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
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
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
