⚠️ SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026).
Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
Plotting:
- Base colours and legends of interpreted MIC and disk values on the interpretation itself instead of matching colours
- Fix SDD in autoplot() for disks, the colours of barplot() for SIR values, and barplot() for MICs ignoring language and expand
- Match a named colours_SIR by name; let keep_operators = TRUE/FALSE in scale_*_mic() behave as "all"/"none"
- Let a named values in scale_*_sir() replace the colours it names, warn in scale_x_sir(), and pass other arguments on
- Let the default of eucast_I follow the guideline option, also for EUCAST before 2019
- Support unquoted column names in facet_sir() without evaluating them
- Correct the documentation and examples
Translations:
- Add SDD, NS, WT and NWT, and correct S, I, R and NI in 18 languages
- Sources of the terms for 'I': NAK via German laboratories (de), SZU national reference laboratory (cs), lex.dk (da), Karolinska University Hospital (sv), COESANT (es), Nordlab (fi), CA-SFM (fr); no by analogy with da and sv
- Not verified against an official source: ar, bn, el, hi, id, ja, ko, pl, ro, ru, sw, tr, uk, ur, vi, zh
Tests:
- Let the grouped antibiogram test use English so it passes in other locales
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
The pruning of blocking rows in the EUCAST reproduction script now compares UTI status too, and the script is fixed for the renamed column of the as.ab() coercion cache. In clinical_breakpoints, only the blocking rows were replaced (356 organism/agent/method combinations newly blocked, none unblocked); other changes of a full rebuild, caused by taxonomy updates in the WHONET-based rows, are not included.
* Update taxonomy of microorganisms (2026-10)
Rebuild of the microorganisms data set from COL 2026-04-18 XR, LPSN and BacDive of October 2026
and MycoBank of January 2026, with v3.0.1 as the previous data set: 111,103 records (v3.0.1:
78,679), 0 changed MO codes of existing names, 522 released codes retired (275 to be reviewed).
Script fixes (data-raw/_reproduction_scripts/reproduction_of_microorganisms.R):
- previous data set from the last release; COL read as COL Data Package (NameUsage.tsv)
- keep COL records without authors (a filter on NA dropped them, e.g. Balamuthia mandrillaris)
- genus homonyms: unclassified MycoBank entries are not authoritative; the released domain of a
genus wins if a source supports it (e.g. Moorella, Serpula, Pirella stay Bacteria)
- protect current names of relevant species instead of whole current genera (data set tripled)
- current names and synonyms only within the same domain and for known names (Brugia -> Lycoperdon)
- MycoBank names in Latin script only; old records outside their source's scope become manually added
- Graphium butterflies of v3.0.1 are not carried over, re-added or restored
- restore released taxa by name and rank; retire older cross-domain homonyms for review
- fill empty families from COL and a commented override list (Ascaris, Balamuthia)
- add Brugia malayi and B. timori; remove Salmonella species synonyms that are serovars
- BacDive: a minority of facultative strain records no longer decides (C. difficile)
- translate codes of other data sets with the development version; review unmatched codes
- scope decisions: COL XR names only if relevant or released; Protozoa follow the Fungi rules
Also: all checkpoints (data-raw/taxonomy*.rds), updated data sets, Bartlett et al. list, accessed
dates in TAXONOMY_VERSION, NEWS, two staphylococci added to CoNS, tests updated for real taxonomic
changes, known defects file removed (all solved), and the findings report with all review files in
data-raw/taxonomy_review/2026-10/.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: note on the .dta export and the single commit
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Fix as.mo() for Salmonella serovars written with the species; add S. xeri to CoNS
- "Salmonella enterica (subsp. enterica) serovar Typhi" returned S. bongori, and
"S. enterica Typhimurium" S. enterica diarizonae; "Paratyphi A/B/C" became serogroups
- Staphylococcus xeri and S. parequorum confirmed as coagulase-negative
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy build: remove lichens (decision of 5 October 2026)
Fungi in the lichen-forming classes and the order Verrucariales are removed unless their genus is
clinically relevant, with the synonyms that point to them (4,155 records); released lichens are
restored. microorganisms now has 107,126 records (Fungi 45,739); all tests pass.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review decisions: microsporidia in Fungi, accepted names, missing protozoa
- all microsporidia in the Fungi (1,394 names of v3.0.1 from P_ to F_, old codes translated by name)
- Enterocytozoon bieneusi and Encephalitozoon cuniculi as accepted names (accepted_name_override)
- Balantidium and Isospora added to MO_RELEVANT_GENERA; Cystoisospora belli as synonym of Isospora belli
- synonym cycles decided: Capillidium and Scolecobasidium are the current genera
- removed the stale data-raw/taxonomy_lpsn0.rds
- microorganisms now has 107,253 records; all tests pass
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: all items reviewed
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Rule matching by accepted taxon; Erysipelatoclostridium as synonym of Thomasclavelia
- interpretive_rules(): species named in a rule (literal names, genus_species/fullname) now also match all other
names of the same accepted taxon, e.g. 'Clostridium ramosum' for Thomasclavelia ramosa; not for genera or regex rules
- Erysipelatoclostridium and its species are synonyms of Thomasclavelia (accepted_name_override); E. merdavium is
