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new species groups, updated clinical breakpoints

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dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
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commit acb534102b
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NEWS.md
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# AMR 2.0.0.9026
# AMR 2.0.0.9027
## 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.
* 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
* 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.
* ECOFF: the `clinical_breakpoints` data set now contains epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using `as.sir(..., breakpoint_type = "ECOFF")`, which is an important new addition for veterinary microbiology.
* Added support for 29 species groups / complexes. They are gathered in a new data set `microorganisms.groups` and are used in clinical breakpoint interpretation. For example, CLSI 2023 contains breakpoints for the RGM group (Rapidly Growing Mycobacterium, containing over 80 species) which is now supported by our package.
* 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
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* Added microbial codes for Gram-negative/positive anaerobic bacteria
## Changed
* Updated algorithm of `as.mo()` by giving more weight to fungi
* `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`
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* Fix for using the `minimum_matching_score` argument
* Updated the code table in `microorganisms.codes`
* Fixed an endless loop if using `reference_df` in `as.mo()`
* Fixed bug for indicating UTIs in `as.sir()`
# AMR 2.0.0