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2.9 KiB
2.9 KiB
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 (needed packages may have other dependencies)
- Function
n_rsito count cases where antibiotic test results were available, to be used in conjunction withdplyr::summarise, see ?rsi - Function
guess_bactidto determine the ID of a microorganism based on genus/species or known abbreviations like MRSA - Function
guess_atcto determine the ATC of an antibiotic based on name, trade name, or known abbreviations - Function
freqto create frequency tables, with additional info in a header - Function
MDROto determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines.- Suggest your own via https://github.com/msberends/AMR/issues/new
- Exceptional resistances defined by EUCAST are also supported instead of countries alone
- Functions
BRMOandMRGNare 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 anddata.tables
Changed
- Fixed
rsiclass for vectors that contain only invalid antimicrobial interpretations - Renamed dataset
ablisttoantibiotics - Renamed dataset
bactlisttomicroorganisms - Added common abbreviations and trade names to the
antibioticsdataset - Added more microorganisms to the
microorganismsdataset - Added analysis examples on help page of dataset
septic_patients - Added support for character vector in
joinfunctions - 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_isolateandEUCAST_rulescolumn names are now case-insensitive - Functions
as.rsiandas.micnow add the package name and version as attributes
Other
- Expanded
README.mdwith more examples - Added ORCID of authors to DESCRIPTION file
- Added unit testing with the
testthatpackage - 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)
0.1.1
EUCAST_rulesapplies for amoxicillin even if ampicillin is missing- Edited column names to comply with GLIMS, the laboratory information system
- Added more valid MIC values
- Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
- Added barplots for
rsiandmicclasses
0.1.0
- First submission to CRAN.