P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-04-28 09:03:51 +02:00
Code Releases Activity

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

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

3
NEWS.md
View File

@@ -1,4 +1,4 @@
# AMR 3.0.1.9052
# AMR 3.0.1.9053
### New
* Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.
@@ -41,6 +41,7 @@
* Fixed `as.sir()` ignoring `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against *E. coli*): an operator-precedence bug (`&&`/`||`) caused the "Interpreting MIC values" intro message to fire unconditionally when `nrow(breakpoints) == 0`, regardless of `info`; the progress bar title was also not gated by `info`
### Updates
* `as.sir()` with `parallel = TRUE` now uses `future.apply::future_lapply()` instead of `parallel::mclapply()`/`parallel::parLapply()`, enabling transparent support for any `future` backend (including `mirai_multisession`) on all platforms; `future` and `future.apply` are now listed under `Suggests`
* `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (#239)
* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).