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
* Fix custom reference_data support in as.sir() (#239)
- custom guideline names now correctly classify values as R: CLSI convention
(>= breakpoint_R for MIC, <= for disk) applies only when guideline contains
"CLSI"; all other guidelines including custom ones use the EUCAST convention
(> breakpoint_R for MIC, < for disk)
- guideline argument is now optional when reference_data is manually set: if
omitted or if its value does not match any row in the custom data, all rows
in reference_data are used; if set to a value present in the data, only
matching rows are filtered — useful for multi-guideline custom tables
- host = NA in custom reference_data now acts as a host-agnostic fallback
when no host-specific breakpoint row exists for the current animal species
- updated reference_data argument documentation to explain these conventions
https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
* Refactor R-classification logic using custom_breakpoints_set flag
Introduce custom_breakpoints_set <- !identical(reference_data, AMR::clinical_breakpoints)
at the top of as_sir_method() and replace all identical() calls inside that
function with this variable.
In the case_when_AMR interpretation blocks (MIC and disk), the R-classification
now has three explicit arms:
- !custom_breakpoints_set & EUCAST guideline -> open interval (> / <)
- !custom_breakpoints_set & CLSI guideline -> closed interval (>= / <=)
- custom_breakpoints_set -> open interval (> / <), always,
regardless of the guideline name in the custom data (e.g. "CLSI_custom"
must not accidentally trigger CLSI convention)
https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
* Fix unit tests for custom reference_data (#239)
- Do not override my_bp$mo / my_bp$ab in tests: assigning plain character
strips the <mo>/<ab> class, which check_reference_data() rejects. Use the
mo/ab values already present in the source row instead.
- Use NA_character_ instead of NA for my_bp$host so the host column keeps
its character class.
- Pass breakpoint_type = "animal" explicitly in the host-fallback test since
the custom reference_data only contains animal-type breakpoints.
https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
* Add coerce_reference_data_columns() for lenient reference_data validation
check_reference_data() now returns the (possibly coerced) reference_data and
the call site captures the result so downstream code sees the fixed columns.
A new coerce_reference_data_columns() helper is called before the strict class
check inside check_reference_data(). It coerces columns to the expected types:
- mo -> as.mo() if not already <mo> class
- ab -> as.ab() if not already <ab> class
- character columns -> as.character() (e.g. host = NA becomes NA_character_)
- numeric columns -> as.double()
- logical columns -> as.logical()
This allows users to build a custom reference_data from a plain data.frame
without having to pre-apply as.mo()/as.ab() or worry about NA column types.
Updated the reference_data roxygen argument to document the auto-coercion and
restored the tests to the simpler form that uses plain character assignments,
relying on the new coercion instead of workarounds.
https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
---------
Co-authored-by: Claude <noreply@anthropic.com>
* Fix parallel computing in as.sir.data.frame
Six bugs in parallel = TRUE mode:
1. PSOCK workers (Windows / R < 4.0) never had AMR loaded, so every
exported/AMR function call failed. Added clusterEvalQ(cl, library(AMR))
with a graceful fallback to sequential when the package cannot be loaded
(e.g. dev-only load_all() environments).
2. clusterExport'd AMR_env was a frozen serialised copy; as.sir() on the
worker wrote to AMR:::AMR_env while run_as_sir_column read from the stale
copy, so the captured log was always wrong. Fixed by resolving AMR_env
dynamically via get("AMR_env", envir = asNamespace("AMR")) inside the
worker function, and removing AMR_env from clusterExport.
3. In the fork-based (mclapply) path each worker inherited the parent's full
sir_interpretation_history. Capturing the whole log then combining across
workers duplicated every pre-existing entry. Fixed by recording the log
row count before the as.sir() call and slicing only the new rows
afterwards.
4. run_as_sir_column used non-exported internals (%pm>%, pm_pull,
as.sir.default) that are inaccessible on PSOCK workers after library(AMR).
Replaced pipe chains with direct as.mic(as.character(x[, col, drop=TRUE]))
and as.disk(...) calls, and changed as.sir.default() to as.sir() which
dispatches correctly via S3.
5. With info = TRUE, worker forks printed per-column progress messages
simultaneously, producing garbled interleaved console output. Per-column
messages are now suppressed inside workers (effective_info = FALSE) while
the outer "Running in parallel" / "DONE" messages still appear.
6. Malformed Unicode escape \u00a (3 hex digits) in the "DONE" banner was
parsed by R as U+00AD (soft hyphen) + "ONE"; corrected to .
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Add parallel computing tests to test-sir.R
Eight targeted tests verify correctness of the parallel as.sir() path:
identical SIR output vs sequential, matching log row counts, no
pre-existing history duplication, reproducibility across runs, results
consistency across max_cores values, single-column fallback, and no
per-column worker messages leaking when info = TRUE. All pass when only
1 core is available (parallel silently falls back to sequential).
