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Code Releases Activity

(v0.7.1.9092) as.ab() improvements

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dr. M.S. (Matthijs) Berends
2019-10-04 15:36:12 +02:00
parent edb599ae0b
commit 8bc4081b03
28 changed files with 176 additions and 71 deletions
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NEWS.md
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# AMR 0.7.1.9091
<small>Last updated: 30-Sep-2019</small>
# AMR 0.7.1.9092
<small>Last updated: 04-Oct-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
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* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
**IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
* More intelligent guessing for `as.ab()`
* Renamed data set `septic_patients` to `example_isolates`
* Function `eucast_rules()`:
* Fixed a bug for *Yersinia pseudotuberculosis*