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(v0.7.0.9005) ab algorithm update

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dr. M.S. (Matthijs) Berends
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions
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6
NEWS.md
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# AMR 0.7.0.9004
# AMR 0.7.0.9005
#### New
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
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mo_fullname("UPEC")
# "Escherichia coli"
```
* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
#### Changed
* Fixed bug in translation of microorganism names
* Fixed bug in determining taxonomic kingdoms
* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
* Function `as.ab()` now allows spaces for coercing antibiotics names
* Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab`
* Added names of object in the header in frequency tables, even when using pipes
* Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP)
* Fixed a bug where setting an antibiotic would not work for `eucast_rules()` and `mdro()`
* Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
* Removed `latest_annual_release` from the `catalogue_of_life_version()` function
* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
#### Other
* Fixed a note thrown by CRAN tests