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(v0.7.0.9013) mo_synonym fix

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dr. M.S. (Matthijs) Berends
2019-06-22 14:49:12 +02:00
parent 409397a337
commit c9156c004a
75 changed files with 465 additions and 507 deletions
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7
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 0.7.0.9012
# AMR 0.7.0.9013
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
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# 3 Ciprofloxacin SI 0.8381831 1181
# 4 Ciprofloxacin R 0.1618169 228
```
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are:
* Support for all scientifically published pathotypes of *E. coli* to date (that we could find). Supported are:
* AIEC (Adherent-Invasive *E. coli*)
* ATEC (Atypical Entero-pathogenic *E. coli*)
@@ -51,9 +51,10 @@
* 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`
* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
* Fixed bug where not all old taxonomic names would be printed, when using a vector as input for `as.mo()`
* Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
* Small improvements to `plot()` and `barplot()` for MIC and RSI classes
* Allow Catalogue of Life IDs to be coerced by `as.mo()`
#### Other
* Fixed a note thrown by CRAN tests