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45 lines
2.9 KiB
Markdown
45 lines
2.9 KiB
Markdown
# 0.2.0
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#### New
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* Full support for Windows, Linux and macOS
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* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
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* Function `n_rsi` to count cases where antibiotic test results were available, to be used in conjunction with `dplyr::summarise`, see ?rsi
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* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
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* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
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* Function `freq` to create **frequency tables**, with additional info in a header
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* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
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* 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)
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* [Exceptional resistances defined by EUCAST](http://www.eucast.org/expert_rules_and_intrinsic_resistance) are also supported instead of countries alone
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* Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
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* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
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* New print format for `tibble`s and `data.table`s
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#### Changed
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* Fixed `rsi` class for vectors that contain only invalid antimicrobial interpretations
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* Renamed dataset `ablist` to `antibiotics`
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* Renamed dataset `bactlist` to `microorganisms`
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* Added common abbreviations and trade names to the `antibiotics` dataset
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* Added more microorganisms to the `microorganisms` dataset
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* Added analysis examples on help page of dataset `septic_patients`
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* Added support for character vector in `join` functions
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* Added warnings when a join results in more rows after than before the join
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* Altered `%like%` to make it case insensitive
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* For parameters of functions `first_isolate` and `EUCAST_rules` column names are now case-insensitive
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* Functions `as.rsi` and `as.mic` now add the package name and version as attributes
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#### Other
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* Expanded `README.md` with more examples
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* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
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* Added unit testing with the `testthat` package
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* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
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* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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# 0.1.1
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* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
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* Edited column names to comply with GLIMS, the laboratory information system
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* Added more valid MIC values
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* Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
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* Added barplots for `rsi` and `mic` classes
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# 0.1.0
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* First submission to CRAN.
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