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new antibiotics

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dr. M.S. (Matthijs) Berends
2019-05-10 16:44:59 +02:00
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NEWS.md
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# AMR 0.6.1.9001
**Note: latest development version**
#### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
#### Changed
* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()`
* Completely reworked the `antibiotics` data set:
* All entries now have 3 different identifiers: a human readable EARS-Net code (`ab`, used by ECDC and WHONET), an ATC code (`atc`, used by WHO), and a CID code (`cid`, Compound ID, used by PubChem)
* Based on the Compound ID, more than a thousand official brand names have been added from many different countries
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
* All output will be translated by using an included, local translation file that can be found after install with:
```r
system.file("translations.tsv", package = "AMR")
```
Please create an issue in one of our repositories if you want additions in this file.
* Improved intelligence of looking up antibiotic tables in data set using `guess_ab_col()`
* Added ~5,000 more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function
* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()`, `rsi()`
* Frequency tables of microbial IDs speed improvement
* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`.
* Added ceftazidim intrinsic resistance to *Streptococci*
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* Fix for `freq()` for when all values are `NA`.
#### Other
* Support for R 3.6.0
* Prevented [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html) in R 3.6.0 and later by adding `StagedInstall: false` to the DESCRIPTION file
# AMR 0.6.1