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(v1.3.0.9016) mo_uncertainties() overhaul

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dr. M.S. (Matthijs) Berends
2020-09-12 08:49:01 +02:00
parent 68e9cb78e9
commit 3ff871afeb
71 changed files with 820 additions and 169 deletions
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NEWS.md
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# AMR 1.3.0.9015
## <small>Last updated: 3 September 2020</small>
# AMR 1.3.0.9016
## <small>Last updated: 12 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
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#> [1] 24 24
```
* Improvements for `as.mo()`:
* Any user input value that could mean more than one taxonomic entry is now considered 'uncertain'. Instead of a warning, a message will be thrown and the accompanying `mo_uncertainties()` has been changed completely; it now prints all possible candidates with their score.
* Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using `mo_*` functions like `mo_name()` on microoganism IDs.
* Added parameter `ignore_pattern` to `as.mo()` which can also be given to `mo_*` functions like `mo_name()`, to exclude known non-relevant input from analysing. This can also be set with the option `AMR_ignore_pattern`.
* `get_locale()` now uses `Sys.getlocale()` instead of `Sys.getlocale("LC_COLLATE")`
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* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
* Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: `tibble` printing support for classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`. When using `tibble`s containing antimicrobial columns (class `<rsi>`), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class `<mo>`) will emphasise on the genus and species, not on the kingdom.
* Names of antiviral agents in data set `antivirals` now have a starting capital letter, like it is the case in the `antibiotics` data set
* Updated the documentation of the `WHONET` data set to clarify that all patient names are fictitious
### Other
* Removed unnecessary references to the `base` package