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EUCAST rules for MDRO

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dr. M.S. (Matthijs) Berends
2018-04-25 15:33:58 +02:00
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commit 970e3ed7f1
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NEWS.md
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# 0.2.0
#### New
* Full support for Windows, Linux and macOS
* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed
* Function `guess_bactid` to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
* Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
* Function `MDRO` to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. Suggest your own via [this link](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E). Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
* Function `freq` to create frequency tables, with additional info in a header
* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
* Functions `clipboard_import` and `clipboard_export` as helper functions to **quickly copy and paste** from/to software like Excel and SPSS
* Function `freq` to create **frequency tables**, with additional info in a header
* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
* Suggest your own via [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E)
* [Exceptional resistances defined by EUCAST](http://www.eucast.org/expert_rules_and_intrinsic_resistance) are also supported instead of countries alone
* Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
* New print format for tibbles and data.tables
* New print format for `tibble`s and `data.table`s
#### Changed
* Renamed dataset `ablist` to `antibiotics`
* Renamed dataset `bactlist` to `microorganisms`
* Added more microorganisms to `bactlist`
* Added common abbreviations and trade names to the `antibiotics` dataset
* Added more microorganisms to the `microorganisms` dataset
* Added analysis examples on help page of dataset `septic_patients`
* Added support for character vector in `join` functions
* Added warnings when a join results in more rows after than before the join
* Altered `%like%` to make it case insensitive
* For parameters of functions `first_isolate` and `EUCAST_rules` the column names are now case-insensitive
* Functions `as.rsi` and `as.mic` now add the package name and version as attribute
* For parameters of functions `first_isolate` and `EUCAST_rules` column names are now case-insensitive
* Functions `as.rsi` and `as.mic` now add the package name and version as attributes
#### Other
* Expanded README.md with more examples
* Added ORC IDs of authors to DESCRIPTION file
* Expanded `README.md` with more examples
* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
* Added unit testing with the `testthat` package
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
* Added Line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
# 0.1.1
* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing