dr. M.S. (Matthijs) BerendsandClaude Opus 5.5
ca5fa333ca
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>
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 ~97 000 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.