diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/multistart.R | 34 |
1 files changed, 24 insertions, 10 deletions
diff --git a/R/multistart.R b/R/multistart.R index beb8194b..cc55feae 100644 --- a/R/multistart.R +++ b/R/multistart.R @@ -7,9 +7,6 @@ #' inspired by the article on practical identifiabiliy in the frame of nonlinear #' mixed-effects models by Duchesne et al (2021). #' -#' Currently, parallel execution of the fits is only supported using -#' [parallel::mclapply], i.e. not available on Windows. -#' #' In case the online version of this help page contains error messages #' in the example code and no plots, this is due to the multistart method #' not working when called by pkgdown. Please refer to the @@ -19,7 +16,9 @@ #' @param object The fit object to work with #' @param n How many different combinations of starting parameters should be #' used? -#' @param cores How many fits should be run in parallel? +#' @param cores How many fits should be run in parallel (only on posix platforms)? +#' @param cluster A cluster as returned by [parallel::makeCluster] to be used +#' for parallel execution. #' @param \dots Passed to the update function. #' @param x The multistart object to print #' @return A list of [saem.mmkin] objects, with class attributes @@ -50,17 +49,26 @@ #' parhist(f_saem_full_multi, lpos = "bottomright") #' #' f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1))) -#' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16) +#' # On Windows, we need to create a cluster first. When working with +#' # such a cluster, we need to export the mmkin object to the cluster +#' # nodes, as it is referred to when updating the saem object on the nodes. +#' library(parallel) +#' cl <- makePSOCKcluster(12) +#' clusterExport(cl, "f_mmkin") +#' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) #' parhist(f_saem_reduced_multi, lpos = "bottomright") #' } -multistart <- function(object, n = 50, cores = 1, ...) +multistart <- function(object, n = 50, + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), + cluster = NULL, ...) { UseMethod("multistart", object) } #' @rdname multistart #' @export -multistart.saem.mmkin <- function(object, n = 50, cores = 1, ...) { +multistart.saem.mmkin <- function(object, n = 50, cores = 1, + cluster = NULL, ...) { if (n <= 1) stop("Please specify an n of at least 2") mmkin_parms <- parms(object$mmkin, errparms = FALSE, @@ -69,9 +77,15 @@ multistart.saem.mmkin <- function(object, n = 50, cores = 1, ...) { mmkin_parms, 1, function(x) stats::runif(n, min(x), max(x))) - res <- parallel::mclapply(1:n, function(x) { - update(object, degparms_start = start_parms[x, ], ...) - }, mc.cores = cores) + if (is.null(cluster)) { + res <- parallel::mclapply(1:n, function (x) { + update(object, degparms_start = start_parms[x, ], ...) + }, mc.cores = cores) + } else { + res <- parallel::parLapply(cluster, 1:n, function(x) { + update(object, degparms_start = start_parms[x, ], ...) + }) + } attr(res, "orig") <- object attr(res, "start_parms") <- start_parms class(res) <- c("multistart.saem.mmkin", "multistart") |