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Fix as.sir() data.frame: preserve already-<sir> columns, exclude metadata
Issue #278: two related bugs in the column-detection / type-assignment pipeline.
Bug 1 – already-<sir> columns deleted on re-run
Line 886 excluded already-sir columns from the type assignment (they
stayed type "") causing the result loop to do x[,col] <- NULL, deleting
them. Fix: drop the !is.sir() guard so all untyped columns fall through
to type "sir" and are re-processed correctly.
Bug 2 – metadata columns treated as antibiotics
as.ab("patient") -> OXY, as.ab("ward") -> PRU. The column detector
accepted any column whose name matched an antibiotic code, regardless of
content. Fix: for name-matched columns that do not already carry an AMR
class, also verify content looks like AMR data (all_valid_mics, all-
numeric, or any SIR-like string). all_valid_disks() is intentionally
avoided here because it strips letters from strings (as.disk("Pt_1")==1).
Also adds tools/benchmark_parallel.R: a standalone script that times
sequential vs parallel as.sir() across n=20/200/2000/20000 rows and
saves a ggplot2 PNG to tools/benchmark_parallel.png.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Update benchmark: two-panel script with warm-up and column-count sweep
Previous single-panel benchmark was misleading: the first sequential run
paid one-time cache-warm-up cost (skewing n=20), and only 6 columns were
used so only 6 cores were ever active on a 16-core machine.
New two-panel design:
Left – vary rows with 16 fixed AB columns (shows memory-bandwidth
saturation for large n)
Right – vary columns with fixed rows (shows the real speedup profile:
parallel wins when n_cols >> 1)
Also adds a warm-up pass before measurements to eliminate first-call bias.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Optimise parallel as.sir(): row-batch mode when n_cols < n_cores
Previously parallel dispatch only parallelised by column, so a 6-column
dataset on a 16-core machine used at most 6 cores with the other 10 idle.
For large n this also caused memory-bandwidth saturation (each worker did
a full n-row scan of clinical_breakpoints simultaneously).
New row-batch mode (fork path, R >= 4.0, non-Windows):
pieces_per_col = ceil(n_cores / n_cols)
Jobs = n_cols × pieces_per_col (≈ n_cores jobs total)
Each job: one column × one row slice
Benefits:
- All cores stay busy regardless of column count
- Per-worker memory footprint shrinks by pieces_per_col ×
- Breakpoints lookup cache pressure reduced per worker
PSOCK path (Windows / R < 4.0) is unchanged: per-job serialisation
overhead makes row batching unprofitable there.
run_as_sir_column() gains an optional `rows` parameter (NULL = all rows,
backward-compatible). Results are reassembled via as.sir(c(as.character(.)))
which is safe for already-clean SIR values.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Fix info=FALSE ignored when no breakpoints found in as_sir_method
Operator-precedence bug at line 1601:
if (isTRUE(info) && nrow(df_unique) < 10 || nrow(breakpoints) == 0)
R evaluates && before ||, so this was equivalent to:
(isTRUE(info) && nrow(df_unique) < 10) || (nrow(breakpoints) == 0)
When nrow(breakpoints) == 0 (e.g. cefoxitin / flucloxacillin / mupirocin
against E. coli in EUCAST) the intro message was always printed regardless
of info. Fix: add parentheses so info gates both conditions:
isTRUE(info) && (nrow(df_unique) < 10 || nrow(breakpoints) == 0)
Also pass print = isTRUE(info) to progress_ticker so the progress bar
(which prints intro_txt as its title) is suppressed when info = FALSE.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Fix cli formatting in as.sir() messages
- stop_if for empty ab_cols: wrap as.mic() and as.disk() in
{.help [{.fun ...}](...)} for clickable links in cli output
- Parallel mode message: use {.field col} formatting for column names
and quotes = FALSE in vector_and(), consistent with the rest of the
codebase (avoids double-quoting from both font_bold and quotes="'")
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Use font_bold() inside {.field} for column names in parallel message
Convention: paste0("{.field ", font_bold(col), "}") gives bold green
column names without quotation marks, consistent with the rest of the
codebase (e.g. the 'Cleaning values' message in run_as_sir_column).
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Add collapse = NULL to font_bold() for column name vectors
font_bold() without collapse = NULL joins a vector with "" into a single
string, breaking paste0() element-wise formatting for length > 1 vectors.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
* Add tools/ to .Rbuildignore
Keeps the benchmark script out of the built package tarball.
https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
---------
Co-authored-by: Claude <noreply@anthropic.com>
* Modernise messaging infrastructure with cli support
Rewrites message_(), warning_(), stop_() to use cli::cli_inform(),
cli::cli_warn(), and cli::cli_abort() when the cli package is available,
with a fully functional plain-text fallback for environments without cli.
