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updated microorganism codes

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dr. M.S. (Matthijs) Berends
2023-05-26 16:10:01 +02:00
parent 0bcf55d3b6
commit c6135d2082
14 changed files with 59 additions and 42 deletions
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NEWS.md
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# AMR 2.0.0.9019
# AMR 2.0.0.9020
## Changed
* Added oxygen tolerance to over 25,000 bacteria in the `microorganisms` data set
* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set
* Added `mo_oxygen_tolerance()` to retrieve the values
* Added `mo_is_anaerobic()` to determine which species are obligate anaerobic bacteria
* Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria
* Added LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()`
* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
* Added microbial codes for Gram-negative/positive anaerobic bacteria
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* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
* Fixed usage of `icu_exclude` in `first_isolates()`
* Improved `as.mo()` algorithm for searching on only species names
* Updated the code table in `microorganisms.codes`
# AMR 2.0.0