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(v2.1.1.9270) Add support for Korean, fix ATCs

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dr. M.S. (Matthijs) Berends
2025-05-04 14:24:43 +02:00
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NEWS.md
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# AMR 2.1.1.9269
# AMR 2.1.1.9270
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
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## tl;dr
- **Scope Expansion**: One Health support (Human + Veterinary + Environmental microbiology).
- **Data Updates**:
- Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).
- Data Updates:
- `antibiotics` renamed to `antimicrobials`.
- Veterinary antimicrobials and WHOCC codes added.
- MycoBank fungal taxonomy integrated (+20,000 fungi).
- **Breakpoints & Interpretations**:
- Breakpoints & Interpretations:
- CLSI/EUCAST 2024-2025 breakpoints added; EUCAST 2025 default.
- `as.sir()` supports NI/SDD levels; parallel computation enabled.
- Custom S/I/R/SDD/NI definitions allowed.
- Improved handling of capped MICs.
- **New Tools & Functions**:
- New Tools & Functions:
- WISCA antibiogram support (`antibiogram()`, `wisca()`).
- New ggplot2 extensions: `scale_*_mic()`, `scale_*_sir()`, `rescale_mic()`.
- New utility functions: `top_n_microorganisms()`, `mo_group_members()`, `mic_p50()`, `mic_p90()`.
- **Predictive Modelling**:
- Predictive Modelling:
- Full tidymodels compatibility for antimicrobial selectors.
- Deprecated `resistance_predict()` and `sir_predict()`.
- **Python Compatibility**: AMR R package now runs in Python.
- **Selector Improvements**:
- Python Compatibility: AMR R package now runs in Python.
- Selector Improvements:
* Added selectors (`isoxazolylpenicillins()`, `monobactams()`, `nitrofurans()`, `phenicols()`, `rifamycins()`, and `sulfonamides()`)
- Selectors renamed from `ab_*` to `amr_*`; old names deprecated.
- **MIC/Disks Handling**:
- MIC/Disks Handling:
- MIC strict comparisons, added levels.
- Disk diffusion range expanded (0–50 mm).
- **EUCAST Rules and MDROs**:
- EUCAST Rules and MDROs:
- EUCAST v12–v15 rules implemented.
- Dutch MDRO 2024 guideline support in `mdro()`.
- **Infrastructure**:
- Infrastructure:
- New website: https://amr-for-r.org.
- Improved `vctrs` integration for tidyverse workflows.
- Dropped SAS `.xpt` file support.
- **Other Fixes & Enhancements**:
- Other Fixes & Enhancements:
- Support for 8 new languages, adding to a total of 28 languages.
- Faster microorganism identification.
- Improved antimicrobial and MIC handling.
- Extended documentation, additional contributors acknowledged.
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* **Support for WISCA antibiograms**
* The `antibiogram()` function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated `wisca()` function is also available for easy usage.
* **More global coverage of languages**
* Added full support for 7 new languages: Arabic, Bengali, Hindi, Indonesian, Swahili, Urdu, and Vietnamese. The `AMR` package is now available in 27 languages.
* Added full support for 8 new languages: Arabic, Bengali, Hindi, Indonesian, Korean, Swahili, Urdu, and Vietnamese. The `AMR` package is now available in 28 languages.
* **Major update to fungal taxonomy and tools for mycologists**
* MycoBank has now been integrated as the primary taxonomic source for fungi. The `microorganisms` data set has been enriched with new columns (`mycobank`, `mycobank_parent`, and `mycobank_renamed_to`) that provide detailed information for fungal species.
* A remarkable addition of over 20,000 new fungal records
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* Added console colours support of `sir` class for Positron
### Other
* New website domain: <https://amr-for-r.org>! The old domain (<http://amr-for-r.org/>) will remain to work.
* New website domain: <https://amr-for-r.org>! The old domain will remain to work.
* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
* Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes