent["DFOP", ]) +#' f_saem_sfo <- saem(f_mmkin_parent["SFO", ]) +#' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) #' -#' # As this returns an SaemixObject, we can use functions from saemix -#' compare.saemix(list(f_saemix_sfo, f_saemix_fomc, f_saemix_dfop)) +#' # The returned saem.mmkin object contains an SaemixObject, we can use +#' # functions from saemix +#' library(saemix) +#' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) #' #' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") -#' f_saemix_fomc_tc <- saemix(f_mmkin_parent_tc["FOMC", ]) -#' compare.saemix(list(f_saemix_fomc, f_saemix_fomc_tc)) +#' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) +#' compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) #' #' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), #' A1 = mkinsub("SFO")) #' 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) +#' f_saem <- saem(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)) -#' +#' # Using a single core, the following takes about 6 minutes, using 10 cores +#' # it is slower instead of faster +#' f_saem_des <- saem(f_mmkin_des, cores = 1) +#' compare.saemix(list(f_saemix$so, f_saemix_des$so)) #' } #' @export -saemix <- function(model, data, control, ...) UseMethod("saemix") +saem <- function(object, control, ...) UseMethod("saem") -#' @rdname saemix +#' @rdname saem #' @export -saemix.mmkin <- function(model, data, +saem.mmkin <- function(object, control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE), cores = 1, verbose = FALSE, suppressPlot = TRUE, ...) { - m_saemix <- saemix_model(model, cores = cores, verbose = verbose) - d_saemix <- saemix_data(model, verbose = verbose) + m_saemix <- saemix_model(object, cores = cores, verbose = verbose) + d_saemix <- saemix_data(object, verbose = verbose) if (suppressPlot) { # We suppress the log-likelihood curve that saemix currently # produces at the end of the fit by plotting to a file # that we discard afterwards tmp <- tempfile() - png(tmp) + grDevices::png(tmp) } - result <- saemix::saemix(m_saemix, d_saemix, control) + f_saemix <- saemix::saemix(m_saemix, d_saemix, control) if (suppressPlot) { - dev.off() + grDevices::dev.off() unlink(tmp) } + result <- list( + mkinmod = object[[1]]$mkinmod, + mmkin = object, + solution_type = object[[1]]$solution_type, + transform_rates = object[[1]]$transform_rates, + transform_fractions = object[[1]]$transform_fractions, + so = f_saemix) + class(result) <- "saem.mmkin" return(result) } -#' @rdname saemix +#' @rdname saem #' @return An [saemix::SaemixModel] object. #' @export saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { @@ -254,7 +259,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { return(res) } -#' @rdname saemix +#' @rdname saem #' @return An [saemix::SaemixData] object. #' @export saemix_data <- function(object, verbose = FALSE, ...) { |