retired by decision of 6 October 2026, and the build removes taxa retired by a human decision
- microorganisms patched with the same logic as the build script (no full rebuild): 107,252 records
- intrinsic_resistant regenerated with the new taxonomy and rule matching: 308,646 rows
- clinical_breakpoints: EUCAST workbook rows merged again, 24 EUCAST 2026 rows moved from C. ramosum to T. ramosa
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy: correct records for names listed twice, no synonyms without a current name, strict data tests
- one record per name keeps the accepted record (e.g. Eggerthella lenta, Gordonia amarae, Anisakis simplex and
Enterobius vermicularis were synonyms without a current name), links to dropped records are moved
- LPSN lookup reads the taxonomic status and correct name; validly published synonyms are no longer 'accepted'
- synonyms without a current name: linked via LPSN or removed, released codes retired (3,668); records with kept
children become 'unknown'; the M. tuberculosis complex is protected (decisions of 7 October 2026)
- subspecies codes reserved, current names of synonyms kept when pruning, missing parent records added or moved,
higher taxonomy harmonised, shared identifiers resolved per domain and rank, pointers and parent links cleaned
- data sets refer only to current names (except intrinsic_resistant); group members only from current names;
internal CoNS/CoPS/streptococcal lists keep a synonym only with its current name
- intrinsic_resistant, clinical_breakpoints (EUCAST workbooks) and microorganisms.groups regenerated
- 28 new tests in test-data.R; devtools::test(): 1,581 expectations, 0 failures
- open decisions listed in data-raw/taxonomy_review/2026-10/REPORT.md, section 6
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy: protect WHO priority genera, follow LPSN for the M. tuberculosis complex, place protist groups in one domain
- all taxa of the genera in MO_WHO_PRIORITY_GENERA are protected, also names that are not validly published
(replaces the hard-coded M. tuberculosis complex; keeps e.g. Klebsiella quasivariicola, M. canettii, M. orygis)
- LPSN is followed for the M. tuberculosis complex: M. bovis, M. africanum, M. caprae, M. microti and M. pinnipedii
are heterotypic synonyms of M. tuberculosis (Riojas et al. 2018); a test enforces this
- labyrinthulids in the Chromista (Aplanochytrium), Dictydiaethalium in the Protozoa (genus_domain_move), and the
rank suffix also between domains ('Acantharia {class}' next to the fungal genus Acantharia)
- devtools::test(): 1,582 expectations, 0 failures
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy build no longer depends on the previous build
- intrinsic_resistant is no input of the microorganisms build anymore (it is computed from it); the genera named in
the interpretive rules are read from the rules instead
- the previous data set no longer makes genera relevant; Debaryomyces added to MO_RELEVANT_GENERA
- new run_after_microorganisms_build.R recreates microorganisms.groups, the EUCAST breakpoints and
intrinsic_resistant in the right order, and the build runs it at its end
- reproduction_of_intrinsic_resistant.R uses devtools::load_all() instead of the installed package
- effect: 24 never released, not relevant COL records less; devtools::test(): 1,582 expectations, 0 failures
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: summary updated to the second round
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* MO code retirements: mark the 265 reviewed retirements as reviewed
The Graphium and v2.x Protozoa retirements were reviewed and accepted on 6 October 2026 (see the taxonomy review
report, section 5); 'NEEDS REVIEW' is replaced by 'reviewed by Matthijs S. Berends on 2026-10-06'.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
The pre-commit URL extractor captured the closing brace of \url{}, which
made the EC server redirect to the dead health.ec.europa.eu domain, after
which urlchecker::url_update() wrote that dead URL back into R/ab.R and R/av.R.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- Aerococcus rules now use `one_of`, so multi-species rules (breakpoints v12 onwards) apply
- Pasteurella rules filed under Neisseria meningitidis moved to their own rule
- Pasteurella rules now apply on genus level
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- test-data-microorganisms.R: warnings are wrapped to the console width, so the expected patterns now
allow a line break between words (failed on GitHub Actions since v3.0.1.9097)
- reproduction_of_microorganisms_CLAUDE.md, step 4: the agent never changes the version number or date,
the human sets them when merging
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- the list of known defects is development data and must not ship with the package
- tests read it from the source repository; mo_repository_root() now walks up from the working
directory, so the tests also find the repository from an R CMD check directory inside it (GitHub Actions)
- the integrity, known-defects and sentinel tests skip when the source repository is not available
- CLAUDE.md: on local commits to main, the git hooks set the version number and date
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
As curated in data-raw/Species groups.xlsx since July 2023; the released v3.0.1 data still
used 'Mycobacterium avium-intracellulare complex' for the same group of organisms.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- taxonomy build: released taxa (since v2.0.0) that are missing are restored from their
last release with their old code and last known status, and are exempt from later
removals (decision by Matthijs S. Berends)
- exceptions are retired on purpose in data-raw/microorganisms_files/mo_code_retirements.csv
