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new WISCA vignette
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NEWS.md
51
NEWS.md
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*(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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#### A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
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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.
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## Breaking
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## tl;dr
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- **Scope Expansion**: One Health support (Human + Veterinary + Environmental microbiology).
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- **Data Updates**:
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- `antibiotics` renamed to `antimicrobials`.
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- Veterinary antimicrobials and WHOCC codes added.
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- MycoBank fungal taxonomy integrated (+20,000 fungi).
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- **Breakpoints & Interpretations**:
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- CLSI/EUCAST 2024-2025 breakpoints added; EUCAST 2025 default.
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- `as.sir()` supports NI/SDD levels; parallel computation enabled.
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- Custom S/I/R/SDD/NI definitions allowed.
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- Improved handling of capped MICs.
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- **New Tools & Functions**:
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- WISCA antibiogram support (`antibiogram()`, `wisca()`).
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- New ggplot2 extensions: `scale_*_mic()`, `scale_*_sir()`, `rescale_mic()`.
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- New utility functions: `top_n_microorganisms()`, `mo_group_members()`, `mic_p50()`, `mic_p90()`.
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- **Predictive Modelling**:
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- Full tidymodels compatibility for antimicrobial selectors.
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- Deprecated `resistance_predict()` and `sir_predict()`.
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- **Python Compatibility**: AMR R package now runs in Python.
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- **Selector Improvements**:
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* Added selectors (`isoxazolylpenicillins()`, `monobactams()`, `nitrofurans()`, `phenicols()`, `rifamycins()`, and `sulfonamides()`)
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- Selectors renamed from `ab_*` to `amr_*`; old names deprecated.
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- **MIC/Disks Handling**:
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- MIC strict comparisons, added levels.
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- Disk diffusion range expanded (0–50 mm).
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- **EUCAST Rules and MDROs**:
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- EUCAST v12–v15 rules implemented.
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- Dutch MDRO 2024 guideline support in `mdro()`.
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- **Infrastructure**:
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- New website: https://amr-for-r.org.
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- Improved `vctrs` integration for tidyverse workflows.
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- Dropped SAS `.xpt` file support.
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- **Other Fixes & Enhancements**:
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- Faster microorganism identification.
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- Improved antimicrobial and MIC handling.
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- Extended documentation, additional contributors acknowledged.
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## Full Changelog
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### Breaking
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* 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.
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* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
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* 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).
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## New
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### New
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* **One Health implementation**
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* 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.
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* 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).
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* 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.
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* New functions `mic_p50()` and `mic_p90()` to retrieve the 50th and 90th percentile of MIC values.
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## Changed
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### Changed
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* SIR interpretation
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* 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.
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* 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.
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* 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)
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* Added console colours support of `sir` class for Positron
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## Other
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* New website domain: <https://amr-for-r.org>! The old domain (<http://amr-for-r.org>) will remain to work.
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### Other
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* New website domain: <https://amr-for-r.org>! The old domain (<https://msberends.github.io/AMR/>) will remain to work.
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* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
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* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
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* Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
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