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Update clinical breakpoints and fix some as.mo() bugs (#117)

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* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
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NEWS.md
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# AMR 2.0.0.9023
# AMR 2.0.0.9024
## Changed
## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for `eucast_rules()` to apply EUCAST Expert Rules.
* The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
* ECOFF: the `clinical_breakpoints` data set now contains the new column `ecoff`, in which the epidemiological cut-off (ECOFF) are available. These ECOFFs can be used for MIC/disk interpretation using `as.sir(..., ecoff = TRUE)`, which is an important new addition for veterinary microbiology.
* 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 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
## Changed
* `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
* Fixed usage of `icu_exclude` in `first_isolates()`
* Improved `as.mo()` algorithm for searching on only species names
* Improved `as.mo()` algorithm:
* Now allows searching on only species names
* Fix for using the `keep_synonyms` argument when using MO codes as input
* Fix for using the `minimum_matching_score` argument
* Updated the code table in `microorganisms.codes`