mirror of https://github.com/msberends/AMR.git
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_rsi
to count cases where antibiotic test results were available, to be used in conjunction withdplyr::summarise
, see ?rsi - 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 - 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
- Exceptional resistances defined by EUCAST are also supported instead of countries alone
- Functions
BRMO
andMRGN
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
tibble
s anddata.table
s
Changed
- Fixed
rsi
class for vectors that contain only invalid antimicrobial interpretations - Renamed dataset
ablist
toantibiotics
- Renamed dataset
bactlist
tomicroorganisms
- 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
andEUCAST_rules
column names are now case-insensitive - Functions
as.rsi
andas.mic
now add the package name and version as attributes
Other
- Expanded
README.md
with more examples - Added ORCID 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)
0.1.1
EUCAST_rules
applies 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
rsi
andmic
classes
0.1.0
- First submission to CRAN.