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Migrate parallel computing in as.sir() from parallel:: to future/future.apply

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Replace parallel::mclapply() and parallel::parLapply() with
future.apply::future_lapply(), enabling transparent support for any
future backend (multisession, multicore, mirai_multisession, cluster)
on all platforms including Windows.

When parallel = TRUE the function now: (1) respects an active
future::plan() set by the user without overriding it on exit, or
(2) sets a temporary multisession plan with parallelly::availableCores()
and tears it down on exit. The max_cores argument controls worker count
only when no user plan is active.

future and future.apply are added to Suggests in DESCRIPTION.

https://claude.ai/code/session_01M1Jvf2Miu6JL4TQrEh1wS8
This commit is contained in:
Claude
2026-04-27 12:21:48 +00:00
parent 3f1b20c304
commit b1cf7a94ad
10 changed files with 80 additions and 101 deletions
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11
man/as.sir.Rd
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@@ -150,9 +150,9 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain
\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}. The \code{parallel} package is part of base \R and no additional packages are required. On Unix/macOS with \R >= 4.0.0, \code{\link[parallel:mclapply]{parallel::mclapply()}} (fork-based) is used; on Windows and \R < 4.0.0, \code{\link[parallel:clusterApply]{parallel::parLapply()}} with a PSOCK cluster is used (requires the AMR package to be installed, not just loaded via \code{devtools::load_all()}). Parallelism distributes columns across cores; it is most beneficial when there are many antibiotic columns and a large number of rows.}
\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. Requires the \code{\link[future.apply:future_lapply]{future.apply}} package. If a non-sequential \code{\link[future:plan]{future::plan()}} is already active (e.g., set by the user via \code{future::plan(future::multisession)}), that plan is respected and left unchanged after the call. Otherwise, a temporary \code{multisession} plan is set automatically and torn down on exit. Parallelism distributes columns across workers; it is most beneficial when there are many antibiotic columns and a large number of rows.}
\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 workers to use if \code{parallel = TRUE} and no \code{\link[future:plan]{future::plan()}} has been set by the user. 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 at most 6 workers will be used. Defaults to \code{-1}. There will never be used more workers than variables to analyse. The number of available cores is detected using \code{\link[parallelly:availableCores]{parallelly::availableCores()}} if that package is installed, and base \R's \code{\link[parallel:detectCores]{parallel::detectCores()}} otherwise. This argument is ignored when the user has already set a \code{\link[future:plan]{future::plan()}}.}
\item{clean}{A \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results.}
}
@@ -183,7 +183,7 @@ your_data \%>\% mutate_if(is.mic, as.sir, ab = c("cipro", "ampicillin", ...), mo
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_species", guideline = "CLSI")
# fast processing with parallel computing:
# fast processing with parallel computing (requires future.apply):
as.sir(your_data, ..., parallel = TRUE)
}\if{html}{\out{</div>}}
\item Operators like "<=" will be considered according to the \code{capped_mic_handling} setting. At default, an MIC value of e.g. ">2" will return "NI" (non-interpretable) if the breakpoint is 4-8; the \emph{true} MIC could be at either side of the breakpoint. This is to prevent that capped values from raw laboratory data would not be treated conservatively.
@@ -201,7 +201,7 @@ your_data \%>\% mutate_if(is.disk, as.sir, ab = c("cipro", "ampicillin", ...), m
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_species", guideline = "CLSI")
# fast processing with parallel computing:
# fast processing with parallel computing (requires future.apply):
as.sir(your_data, ..., parallel = TRUE)
}\if{html}{\out{</div>}}
}
@@ -313,7 +313,8 @@ as.sir(df_wide)
sir_interpretation_history()
\donttest{
# using parallel computing, which is available in base R:
# using parallel computing (requires the future.apply package):
# future::plan(future::multisession) # optional: set your own plan first
as.sir(df_wide, parallel = TRUE, info = TRUE)