Key changes:
- New cli_to_plain() helper converts cli inline markup ({.fun}, {.arg},
{.val}, {.field}, {.cls}, {.pkg}, {.href}, {.url}, etc.) to readable
plain-text equivalents for the non-cli fallback path
- word_wrap() simplified: drops add_fn, ANSI re-index algorithm, RStudio
link injection, and operator spacing hack; returns pasted input unchanged
when cli is available
- stop_() no longer references AMR_env$cli_abort; uses pkg_is_available()
directly; passes sys.call() objects to cli::cli_abort() call= argument
- Removed add_fn parameter from message_(), warning_(), and word_wrap()
- All call sites across R/ updated: add_fn arguments removed, some paste0-
based string construction converted to cli glue syntax ({.fun as.mo},
{.arg col_mo}, {n} results, etc.)
- cli already listed in Suggests; no DESCRIPTION dependency changes needed
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace {.fun} with {.help} for all exported functions in messaging
All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Qualify all {.help} tags with AMR:: and convert backtick ?func references
- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Require cli >= 3.0.0 for cli_inform/cli_warn/cli_abort availability checks
cli_inform, cli_warn, and cli_abort were introduced in cli 3.0.0.
Add min_version = "3.0.0" (as character) to all four pkg_is_available("cli")
checks so older cli versions fall back to base R messaging.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Implement cli::code_highlight() for R code examples in messages (issue #191)
Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.
Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.
Fixes#191https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.
Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.
Dynamic cases in amr_selectors.R and mo_property.R also updated.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Add {.topic} markup for non-function help page references
Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.
Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).
Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.
Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix {.topic} to use required pkg::topic format with display text
{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).
Use the [display_text](pkg::topic) form throughout:
{.topic [AMR-options](AMR::AMR-options)}
{.topic [AMR-deprecated](AMR::AMR-deprecated)}
The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.
The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix regexec() calls: remove perl=TRUE unsupported in older R
regexec() only gained the perl argument in R 4.1.0. The CI matrix
covers oldrel-1 through oldrel-4 (R 3.x/4.0.x), so perl=TRUE caused
an 'unused argument' error on every message_() call in those
environments.
All four affected regexec() calls use POSIX-extended compatible
patterns, so dropping perl=TRUE is safe.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Slim CI matrix for PRs to ubuntu-latest / r-release only
For pull requests, check-recent now runs a single job (ubuntu-latest,
r-release) via a setup job that emits the matrix as JSON. On push and
schedule the full matrix is unchanged (devel + release on all OSes,
oldrel-1 through oldrel-4).
Also removed the pull_request trigger from check-recent-dev-pkgs; the
dev-packages check only needs to run on push/schedule.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Restrict dev-versions and old-tinytest CI to main branch only
Both workflows were triggering on every push to every branch.
Narrowed push trigger to [main] so they only run after merging,
not on every feature/PR branch push.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Update NEWS.md to continuous log + add concise style rules to CLAUDE.md
NEWS.md is now a single continuous log under one heading per dev series,
not a new section per version bump. CLAUDE.md documents: only replace
line 1 (heading), append new entries, keep them extremely concise with
no trailing full stop.
Merged 9035 and 9036 entries into one section; condensed verbose 9036
bullets; added CI workflow change entry.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace single-quoted literals in messaging calls with cli markup
Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')
Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging
- 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)}
- "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax
- Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}}
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace glue-style dynamic markup with paste0() construction
{.field {variable}} and {.cls {variable}} patterns rely on glue
evaluation which is not safe in a zero-dependency package. Replace
all four occurrences with paste0("{.field ", var, "}") so the value
is baked into the markup string before reaching message_()/stop_().
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in check-recent workflow
push: branches: '**' caused both the push event (9-worker matrix) and
the pull_request event (1-worker matrix) to fire simultaneously on every
PR commit. Restricting push to [main] means PR pushes only trigger the
pull_request path (1 worker), while direct pushes to main still get the
full 9-worker matrix.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in code-coverage workflow
Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace bare backticks with cli inline markup across all messaging calls
- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Pre-evaluate inline expressions, add format_inline_(), fix print.ab
- All bare {variable}/{expression} in message_()/warning_()/stop_() calls
are now pre-evaluated via paste0(), so users without cli/glue never see
raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R,
antibiogram.R, atc_online.R)
- Add format_inline_() helper: formats a cli-markup string and returns it
(not emits it), using cli::format_inline() when available and cli_to_plain()
otherwise
- Rewrite .onAttach to use format_inline_() for all packageStartupMessage
calls; also adds {.topic} link and {.code} markup for option names
- print.ab: pre-evaluate function_name via paste0 (no .envir needed),
apply highlight_code() to each example bullet for R syntax highlighting
- join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* Replace all "in \`funcname()\`:" with {.help [{.fun funcname}](AMR::funcname)}
Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.
Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* definitive
* version fix
---------
Co-authored-by: Claude <noreply@anthropic.com>
* 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>
