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(v0.9.0.9016) Support SNOMED codes

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dr. M.S. (Matthijs) Berends
2020-01-27 19:14:23 +01:00
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NEWS.md
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# AMR 0.9.0.9015
# AMR 0.9.0.9016
## <small>Last updated: 27-Jan-2020</small>
### New
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
```r
ab_loinc("ampicillin")
#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"
ab_name("21066-6")
#> [1] "Ampicillin"
ab_atc("21066-6")
#> [1] "J01CA01"
```
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows machine reading these guidelines**, which is currently almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
* Support for LOINC and SNOMED codes
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
```r
ab_loinc("ampicillin")
#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"
ab_name("21066-6")
#> [1] "Ampicillin"
ab_atc("21066-6")
#> [1] "J01CA01"
```
* Support for SNOMED CT codes in the `microorganisms` data set. Use `mo_snomed()` to retrieve SNOMED codes, or use a SNOMED code for input in any `mo_*` function:
```r
mo_snomed("S. aureus")
#> [1] 115329001 3092008 113961008
mo_name(115329001)
#> [1] "Staphylococcus aureus"
mo_gramstain(115329001)
#> [1] "Gram-positive"
```
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
### Changes
* Bugfix for some WHONET microorganism codes that were not interpreted correctly when using `as.rsi()`