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(v2.1.1.9081) HUGE microorganisms update for fungi!

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dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
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NEWS.md
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# AMR 2.1.1.9080
# AMR 2.1.1.9081
*(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).)*
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* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
## New
* One Health implementation
* Function `as.sir()` now has extensive support for animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* **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 CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when `guideline` is set to CLSI)
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
* Clinical breakpoints
* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disks diffusion interpretations.
* **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
* New function `mo_mycobank()` to retrieve the MycoBank record number, analogous to existing functions such as `mo_lpsn()` and `mo_gbif()`.
* The `as.mo()` function and all `mo_*()` functions now includes an `only_fungi` argument, allowing users to restrict results solely to fungal species. This ensures fungi are prioritised over bacteria during microorganism identification. This can also be set globally with the new `AMR_only_fungi` option.
* Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.
* **Updated clinical breakpoints**
* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
* MIC plotting and transforming
* **New forms for MIC plotting and transforming**
* New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* New function `rescale_mic()`, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
* Microbiological taxonomy (`microorganisms` data set) updated to June 2024, with some exciting new features:
* Added MycoBank as the primary taxonomic source for fungi
* 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.
* New function `rescale_mic()`, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.
* **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 belong to that group.
## Changed
* SIR interpretation
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## Other
* Greatly updated and expanded documentation
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
* Stopped support for SAS (`.xpt`) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
# Older Versions
## Older Versions
This changelog only contains changes from AMR v3.0 (October 2024) and later.