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update dependencies

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dr. M.S. (Matthijs) Berends
2018-04-02 16:05:09 +02:00
parent cee64ef050
commit 07bdd61241
15 changed files with 172 additions and 221 deletions
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NEWS
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## 0.1.2
- NEW: Function `guess_bactid` to determine the ID of a microorganism based on genus/species
- NEW: Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- NEW: New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
- EDIT: Renamed dataset `ablist` to `antibiotics`
- EDIT: Renamed dataset `bactlist` to `microorganisms`
- EDIT: Added support for character vector in join functions
- EDIT: Altered `%like%` to make it case insensitive
- EDIT: Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- EDIT: For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive
- EDIT: Functions `as.rsi` and `as.mic` now add the package name and version as attribute
- Added full support for Windows, Linux and macOS; this package now works everywhere :)
- New function `guess_bactid` to determine the ID of a microorganism based on genus/species
- New functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
- Renamed dataset `ablist` to `antibiotics`
- Renamed dataset `bactlist` to `microorganisms`
- Added analysis examples on help page of dataset `septic_patients`
- Added support for character vector in join functions
- Added warnings when applying a join results in more rows after than before the join
- Altered `%like%` to make it case insensitive
- For parameters of functions `first_isolate`, `EUCAST_rules` the column names are now case-insensitive
- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
- Expanded README.md
- Added unit testing with Travis CI (https://travis-ci.org/msberends/AMR)
- Added code coverage checking with Codecov (https://codecov.io/gh/msberends/AMR/tree/master/R)
## 0.1.1
- `EUCAST_rules` applies for amoxicillin even if ampicillin is missing