Commit Graph - AMR

P281424/AMR

Fork 0

mirror of https://github.com/msberends/AMR.git synced 2025-09-15 11:49:41 +02:00

Commit Graph

Select branches

Hide Pull Requests

gh-pages

main

python-wrapper

sir-s3-update

#109

#117

#134

#181

#192

#205

#212

#221

#226

#226

#65

#67

#68

#71

#72

#77

#93

#97

v0.1.0

v0.1.1

v0.2.0

v0.3.0

v0.4.0

v0.5.0

v0.6.0

v0.6.1

v0.7.0

v0.7.1

v0.8.0

v0.9.0

v1.0.0

v1.0.1

v1.1.0

v1.2.0

v1.3.0

v1.4.0

v1.5.0

v1.6.0

v1.7.0

v1.7.1

v1.8.0

v1.8.1

v1.8.2

v2.0.0

v2.1.0

v2.1.1

v3.0.0

e3e10c2e88 fix for macOS and older tidyr versions dr. M.S. (Matthijs) Berends 2018-07-11 12:34:02 +02:00
eca406b18b travis build fails for macos dr. M.S. (Matthijs) Berends 2018-07-11 11:46:06 +02:00
673ea81c0a libgit2 for macOS dr. M.S. (Matthijs) Berends 2018-07-11 11:04:54 +02:00
330558e0f1 travis update dr. M.S. (Matthijs) Berends 2018-07-11 10:39:47 +02:00
9e40771a17 get travis working again dr. M.S. (Matthijs) Berends 2018-07-10 16:36:30 +02:00
490990c8cb no errors on 3.1 and 3.2 dr. M.S. (Matthijs) Berends 2018-07-10 16:31:13 +02:00
0da1071cd8 latest R version on both linux and macOS dr. M.S. (Matthijs) Berends 2018-07-10 16:17:09 +02:00
f2684b29e7 test R 3.1 to latest dr. M.S. (Matthijs) Berends 2018-07-10 16:05:11 +02:00
cde1892e25 allow failure of covr dr. M.S. (Matthijs) Berends 2018-07-10 15:56:00 +02:00
f63414d519 new g.test, extra unit tests dr. M.S. (Matthijs) Berends 2018-07-10 12:27:07 +02:00
fc30d3fb13 freq: support for table dr. M.S. (Matthijs) Berends 2018-07-09 14:02:58 +02:00
18c91786bf Merge branch 'master' of https://github.com/msberends/AMR dr. M.S. (Matthijs) Berends 2018-07-08 22:15:31 +02:00
14b990d769 kurtosis, skewness, start with ML dr. M.S. (Matthijs) Berends 2018-07-08 22:14:55 +02:00
e4ca66e3ee support zenodo MS Berends 2018-07-04 23:42:43 +02:00
c768ba0d9c A. lwoffi to A. lwoffii dr. M.S. (Matthijs) Berends 2018-07-04 17:34:23 +02:00
34ee0247ac addins and small improvements to microorganisms dataset dr. M.S. (Matthijs) Berends 2018-07-04 17:20:03 +02:00
10fce8382c include IQR and MAD in freq dr. M.S. (Matthijs) Berends 2018-07-03 11:30:40 +02:00
3d0d21f322 rename vector2ratio to ratio dr. M.S. (Matthijs) Berends 2018-07-02 11:14:20 +02:00
a1acb2f3ac extra unit tests dr. M.S. (Matthijs) Berends 2018-07-02 09:34:20 +02:00
2c8d4cb8bf forgot namespace... dr. M.S. (Matthijs) Berends 2018-07-01 22:37:47 +02:00
2ca01e2d8d remove rlang dependency dr. M.S. (Matthijs) Berends 2018-07-01 22:23:34 +02:00
965fe8681b rlang dep for Travis/macOS dr. M.S. (Matthijs) Berends 2018-07-01 21:50:34 +02:00
3527894b49 new g.test() and edited freq() dr. M.S. (Matthijs) Berends 2018-07-01 21:40:37 +02:00
f7af8a81da update man page dr. M.S. (Matthijs) Berends 2018-06-29 09:06:47 +02:00
6ee713cec1 move tbl_parse_guess dr. M.S. (Matthijs) Berends 2018-06-29 08:56:03 +02:00
4bdcde9a00 allow clipboard on travis MS Berends 2018-06-27 15:56:59 +02:00
649a8025aa add clipboard functions again dr. M.S. (Matthijs) Berends 2018-06-27 15:54:56 +02:00
