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Matthijs BerendsandClaude Opus 5.5
0ca43df459
* 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>
3.2 KiB
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3.2 KiB
Executable File
The AMR Package for R
Please visit our comprehensive package website https://amr-for-r.org to read more about this package, including many examples and tutorials.
Overview:
- Provides an all-in-one solution for antimicrobial resistance (AMR) data analysis in a One Health approach
- Peer-reviewed, used in over 175 countries, cited over 100 times, available in 28 languages
- Generates antibiograms - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
- Provides the full microbiological taxonomy of ~103 000 distinct species and extensive info of ~620 antimicrobial drugs
- Applies CLSI 2011-2026 and EUCAST 2011-2026 clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
- Corrects for duplicate isolates, calculates and predicts AMR per antimicrobial class
- Integrates with WHONET, ATC, EARS-Net, PubChem, LOINC, SNOMED CT, and NCBI
- 100% free of costs and dependencies, highly suitable for places with limited resources
The AMR package is a peer-reviewed, free and open-source R package
with zero dependencies to simplify the analysis and prediction of
Antimicrobial Resistance (AMR) and to work with microbial and
antimicrobial data and properties, by using evidence-based methods.
Our aim has always been to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
The AMR package supports and can read any data format, including
WHONET data. This package works on Windows, macOS and Linux with all
versions of R since R-3.0 (April 2013). It was designed to work in any
setting, including those with very limited resources. It was created
for both routine data analysis and academic research at the Faculty of
Medical Sciences of the University of Groningen
and the University Medical Center Groningen.
How to get this package
To install the latest ‘release’ version from CRAN:
install.packages("AMR")
To install the latest ‘beta’ version:
install.packages("AMR", repos = "beta.amr-for-r.org")
If this does not work, try to install directly from GitHub using the
remotes package:
remotes::install_github("msberends/AMR")
This AMR package for R is free, open-source software and licensed under the GNU General Public License v2.0 (GPL-2). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.