diff options
Diffstat (limited to 'R/saemix.R')
| -rw-r--r-- | R/saemix.R | 31 |
1 files changed, 24 insertions, 7 deletions
@@ -5,25 +5,37 @@ #' list of mkinfit objects that have been obtained by fitting the same model to #' a list of datasets. #' +#' 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 variances of the random effects (argument omega.init) are the +#' variances of the deviations of the parameters from these mean values. +#' #' @param object An mmkin row object containing several fits of the same model to different datasets +#' @param cores The number of cores to be used for multicore processing. +#' On Windows machines, cores > 1 is currently not supported. #' @rdname saemix #' @importFrom saemix saemixData saemixModel +#' @importFrom stats var #' @examples #' ds <- lapply(experimental_data_for_UBA_2019[6:10], #' function(x) subset(x$data[c("name", "time", "value")])) #' names(ds) <- paste("Dataset", 6:10) #' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), #' A1 = mkinsub("SFO")) -#' f_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo), ds, quiet = TRUE, cores = 5) +#' \dontrun{ +#' f_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo), ds, quiet = TRUE) +#' library(saemix) #' m_saemix <- saemix_model(f_mmkin) #' d_saemix <- saemix_data(f_mmkin) -#' saemix_options <- list(seed = 123456, save = FALSE, save.graphs = FALSE) -#' \dontrun{ -#' saemix(m_saemix, d_saemix, saemix_options) +#' saemix_options <- list(seed = 123456, +#' save = FALSE, save.graphs = FALSE, displayProgress = FALSE, +#' nbiter.saemix = c(200, 80)) +#' f_saemix <- saemix(m_saemix, d_saemix, saemix_options) +#' plot(f_saemix, plot.type = "convergence") #' } #' @return An [saemix::SaemixModel] object. #' @export -saemix_model <- function(object) { +saemix_model <- function(object, cores = parallel::detectCores()) { if (nrow(object) > 1) stop("Only row objects allowed") mkin_model <- object[[1]]$mkinmod @@ -81,14 +93,19 @@ saemix_model <- function(object) { out_values <- out_wide[out_index] } return(out_values) - }, mc.cores = 15) + }, mc.cores = cores) res <- unlist(res_list) return(res) } + raneff_0 <- mean_degparms(object, random = TRUE)$random$ds + var_raneff_0 <- apply(raneff_0, 2, var) + res <- saemixModel(model_function, psi0, "Mixed model generated from mmkin object", - transform.par = rep(0, length(degparms_optim))) + transform.par = rep(0, length(degparms_optim)), + omega.init = diag(var_raneff_0) + ) return(res) } |