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Code Releases Activity

(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
parent f553a08a7b
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NEWS.md
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# AMR 0.7.1.9074
<small>Last updated: 16-Sep-2019</small>
# AMR 0.7.1.9075
<small>Last updated: 18-Sep-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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```
### Changed
* Many algorithm improvements for `as.mo()` (of which some led to additions to the `microorganisms` data set):
* Many algorithm improvements for `as.mo()` (of which some led to additions to the `microorganisms` data set). Many thanks to all contributors that helped improving the algorithms.
* Self-learning algorithm - the function now gains experience from previously determined microorganism IDs and learns from it (yielding 80-95% speed improvement for any guess after the first try)
* Big improvement for misspelled input
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
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* Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. **IMPORTANT:** Because of these changes, the microorganism IDs have been changed to a slightly different format. 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.
* Renamed data set `septic_patients` to `example_isolates`
* Function `eucast_rules()`:
* Fixed a bug for *Yersinia pseudotuberculosis*
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* Fix for `key_antibiotics()` on foreign systems
#### Other
* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
# AMR 0.7.1