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(v2.1.1.9259) Parallel computing for R < 4

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dr. M.S. (Matthijs) Berends 2025-04-27 20:25:39 +02:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.1.1.9258 Version: 2.1.1.9259
Date: 2025-04-27 Date: 2025-04-27
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 2.1.1.9258 # AMR 2.1.1.9259
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)* *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*

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R/sir.R
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@ -680,7 +680,7 @@ as.sir.disk <- function(x,
} }
#' @rdname as.sir #' @rdname as.sir
#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. This requires no additional packages, as the used `parallel` package is part of base \R. On Windows and on \R < 4.0.0 [parallel::parLapply()] will be used; in all other cases the most efficient [parallel::mclapply()] will be used. #' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. This requires no additional packages, as the used `parallel` package is part of base \R. On Windows and on \R < 4.0.0 [parallel::parLapply()] will be used, in all other cases the most efficient [parallel::mclapply()] will be used.
#' @param max_cores Maximum number of cores to use if `parallel = TRUE`. Use a negative value to subtract that number from the available number of cores, e.g. a value of `-2` on an 8-core machine means that at most 6 cores will be used. Defaults to `-1`. There will never be used more cores than variables to analyse. The available number of cores are detected using [parallelly::availableCores()] if that package is installed, and base \R's [parallel::detectCores()] otherwise. #' @param max_cores Maximum number of cores to use if `parallel = TRUE`. Use a negative value to subtract that number from the available number of cores, e.g. a value of `-2` on an 8-core machine means that at most 6 cores will be used. Defaults to `-1`. There will never be used more cores than variables to analyse. The available number of cores are detected using [parallelly::availableCores()] if that package is installed, and base \R's [parallel::detectCores()] otherwise.
#' @export #' @export
as.sir.data.frame <- function(x, as.sir.data.frame <- function(x,
@ -854,6 +854,12 @@ as.sir.data.frame <- function(x,
# set up parallel computing # set up parallel computing
n_cores <- get_n_cores(max_cores = max_cores) n_cores <- get_n_cores(max_cores = max_cores)
n_cores <- min(n_cores, length(ab_cols)) # never more cores than variables required n_cores <- min(n_cores, length(ab_cols)) # never more cores than variables required
if (isTRUE(parallel) && .Platform$OS.type != "windows" && getRversion() < "4.0.0") {
n_cores <- 1
if (isTRUE(info)) {
warning("Parallel computing is not available on unix in R < 4.0", call. = FALSE)
}
}
run_as_sir_column <- function(i) { run_as_sir_column <- function(i) {
ab_col <- ab_cols[i] ab_col <- ab_cols[i]

2
man/as.sir.Rd
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@ -138,7 +138,7 @@ The default \code{"standard"} setting ensures cautious handling of uncertain val
\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. This requires no additional packages, as the used \code{parallel} package is part of base \R. On Windows and on \R < 4.0.0 \code{\link[parallel:clusterApply]{parallel::parLapply()}} will be used; in all other cases the most efficient \code{\link[parallel:mclapply]{parallel::mclapply()}} will be used.} \item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. This requires no additional packages, as the used \code{parallel} package is part of base \R. On Windows and on \R < 4.0.0 \code{\link[parallel:clusterApply]{parallel::parLapply()}} will be used, in all other cases the most efficient \code{\link[parallel:mclapply]{parallel::mclapply()}} will be used.}
\item{max_cores}{Maximum number of cores to use if \code{parallel = TRUE}. Use a negative value to subtract that number from the available number of cores, e.g. a value of \code{-2} on an 8-core machine means that at most 6 cores will be used. Defaults to \code{-1}. There will never be used more cores than variables to analyse. The available number of cores are detected using \code{\link[parallelly:availableCores]{parallelly::availableCores()}} if that package is installed, and base \R's \code{\link[parallel:detectCores]{parallel::detectCores()}} otherwise.} \item{max_cores}{Maximum number of cores to use if \code{parallel = TRUE}. Use a negative value to subtract that number from the available number of cores, e.g. a value of \code{-2} on an 8-core machine means that at most 6 cores will be used. Defaults to \code{-1}. There will never be used more cores than variables to analyse. The available number of cores are detected using \code{\link[parallelly:availableCores]{parallelly::availableCores()}} if that package is installed, and base \R's \code{\link[parallel:detectCores]{parallel::detectCores()}} otherwise.}