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(v0.7.0.9003) scale fix

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dr. M.S. (Matthijs) Berends
2019-06-08 23:50:06 +02:00
parent f50d3a5ba1
commit ec48f1d83b
16 changed files with 403 additions and 32 deletions
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NEWS.md
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# AMR 0.7.0.9002
# AMR 0.7.0.9003
#### 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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#### 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 severe misspelled input
* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
* 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)