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(v0.6.1.9053) prerelease fixes

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dr. M.S. (Matthijs) Berends
2019-06-02 19:23:19 +02:00
parent 8de0495008
commit bd73988f15
38 changed files with 337 additions and 327 deletions
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NEWS.md
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# AMR 0.6.1.9052
**Note: latest development version**
# AMR 0.6.1.9053
#### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
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* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()`, `rsi()`
* Frequency tables (`freq()`):
* speed improvement for microbial IDs
* fixed level names in markdown
* fixed factor level names for R Markdown
* when all values are unique it now shows a message instead of a warning
* support for boxplots:
```r
septic_patients %>%
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* Fix for `first_isolate()` for when dates are missing
* Improved speed of `guess_ab_col()`
* Function `as.mo()` now gently interprets any number of whitespace characters (like tabs) as one space
* Function `as.mo()` now returns `UNKNOWN` for `"con"` (WHONET ID of 'contamination') and returns `NA` for `"xxx"`(WHONET ID of 'no growth')
* Small algorithm fix for `as.mo()`
* Removed viruses from data set `microorganisms.codes` and cleaned it up
* Fix for `mo_shortname()` where species would not be determined correctly