diff options
| -rw-r--r-- | R/multistart.R | 34 | ||||
| -rw-r--r-- | man/multistart.Rd | 26 |
2 files changed, 43 insertions, 17 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") diff --git a/man/multistart.Rd b/man/multistart.Rd index d145aa63..aa352267 100644 --- a/man/multistart.Rd +++ b/man/multistart.Rd @@ -7,9 +7,15 @@ \alias{parms.multistart} \title{Perform a hierarchical model fit with multiple starting values} \usage{ -multistart(object, n = 50, cores = 1, ...) +multistart( + object, + n = 50, + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), + cluster = NULL, + ... +) -\method{multistart}{saem.mmkin}(object, n = 50, cores = 1, ...) +\method{multistart}{saem.mmkin}(object, n = 50, cores = 1, cluster = NULL, ...) \method{print}{multistart}(x, ...) @@ -21,7 +27,10 @@ multistart(object, n = 50, cores = 1, ...) \item{n}{How many different combinations of starting parameters should be used?} -\item{cores}{How many fits should be run in parallel?} +\item{cores}{How many fits should be run in parallel (only on posix platforms)?} + +\item{cluster}{A cluster as returned by \link[parallel:makeCluster]{parallel::makeCluster} to be used +for parallel execution.} \item{\dots}{Passed to the update function.} @@ -40,9 +49,6 @@ inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021). } \details{ -Currently, parallel execution of the fits is only supported using -\link[parallel:mclapply]{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 @@ -68,7 +74,13 @@ f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) 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") } } |