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(v0.8.0.9031) as.mo() improvements

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dr. M.S. (Matthijs) Berends
2019-11-15 15:25:03 +01:00
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NEWS.md
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# AMR 0.8.0.9030
<small>Last updated: 11-Nov-2019</small>
# AMR 0.8.0.9031
<small>Last updated: 15-Nov-2019</small>
### Breaking
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
* If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:
```r
if (mo_family(somebugs) == "Enterobacteriaceae") ...
```
then please adjust this to:
```r
if (mo_order(somebugs) == "Enterobacterales") ...
```
### New
* Functions `susceptibility()` and `resistance()` as aliases of `proportion_SI()` and `proportion_R()`, respectively. These functions were added to make it more clear that "I" should be considered susceptible and not resistant.
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* The new Verbose mode (`mdro(...., verbose = TRUE)`) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents
### Changes
* Improvements to algorithm in `as.mo()`:
* Now allows "ou" where "au" should have been used and vice versa
* More intelligent way of coping with some consonants like "l" and "r"
* Added a score (a certainty percentage) to `mo_uncertainties()`, that is calculated using the [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance):
```r
as.mo(c("Stafylococcus aureus",
"staphylokok aureuz"))
#> Warning:
#> Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them.
#> Class 'mo'
#> [1] B_STPHY_AURS B_STPHY_AURS
mo_uncertainties()
#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)
#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)
```
* Removed previously deprecated function `as.atc()` - this function was replaced by `ab_atc()`
* Renamed all `portion_*` functions to `proportion_*`. All `portion_*` functions are still available as deprecated functions, and will return a warning when used.
* When running `as.rsi()` over a data set, it will now print the guideline that will be used if it is not specified by the user
* Fix for `eucast_rules()`: *Stenotrophomonas maltophilia* not interpreted "R" to ceftazidime anymore (following EUCAST v3.1)
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family *Enterobacteriaceae*, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016.
* Improvements for `eucast_rules()`:
* Fix where *Stenotrophomonas maltophilia* would always become ceftazidime R (following EUCAST v3.1)
* Fix where *Leuconostoc* and *Pediococcus* would not always become glyopeptides R
* non-EUCAST rules in `eucast_rules()` are now applied first and not as last anymore. This is to improve the dependency on certain antibiotics for the official EUCAST rules. Please see `?eucast_rules`.
* Fix for interpreting MIC values with `as.rsi()` where the input is `NA`
* Added "imi" and "imp" as allowed abbreviation for Imipenem (IPM)
* Fix for automatically determining columns with antibiotic results in `mdro()` and `eucast_rules()`