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AMR
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112 Commits

Author SHA1 Message Date
dr. M.S. (Matthijs) Berends 4b5530ed64 Try to support older R versions 2018-04-18 15:19:00 +02:00
dr. M.S. (Matthijs) Berends a814d82b4b try to support older R versions 2018-04-18 14:50:16 +02:00
dr. M.S. (Matthijs) Berends 2509e2413d MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00
dr. M.S. (Matthijs) Berends 3165c50d06 more MOs 2018-04-03 16:07:32 +02:00
dr. M.S. (Matthijs) Berends 4a47e59e6f fortify code with more tests 2018-04-03 11:08:31 +02:00
dr. M.S. (Matthijs) Berends 972e923484 testthat for macOS 2018-04-02 16:21:03 +02:00
dr. M.S. (Matthijs) Berends 07bdd61241 update dependencies 2018-04-02 16:05:09 +02:00
dr. M.S. (Matthijs) Berends cee64ef050 fix Travis 2018-04-02 15:03:22 +02:00
dr. M.S. (Matthijs) Berends c182a9673d fix clipboard on linux 2018-04-02 11:11:21 +02:00
MS Berends abcb4accbd
Update .travis.yml 2018-03-29 15:17:48 +02:00
MS Berends b7f29aa748
Update first_isolates.R 2018-03-29 15:15:31 +02:00
MS Berends 2647dacc0a
add clipbaord support for Linux and macOS 2018-03-29 15:07:36 +02:00
MS Berends f1dbed6fcc
Update clipboard.R 2018-03-29 14:56:40 +02:00
MS Berends e2a5202b69
Update test-clipboard.R 2018-03-29 14:47:52 +02:00
MS Berends 258e080756
Update test-clipboard.R 2018-03-29 14:26:26 +02:00
MS Berends 136272cb71
Update clipboard.R 2018-03-29 14:16:42 +02:00
MS Berends 9f943708cc
Update .travis.yml 2018-03-29 14:07:54 +02:00
MS Berends fd04df5f9d
Update clipboard.R 2018-03-29 13:23:02 +02:00
MS Berends dbec56c68a
Update .travis.yml 2018-03-29 13:16:08 +02:00
MS Berends 339b445a30
Update test-clipboard.R 2018-03-29 13:12:49 +02:00
MS Berends 2f4823f7a7
Update clipboard.R 2018-03-29 13:10:55 +02:00
MS Berends ff90188f41
Update .travis.yml 2018-03-29 12:56:03 +02:00
dr. M.S. (Matthijs) Berends 1b3cc41c08
fix tests 2018-03-27 17:58:46 +02:00
dr. M.S. (Matthijs) Berends 6f7730dcaa
add tests using testthat 2018-03-27 17:43:42 +02:00
MS Berends c26839b08e
Test on Linux and Mac 2018-03-23 14:59:50 +01:00
MS Berends 9637b43357
Remove Windows only function 2018-03-23 14:59:02 +01:00
MS Berends 39eb307968
Remove Windows only function 2018-03-23 14:58:46 +01:00
MS Berends 1b3daebc84
Remove Windows only function 2018-03-23 14:52:56 +01:00
dr. M.S. (Matthijs) Berends 53464ff1c8
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive 
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
 2018-03-23 14:46:02 +01:00
dr. M.S. (Matthijs) Berends e1e19af625
README update 2018-03-22 13:45:04 +01:00
dr. M.S. (Matthijs) Berends fe803f7279
use guess_bactid for GLIMS codes 2018-03-19 21:23:21 +01:00
dr. M.S. (Matthijs) Berends c765f424ab
typo 2018-03-19 21:03:23 +01:00
dr. M.S. (Matthijs) Berends dd2517ecb7
- Added new algorithm to determine weighted isolates, can now be `points` or `keyantibiotics, see `?first_isolate` 
- Function `first_isolate` supports tidyverse-like evaluation of parameters (no need to quote them anymore)
- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
 2018-03-19 20:39:23 +01:00
MS Berends 2db25b3b38
Use R 3.2 to make `covr` work 2018-03-19 12:49:22 +01:00
dr. M.S. (Matthijs) Berends 502a44eb25
- Added new function `guess_bactid` to determine the ID of a microorganism based on genus/species 
- Renamed `ablist` to `antibiotics`
- Added support for character vector in join functions
- Altered `%like%` to make it case insensitive
 2018-03-19 12:43:22 +01:00
ceefluz 0fec64a240 Add ORCID identifier 2018-03-19 10:28:35 +01:00
dr. M.S. (Matthijs) Berends 6c67c8f6c1
examples edit 2018-03-14 09:58:58 +01:00
dr. M.S. (Matthijs) Berends 46db3f7b13
import from graphics 2018-03-13 15:40:10 +01:00
dr. M.S. (Matthijs) Berends 53959d40c7
typo in examples 2018-03-13 14:40:52 +01:00
dr. M.S. (Matthijs) Berends 04fc3573ec
add barplots 2018-03-13 14:34:10 +01:00
dr. M.S. (Matthijs) Berends e4b371d30a
add MIC values 
add badges to readme
 2018-03-13 11:57:30 +01:00
ceefluz 4ea0333349 Minor text changes for DDD definition 2018-03-13 11:48:30 +01:00
MS Berends aae393f2a9
Update .Rbuildignore 2018-03-11 21:20:28 +01:00
MS Berends 692116b4dc
Create .travis.yml 2018-03-11 21:00:11 +01:00
dr. M.S. (Matthijs) Berends 34e70a65ed
added septic_patients 2018-02-27 20:01:02 +01:00
dr. M.S. (Matthijs) Berends 98b2b99913
new atc codes 2018-02-26 16:06:49 +01:00
dr. M.S. (Matthijs) Berends 8a603876d2
misc 2018-02-26 15:53:09 +01:00
dr. M.S. (Matthijs) Berends 915d4db23b
add rows to summary 2018-02-26 14:37:40 +01:00
dr. M.S. (Matthijs) Berends 6fa05fe33b
first isolates 2018-02-26 14:06:31 +01:00
dr. M.S. (Matthijs) Berends d36a391747
export first_isolate 2018-02-26 12:15:52 +01:00