dab085d7ad Update README.md MS Berends 2018-06-27 10:44:24 +02:00
a9bd5472d0 top_freq dr. M.S. (Matthijs) Berends 2018-06-20 14:47:37 +02:00
4a027f3c34 extra unit tests, add row.names to freq dr. M.S. (Matthijs) Berends 2018-06-19 15:20:14 +02:00
bdc860e29c atc_groups dr. M.S. (Matthijs) Berends 2018-06-19 10:05:38 +02:00
0a5898b17d fix for printing tibbles, improve guess_bactid dr. M.S. (Matthijs) Berends 2018-06-08 12:06:54 +02:00
efdf5a3dc5 prevent dplyr:row_number warning dr. M.S. (Matthijs) Berends 2018-05-31 14:19:25 +02:00
7a6d5fb6b7 rsi/mic fix MS Berends 2018-05-31 09:02:49 +02:00
5593aee19e edit as.rsi algor. dr. M.S. (Matthijs) Berends 2018-05-30 23:02:16 +02:00
dcc26dd942 Update freq function uscloud 2018-05-22 16:34:22 +02:00
0d80647d41 fix SI and IR MS Berends 2018-05-16 11:19:45 +02:00
af524626b6 Merge branch 'master' of https://github.com/msberends/AMR dr. M.S. (Matthijs) Berends 2018-05-14 11:54:25 +02:00
95f7c78fd6 edit vignette title dr. M.S. (Matthijs) Berends 2018-05-14 11:54:08 +02:00
eecd7a11e8 Set theme jekyll-theme-cayman MS Berends 2018-05-09 11:49:50 +02:00
c690db145e Set theme jekyll-theme-slate MS Berends 2018-05-09 11:48:10 +02:00
f05e7178cb added vignette of freq dr. M.S. (Matthijs) Berends 2018-05-09 11:44:46 +02:00
25b3346d9a edit methodology of rsi v0.2.0 dr. M.S. (Matthijs) Berends 2018-05-03 10:19:02 +02:00
c0fc82c794 Added function n_rsi dr. M.S. (Matthijs) Berends 2018-05-02 14:56:25 +02:00
e5ae7b98ac update logo dr. M.S. (Matthijs) Berends 2018-05-01 09:59:37 +02:00
6eaf594cb7 update data info dr. M.S. (Matthijs) Berends 2018-05-01 09:57:50 +02:00
be5d714639 update README dr. M.S. (Matthijs) Berends 2018-05-01 09:43:47 +02:00
19ccc51f40 remove clipboard functions dr. M.S. (Matthijs) Berends 2018-05-01 09:36:45 +02:00
6fa93fc286 fix clipboard check dr. M.S. (Matthijs) Berends 2018-04-30 16:54:37 +02:00
8fe70d5652 Fix Latex PDF error dr. M.S. (Matthijs) Berends 2018-04-30 16:24:11 +02:00
970e3ed7f1 EUCAST rules for MDRO dr. M.S. (Matthijs) Berends 2018-04-25 15:33:58 +02:00
0b22ddef8e more unit tests dr. M.S. (Matthijs) Berends 2018-04-20 13:45:34 +02:00
82fec5cc51 Try to support older R versions dr. M.S. (Matthijs) Berends 2018-04-19 14:10:57 +02:00
e7396b8f39 Try to support older R versions dr. M.S. (Matthijs) Berends 2018-04-19 12:50:23 +02:00
d79132b29f Try to support older R versions dr. M.S. (Matthijs) Berends 2018-04-18 15:41:27 +02:00
4b5530ed64 Try to support older R versions dr. M.S. (Matthijs) Berends 2018-04-18 15:19:00 +02:00
a814d82b4b try to support older R versions dr. M.S. (Matthijs) Berends 2018-04-18 14:50:16 +02:00
2509e2413d MDRO, freq tables, new print format for tibbles dr. M.S. (Matthijs) Berends 2018-04-18 12:24:54 +02:00
3165c50d06 more MOs dr. M.S. (Matthijs) Berends 2018-04-03 16:07:32 +02:00
4a47e59e6f fortify code with more tests dr. M.S. (Matthijs) Berends 2018-04-03 11:08:31 +02:00
972e923484 testthat for macOS dr. M.S. (Matthijs) Berends 2018-04-02 16:21:03 +02:00
07bdd61241 update dependencies dr. M.S. (Matthijs) Berends 2018-04-02 16:05:09 +02:00
