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* mdro(): infer base drug resistance from drug+inhibitor combination columns (#209) When a base beta-lactam column (e.g., piperacillin/PIP) is absent but a corresponding drug+inhibitor combination (e.g., piperacillin/tazobactam/TZP) is present and resistant, resistance in the base drug is now correctly inferred. This is clinically sound: resistance in a combination implies the inhibitor provided no benefit, so the base drug is also resistant. Susceptibility in a combination is NOT propagated to the base drug (the inhibitor may be responsible for susceptibility), so only R values are inferred; missing base drugs remain NA otherwise. Implementation details: - Uses AB_BETALACTAMS_WITH_INHIBITOR to identify all beta-lactam+inhibitor combinations present in the user's data - Derives base drug AB codes by stripping the "/inhibitor" part from names - Creates synthetic proxy columns (.sir_proxy_<AB>) in x, set to "R" when any matching combination is R, otherwise NA - Proxy columns are added to cols_ab before drug variable assignment, so all existing guideline logic benefits without any changes - Multiple combos for the same base drug are OR-ed (any R → R) - Adds internal ab_without_inhibitor() helper for the name->base mapping - Verbose mode reports which combinations are used for inference Bumps version: 3.0.1.9028 -> 3.0.1.9029 https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG * Add sir.R/mic.R fixes and mdro() unit tests; bump to 3.0.1.9030 R/sir.R (line 571): Guard purely numeric strings (e.g. "1", "8") from the Unicode letter filter. Values matching the broad SIR regex but consisting only of digits must not be stripped; add `x %unlike% "^[0-9+]$"` predicate. R/mic.R (lines 220-222): Preserve the letter 'e' during Unicode-letter removal so that MIC values in scientific notation (e.g. "1e-3", "2.5e-2") survive the cleaning step. - Line 220: [\\p{L}] → [^e\\P{L}] (remove all letters except 'e') - Line 222: [^0-9.><= -]+ → [^0-9e.><= -]+ (allow 'e' in whitelist) tests/testthat/test-mdro.R: New tests for the drug+inhibitor inference added in the previous commit (issue #209): - TZP=R with no PIP column → PIP inferred R → MDRO class elevated - TZP=S with no PIP column → proxy col is NA (not S) → class lower - verbose mode emits "Inferring resistance" message - AMC=R with no AMX column runs without error (Enterococcus faecium) https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG * Fix version to single bump (9029) and update CLAUDE.md versioning rules CLAUDE.md: Rewrite the "Version and date bump" subsection to document that: - Exactly ONE version bump is allowed per PR (PRs are squash-merged into one commit on the default branch, so one commit = one version increment) - The correct version is computed from git history: currentversion="${currenttag}.$((commits_since_tag + 9001 + 1))" with the +1 accounting for the PR's own squash commit not yet on the default branch - Fall back to incrementing DESCRIPTION's version by 1 if git describe fails - The Date: field tracks the date of the *last* PR commit (updated each time) DESCRIPTION / NEWS.md: Correct the version from 3.0.1.9030 back to 3.0.1.9029. Two version bumps were made across two commits in this PR; since it will be squash-merged as one commit only one bump is correct. Also update Date to today (2026-03-07). https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG * Fix stats::setNames, test accessor bug, and version script verification R/mdro.R: Qualify setNames() as stats::setNames() in the drug+inhibitor inference block to satisfy R CMD CHECK's global-function checks. tests/testthat/test-mdro.R: mdro() with verbose=FALSE returns an atomic ordered factor, not a data.frame. Fix three test errors introduced in the previous commit: - Line 320: result_no_pip$MDRO -> result_no_pip (factor, no $ accessor) - Line 328: result_tzp_s$MDRO / result_no_pip$MDRO -> direct factor refs - Line 347: expect_inherits(..., "data.frame") -> c("factor","ordered") Also fix the comment on line 347 to match the actual return type. Version: confirmed at 3.0.1.9029 (no further bump; one bump already made this PR). git describe failed (no tags in dev environment) — fallback applies. The +1 in CLAUDE.md's formula is correct for tagged repos: currentcommit + 9001 + 1 = 27 + 9001 + 1 = 9029 ✓ https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG * Fix unit tests: use mrgn guideline and expect_message() for proxy tests Three failures corrected: 1. Classification tests (lines 321, 329): The EUCAST guideline for P. aeruginosa already has OR logic (PIP OR TZP), so TZP=R alone satisfies it regardless of whether the PIP proxy exists. Switch to guideline="mrgn": the MRGN 4MRGN criterion for P. aeruginosa requires PIP=R explicitly (lines 1488-1496 of mdro.R), with no TZP fallback. Without the proxy: PIP missing -> not 4MRGN -> level 1. With the proxy (TZP=R infers PIP=R): 4MRGN reached -> level 3. The TZP=S case leaves proxy=NA, so PIP is still absent effectively -> level 1, which is < level 3 as expected. 2. Verbose/message test (line 335): message_() routes through message() to stderr, not cat() to stdout. expect_output() only captures stdout so it always saw nothing. Fix: use expect_message() instead, and remove the inner suppressMessages() that was swallowing the message before expect_message() could capture it. Also trim two stale lines left over from the old expect_output block. https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG --------- Co-authored-by: Claude <noreply@anthropic.com>
75 lines
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75 lines
4.6 KiB
Plaintext
Package: AMR
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Version: 3.0.1.9029
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Date: 2026-03-07
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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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ggplot2,
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knitr,
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openxlsx,
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parallelly,
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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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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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