- parallel = TRUE now errors with a cli-styled message if no non-sequential
future::plan() is active; users must call e.g. future::plan(future::multisession)
before using parallel = TRUE (breaking change)
- Removed auto-setup/teardown of multisession plan inside as.sir(), which was
slow and caused version-mismatch issues with load_all() workflows
- Added as_wt_nwt to the exclusion list in as_sir_method() to suppress
false-positive "no longer used" warnings during parallel runs
- Fixed pieces_per_col row-batch calculation to use n_workers (total available
workers from the active plan) instead of n_cores (workers clipped to n_cols),
so row-batch mode activates correctly when n_cols < n_workers
- Updated @param parallel and @param max_cores roxygen docs; regenerated man/as.sir.Rd
- Updated sequential-mode hint to instruct users to set plan() first
https://claude.ai/code/session_01M1Jvf2Miu6JL4TQrEh1wS8
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>
* fix: convert Python lists to R vectors in wrapper to prevent R list coercion errors
Fixes#267. Python lists passed to R functions via rpy2 are received as
R lists, not R character/numeric vectors. This causes is.mic(), is.sir(),
is.disk() etc. to return length > 1 logicals, which break R's && operator.
Added convert_to_r() helper that maps Python list/tuple to the appropriate
typed R vector (StrVector, IntVector, FloatVector) based on element types.
The r_to_python decorator now applies this to all args and kwargs before
calling the R function.
* docs: instruct Claude to install git and gh before computing version
* 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>
* fix: restore valid AB codes mangled by generalise_antibiotic_name() (#245)
When as.ab() received a vector containing both valid AB codes (like ETH,
PHN, PHE, STH, THA, MTH, THI1) and an untranslatable value, the fast
path at line 100 was skipped. The slow path then applied
generalise_antibiotic_name(), which rewrites "TH"->"T" and "PH"->"F",
mangling these short AB codes (e.g. ETH->"ET", PHN->"FN") so they could
no longer be found in the lookup table.
Fix: save the pre-generalised values before applying
generalise_antibiotic_name(), then restore any elements that were already
valid AB codes in their original form.
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* fix: use toupper() in AB code restoration to handle lowercase input (#245)
Ensures that lowercase user input (e.g. 'eth', 'phn') is matched
case-insensitively against the uppercase AB codes in $ab, and that
the restored value is stored in uppercase to match the lookup table.
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* revert: remove unnecessary toupper() since x is already uppercased
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* Revise versioning and date bump requirements for PRs
Updated versioning instructions for pull requests to include date bump.
---------
Co-authored-by: Claude <noreply@anthropic.com>
* add CLAUDE.md with project context for Claude Code
Provides development commands, architecture overview, file conventions,
custom S3 classes, data files, testing setup, and versioning guidelines
to help Claude Code assist effectively in this repository.
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
* add CLAUDE.md to .Rbuildignore
Excludes the Claude Code context file from the R package build tarball.
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
* document version-bump requirement for every PR in CLAUDE.md
Each PR must increment the .9zzz dev counter by 1 in both
DESCRIPTION (Version: field) and NEWS.md (top-level heading).
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
---------
Co-authored-by: Claude <noreply@anthropic.com>