cee64ef050 fix Travis dr. M.S. (Matthijs) Berends 2018-04-02 15:03:22 +02:00
c182a9673d fix clipboard on linux dr. M.S. (Matthijs) Berends 2018-04-02 11:11:21 +02:00
abcb4accbd Update .travis.yml MS Berends 2018-03-29 15:17:48 +02:00
b7f29aa748 Update first_isolates.R MS Berends 2018-03-29 15:15:31 +02:00
2647dacc0a add clipbaord support for Linux and macOS MS Berends 2018-03-29 15:07:36 +02:00
f1dbed6fcc Update clipboard.R MS Berends 2018-03-29 14:56:40 +02:00
e2a5202b69 Update test-clipboard.R MS Berends 2018-03-29 14:47:52 +02:00
258e080756 Update test-clipboard.R MS Berends 2018-03-29 14:26:26 +02:00
136272cb71 Update clipboard.R MS Berends 2018-03-29 14:16:42 +02:00
9f943708cc Update .travis.yml MS Berends 2018-03-29 14:07:54 +02:00
fd04df5f9d Update clipboard.R MS Berends 2018-03-29 13:23:02 +02:00
dbec56c68a Update .travis.yml MS Berends 2018-03-29 13:16:08 +02:00
339b445a30 Update test-clipboard.R MS Berends 2018-03-29 13:12:49 +02:00
2f4823f7a7 Update clipboard.R MS Berends 2018-03-29 13:10:55 +02:00
ff90188f41 Update .travis.yml MS Berends 2018-03-29 12:56:03 +02:00
1b3cc41c08 fix tests dr. M.S. (Matthijs) Berends 2018-03-27 17:58:46 +02:00
6f7730dcaa add tests using testthat dr. M.S. (Matthijs) Berends 2018-03-27 17:43:42 +02:00
c26839b08e Test on Linux and Mac MS Berends 2018-03-23 14:59:50 +01:00
9637b43357 Remove Windows only function MS Berends 2018-03-23 14:59:02 +01:00
39eb307968 Remove Windows only function MS Berends 2018-03-23 14:58:46 +01:00
1b3daebc84 Remove Windows only function MS Berends 2018-03-23 14:52:56 +01:00
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 dr. M.S. (Matthijs) Berends 2018-03-23 14:46:02 +01:00
e1e19af625 README update dr. M.S. (Matthijs) Berends 2018-03-22 13:45:04 +01:00
fe803f7279 use guess_bactid for GLIMS codes dr. M.S. (Matthijs) Berends 2018-03-19 21:23:21 +01:00
c765f424ab typo dr. M.S. (Matthijs) Berends 2018-03-19 21:03:23 +01:00
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 dr. M.S. (Matthijs) Berends 2018-03-19 20:39:23 +01:00
2db25b3b38 Use R 3.2 to make covr work MS Berends 2018-03-19 12:49:22 +01:00
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 dr. M.S. (Matthijs) Berends 2018-03-19 12:43:22 +01:00
0fec64a240 Add ORCID identifier ceefluz 2018-03-19 10:28:35 +01:00
6c67c8f6c1 examples edit v0.1.1 dr. M.S. (Matthijs) Berends 2018-03-14 09:58:58 +01:00
46db3f7b13 import from graphics dr. M.S. (Matthijs) Berends 2018-03-13 15:40:10 +01:00
53959d40c7 typo in examples dr. M.S. (Matthijs) Berends 2018-03-13 14:40:52 +01:00
04fc3573ec add barplots dr. M.S. (Matthijs) Berends 2018-03-13 14:34:10 +01:00
e4b371d30a add MIC values add badges to readme dr. M.S. (Matthijs) Berends 2018-03-13 11:57:30 +01:00
4ea0333349 Minor text changes for DDD definition ceefluz 2018-03-13 11:48:30 +01:00
aae393f2a9 Update .Rbuildignore MS Berends 2018-03-11 21:20:28 +01:00
692116b4dc Create .travis.yml MS Berends 2018-03-11 21:00:11 +01:00
34e70a65ed added septic_patients dr. M.S. (Matthijs) Berends 2018-02-27 20:01:02 +01:00