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(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi

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dr. M.S. (Matthijs) Berends
2024-09-19 11:44:56 +02:00
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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://msberends.github.io/AMR/#latest-development-version).)*
#### 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](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
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
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
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* The `microorganisms` data set now contains additional columns `mycobank`, `mycobank_parent`, and `mycobank_renamed_to`
* New function `mo_mycobank()` to get the MycoBank record number, analogous to existing functions `mo_lpsn()` and `mo_gbif()`
* We've welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi
* Improved support for mycologists:
* The `as.mo()` function now includes a new argument, `only_fungi` (TRUE/FALSE), which limits the results to fungi only. Normally, bacteria are often prioritised by the algorithm, but setting `only_fungi = TRUE` ensures only fungi are returned.
* You can also set this globally using the new R option `AMR_only_fungi`, e.g., `options(AMR_only_fungi = TRUE)`.
* Other
* 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 are in that group.
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* Fixed a bug for when `antibiogram()` returns an empty data set
## Other
* Greatly updated and expanded documentation
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input