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Code Releases Activity

icu_exclude in first_isolate(), fixes #110

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dr. M.S. (Matthijs) Berends
2023-05-17 22:12:10 +02:00
parent 5f9769a4f7
commit 3018fb87a9
3 changed files with 35 additions and 43 deletions
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NEWS.md
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# AMR 2.0.0.9015
# AMR 2.0.0.9018
## Changed
* Added oxygen tolerance 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 LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()`
* formatting fix for `sir_interpretation_history()`
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
* 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
* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
* Fixed formatting for `sir_interpretation_history()`
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
* Fixed usage of `icu_exclude` in `first_isolates()`
# AMR 2.0.0