P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 05:02:03 +02:00
Code Releases Activity

new WISCA vignette

Browse Source
This commit is contained in:
github-actions[bot]
2025-04-30 17:33:03 +02:00
parent 04aec39371
commit c70ac149ff
8 changed files with 284 additions and 79 deletions
Download Patch File Download Diff File Expand all files Collapse all files

51
NEWS.md
View File

@ -2,15 +2,54 @@
*(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).)*
#### A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
## Breaking
## tl;dr
- **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**:
- 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**:
- 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**:
- Full tidymodels compatibility for antimicrobial selectors.
- Deprecated `resistance_predict()` and `sir_predict()`.
- **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 strict comparisons, added levels.
- Disk diffusion range expanded (0–50 mm).
- **EUCAST Rules and MDROs**:
- EUCAST v12–v15 rules implemented.
- Dutch MDRO 2024 guideline support in `mdro()`.
- **Infrastructure**:
- New website: https://amr-for-r.org.
- Improved `vctrs` integration for tidyverse workflows.
- Dropped SAS `.xpt` file support.
- **Other Fixes & Enhancements**:
- Faster microorganism identification.
- Improved antimicrobial and MIC handling.
- Extended documentation, additional contributors acknowledged.
## Full Changelog
### Breaking
* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
* Functions `resistance_predict()` and `sir_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
## New
### New
* **One Health implementation**
* Function `as.sir()` now has extensive support for veterinary breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://amr-for-r.org/articles/datasets.html).
@ -45,7 +84,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that belong to that group.
* New functions `mic_p50()` and `mic_p90()` to retrieve the 50th and 90th percentile of MIC values.
## Changed
### Changed
* SIR interpretation
* Support for parallel computing to greatly improve speed using the `parallel` package (part of base R). Use `as.sir(your_data, parallel = TRUE)` to run SIR interpretation using multiple cores.
* It is now possible to use column names for arguments `guideline`, `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
@ -108,8 +147,8 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Added arguments `esbl`, `carbapenemase`, `mecA`, `mecC`, `vanA`, `vanB` to denote column names or logical values indicating presence of these genes (or production of their proteins)
* 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.
### Other
* New website domain: <https://amr-for-r.org>! The old domain (<https://msberends.github.io/AMR/>) 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