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(v0.7.1.9055) algorithm improvements

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dr. M.S. (Matthijs) Berends
2019-08-13 16:15:08 +02:00
parent 6c4822164c
commit 7108454ba5
77 changed files with 644 additions and 582 deletions
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NEWS.md
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# AMR 0.7.1.9038
# AMR 0.7.1.9055
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
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* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
* Fix and speed improvement for `mo_shortname()`
* Algorithm improvements for `as.mo()`:
* Some misspelled input were not understood
* Algorithm improvements for `as.mo()` (by which some additions were made to the `microorganisms` data set:
* Big improvement for misspelled input
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
* Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology
* Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Updated the `microorganisms` data set to contain the latest taxonomic data from the IJSEM journal (now up to date until August 2019)
* Added almost 5,000 new fungi to the `microorganisms` data set
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* The `name` of `RIF` is now Rifampicin instead of Rifampin
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#### Changed
* Fixed a critical bug in `first_isolate()` where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.
* Fixedd a bug in `eucast_rules()` where antibiotics from WHONET software would not be recognised
* Fixed a bug in `eucast_rules()` where antibiotics from WHONET software would not be recognised
* Completely reworked the `antibiotics` data set:
* All entries now have 3 different identifiers:
* Column `ab` contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package