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unknown codes, rsi fix

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dr. M.S. (Matthijs) Berends
2019-03-02 22:47:04 +01:00
parent c5efb272fd
commit e835525cf6
31 changed files with 528 additions and 409 deletions
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15
NEWS.md
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@ -78,11 +78,18 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Functions `atc_ddd()` and `atc_groups()` have been renamed `atc_online_ddd()` and `atc_online_groups()`. The old functions are deprecated and will be removed in a future version.
* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
* Function `guess_atc()` is now deprecated in favour of `as.atc()` and will be removed in future versions
* Improvements for `as.mo()`:
* Improvements for `as.mo()`:\
* Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. Properties of these will be translated on foreign systems in all language already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
```r
mo_genus("qwerty", language = "es")
# Warning:
# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
#> [1] "(género desconocido)"
```
* Fix for vector containing only empty values
* Finds better results when input is in other languages
* Better handling for subspecies
* Better handling for *Salmonellae*
* Better handling for *Salmonellae*, especially the 'city like' serovars like *Salmonella London*
* Understanding of highly virulent *E. coli* strains like EIEC, EPEC and STEC
* There will be looked for uncertain results at default - these results will be returned with an informative warning
* Manual (help page) now contains more info about the algorithms
@ -102,7 +109,9 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* New colours for `scale_rsi_colours()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
* Small text updates to summaries of class `rsi` and `mic`
* Function `as.rsi()` now gives a warning when inputting MIC values
* Function `as.rsi()`:
* Now gives a warning when inputting MIC values
* Now accepts high and low resistance: `"HIGH S"` will return `S`
* Frequency tables (`freq()` function):
* Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
```r