with a reason: other organisms with the same genus name (e.g. the Graphium butterflies,
wrongly in the Fungi until v3.0.1) and taxa whose genus is now only known in another
domain; as.mo() translates these codes to NA with that reason
- synonyms without a current name are linked to an accepted name in the same genus that
only differs by a Latin gender ending (e.g. Candida glabratus -> Nakaseomyces glabratus)
- placeholders such as "(unknown class)" never become records; codes of manually added
records are matched by domain and name
- integrity rule released_taxon_missing; known defects of the data on main updated
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- data-raw/microorganisms_files/: registry of all MO codes of every release since v2.0.0
(78,992 codes, built from the git tags), approved renames, and README with the rules;
decision by Matthijs S. Berends: MO codes from before v2.0.0 are not supported
- as.mo(): codes of earlier releases are translated deterministically via the internal
MO_RETIRED_CODES (generated from the registry); unknown codes are no longer guessed
(previously F_TRCHP, Trichophyton in v3.0.1, became Talaromyces chlamydosporus)
- synonym_mo_to_accepted_mo(): a missing target of one source no longer overwrites a valid
target of another source (e.g. Chaetomium abuense), and no 'renamed to itself'
- taxonomy build: codes are reused and reserved from the registry instead of the development
data (fixes 40 codes reused in the 2026 development data), also for phylum to family;
synonym cycles are broken; dangling 'renamed to' identifiers are removed; the build stops
on any broken integrity rule before saving
- run_microorganisms_build.R: runs the build in chunks at its checkpoints in one R process,
with progress logging and resuming from any checkpoint; prompt updated accordingly
- tests: shared integrity rules (helper-microorganisms.R) used by build and testthat, registry
tests over all codes, sentinel organisms, regression tests; current defects of the data on
main are listed in microorganisms_known_defects.csv until the next rebuild
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Review of reproduction_of_microorganisms.R against the 2026 intermediates:
- genus homonyms: overrides, LPSN/MycoBank first, status within LPSN/MycoBank,
move misplaced protists, remove true homonyms (Necator, Capillaria, Graphium)
- keep clinically relevant names that are not validly published (Tropheryma)
- one set of relevant genera for all filters; 30 genera added to MO_RELEVANT_GENERA
- MycoBank classification parsed from all columns; empty values never overwrite
- GBIF synonyms in another genus get the lineage of their own genus
- prevalence no longer copied from genus; current names inherit from synonyms
- inferred records follow the relevance filters (no more unrelated lichens)
- ASCII names before deduplication (12 duplicate full names in 2026)
- MO codes: robust code parsing, reserved old codes, single allocator,
domain column used directly (2026 rename would now fail)
- name clean-up applied to taxonomy before MO codes, BacDive rows filled
- unattended running: review() instead of View(), CSV export of reviews,
LPSN cache and retries, stops when raw source files are missing
- reproduction_of_microorganisms_CLAUDE.md: prompt for an unattended run with
findings report and checklist for human review in the PR
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Genus resolution now prefers LPSN/MycoBank over GBIF, then accepted over
synonym, then source, then rank, and only then domain. Losing LPSN/MycoBank
homonyms are removed instead of moved into another domain. Adds integrity
checks that LPSN records stay prokaryotic and MycoBank records stay fungal.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Make the EUCAST Clinical Breakpoint Tables import (2019-2026) fail-safe:
- Add blocking rows (NA breakpoints, reason in `note`) where EUCAST gives
no breakpoint for an organism (IE, "-", Note, brackets, "except"
clauses, table scope), so as.sir() no longer falls back to broader taxa
- Apply restrictions from EUCAST notes via a curated rule table with a
completeness guard (e.g. zone diameters for E. coli only)
- Import PK-PD (non-species related) breakpoints 2019-2023, H.
parainfluenzae MIC breakpoints, and explicit screening thresholds from
notes (high-level aminoglycosides, cefoxitin MIC, unidentified CoNS)
- Parser fixes: lost Staphylococcus sheets 2019/2020, note keys and
bodies, struck-through cells, hidden sheets, missing disk contents,
organism groups, site vocabulary, MIC dilution levels, off-scale
breakpoints stored as 0.0001
- Keep EUCAST antifungal breakpoints 2019-2025 from WHONET; code WHONET
streptomycin as STR1 instead of STR (streptoduocin)
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
* Generalise interpretive rules for multi-guideline support (#268)
- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider
column (value: "EUCAST") to distinguish future CLSI rows
- Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R;
filter by rule.provider == guideline when applying rules in interpretive_rules()
- Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class
"custom_interpretive_rules"; old function becomes a deprecated wrapper in
zz_deprecated.R; backward-compat S3 dispatch shims added for old class
- Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors
- Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF
for transitional compatibility until sysdata.rda is regenerated
https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
* Fix namespace load failure: remove assignInNamespace from .onLoad (#268)
assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.
https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
* fixes
* fixes
---------
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
