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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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man/custom_eucast_rules.Rd
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@@ -19,7 +19,7 @@ Define custom EUCAST rules for your organisation or specific analysis and use th
Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function.
\subsection{Basics}{
If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
TZP == "R" ~ aminopenicillins == "R")