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* Add parallel computing support to antibiogram() and wisca() (#281) For WISCA: simulations are distributed across (group, chunk) job pairs via future.apply::future_lapply(), keeping all workers active even when the regimen count is smaller than nbrOfWorkers(). Sequential fallback with progress ticker is preserved when parallel = FALSE or workers = 1. For grouped antibiograms: each group is processed by a separate worker, mirroring the row-batch approach in as.sir(). Same gate pattern as as.sir() (PR #280): requires a non-sequential future::plan() to be active; auto-upgrades to parallel = TRUE when a parallel plan is detected; throws an informative error otherwise. https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF * Fix version to 3.0.1.9055 and update CLAUDE.md version formula Uses origin/${defaultbranch} (with a fetch) instead of the local branch ref so the commit count is never stale after a merge. https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF * Fix non-ASCII characters in antibiogram.R Replace en/em dashes and non-breaking spaces with ASCII equivalents to satisfy R CMD check portability requirement. https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF * Update auto-generated Rd files after documentation rebuild https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF * Move parallel gate to top of antibiogram.default() like sir.R The gate was inside the wisca==TRUE block, so parallel=TRUE with a sequential plan was silently ignored for non-WISCA antibiograms. Now the gate runs unconditionally at the top of the function, identical to the as.sir() pattern: error on explicit parallel=TRUE with sequential plan, auto-upgrade when a non-sequential plan is already active. https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF * Fix parallel WISCA returning all NA; strengthen tests; add sequential hint Bug: lapply() over a factor yields length-1 factor elements (integer codes), while for() over a factor yields character strings. The job list stored j\$group as a factor integer, but the reassembly loop compared it with identical(j\$group, g) where g was character -- always FALSE, so no simulation chunks were ever assembled and coverage stayed NA throughout. Fix: convert unique_groups to character before building jobs so both the job list and the reassembly loop use the same type. Tests: replaced na.rm = TRUE guards with explicit anyNA() checks so the test suite would have caught the all-NA result immediately. Also adds a sequential-mode performance hint (analogous to sir.R lines 1116-1127) when simulations >= 500 and >= 3 regimens. https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF --------- Co-authored-by: Claude <noreply@anthropic.com>
77 lines
4.6 KiB
Plaintext
77 lines
4.6 KiB
Plaintext
Package: AMR
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Version: 3.0.1.9055
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Date: 2026-04-30
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
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Authors@R: c(
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person(given = c("Matthijs", "S."), family = "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
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person(given = c("Dennis"), family = "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
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person(given = c("Erwin", "E.", "A."), family = "Hassing", role = c("aut", "ctb")),
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person(given = c("Aislinn"), family = "Cook", role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
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person(given = c("Andrew", "P."), family = "Norgan", role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
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person(given = c("Anita"), family = "Williams", role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
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person(given = c("Annick"), family = "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
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person(given = c("Anthony"), family = "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
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person(given = c("Anton"), family = "Mymrikov", role = "ctb"),
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person(given = c("Bart", "C."), family = "Meijer", role = "ctb"),
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person(given = c("Christian", "F."), family = "Luz", role = "ctb", comment = c(ORCID = "0000-0001-5809-5995")),
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person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
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person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
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person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
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person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
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person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
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person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
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person(given = c("Jonas"), family = "Salm", role = "ctb"),
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person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
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person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
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person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
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person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
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person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
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person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
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person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
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person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
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person(given = c("Casper", "J."), family = "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
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person(given = c("Corinna"), family = "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")))
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Depends: R (>= 3.0.0)
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Suggests:
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cleaner,
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cli,
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crayon,
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curl,
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data.table,
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dplyr,
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future,
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future.apply,
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ggplot2,
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knitr,
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openxlsx,
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pillar,
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progress,
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readxl,
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recipes,
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rlang,
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rmarkdown,
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rstudioapi,
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rvest,
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skimr,
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testthat,
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tibble,
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tidymodels,
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tidyselect,
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tinytest,
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vctrs,
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xml2,
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usethis
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VignetteBuilder: knitr,rmarkdown
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URL: https://amr-for-r.org, https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.3
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Roxygen: list(markdown = TRUE, old_usage = TRUE)
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