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AMR
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310 Commits

Author SHA1 Message Date
dr. M.S. (Matthijs) Berends fbc9191b13 new EUCAST rules algorithm 2019-04-05 18:47:39 +02:00
dr. M.S. (Matthijs) Berends 248e508e9b CI - test also on r-devel 2019-03-29 14:34:39 +01:00
dr. M.S. (Matthijs) Berends b25f2d6213 v0.6.1 2019-03-28 21:33:28 +01:00
dr. M.S. (Matthijs) Berends 429814c29b v0.6.0 2019-03-27 11:22:36 +01:00
dr. M.S. (Matthijs) Berends 29f444543d added Becker 2019 2019-03-26 14:24:03 +01:00
dr. M.S. (Matthijs) Berends c6a12266e7 DSMZ data 2019-03-18 14:29:41 +01:00
dr. M.S. (Matthijs) Berends fdffc2791b memory for as.mo() 2019-03-15 13:57:25 +01:00
dr. M.S. (Matthijs) Berends 504a042fba uncertainty levels, new WHONET codes 2019-03-12 12:19:27 +01:00
dr. M.S. (Matthijs) Berends b319b89750 WHONET fix 2019-03-09 08:21:00 +01:00
dr. M.S. (Matthijs) Berends 5c7a061a5d filter_ab_class fix 2019-03-06 09:32:48 +01:00
dr. M.S. (Matthijs) Berends 74e0ae21fd con WHONET, filter ab class 2019-03-05 22:47:42 +01:00
dr. M.S. (Matthijs) Berends e835525cf6 unknown codes, rsi fix 2019-03-02 22:47:04 +01:00
dr. M.S. (Matthijs) Berends c5efb272fd mo_source improvement 2019-03-01 09:34:04 +01:00
dr. M.S. (Matthijs) Berends 2565b60024 rlang dependency, new fungi 2019-02-28 13:56:28 +01:00
dr. M.S. (Matthijs) Berends 54162522bd age_groups fix 2019-02-27 11:36:12 +01:00
dr. M.S. (Matthijs) Berends f9ded23023 as.mo improvement 2019-02-26 12:33:26 +01:00
dr. M.S. (Matthijs) Berends 0ec76cfa98 as.mo improvement 2019-02-25 10:42:57 +01:00
dr. M.S. (Matthijs) Berends 1a6314769b as.mo improvement 2019-02-23 16:02:31 +01:00
dr. M.S. (Matthijs) Berends 41ad7a22c8 mo_rank mo_url, added Tremellales 2019-02-22 22:12:10 +01:00
dr. M.S. (Matthijs) Berends 68a9a35ed6 algorithm update 2019-02-21 18:55:52 +01:00
dr. M.S. (Matthijs) Berends 13120f465f website update 2019-02-20 13:57:23 +01:00
dr. M.S. (Matthijs) Berends fb1fc3686c Catalogue of life 2019-02-20 00:04:48 +01:00
dr. M.S. (Matthijs) Berends 54f8258f8c Catalogue of Life, replaces ITIS 2019-02-18 02:33:37 +01:00
dr. M.S. (Matthijs) Berends 9209787a53 SPSS tutorial 2019-02-14 15:18:17 +01:00
dr. M.S. (Matthijs) Berends efb2af9e3a benchmarks plots 2019-02-14 10:23:51 +01:00
dr. M.S. (Matthijs) Berends ae44b185e6 fix freq length calculation 2019-02-13 17:14:59 +01:00
dr. M.S. (Matthijs) Berends 30ff770c93 freq update 2019-02-12 15:38:31 +01:00
dr. M.S. (Matthijs) Berends 76ed26d27e resistance predict update 2019-02-11 10:27:10 +01:00
dr. M.S. (Matthijs) Berends 70105086c8 as.rsi warning, site update 2019-02-10 08:42:28 +01:00
dr. M.S. (Matthijs) Berends c56b179857 as.rsi warning, site update 2019-02-09 22:16:24 +01:00
dr. M.S. (Matthijs) Berends ed30312048 mo codes for WHONET 2019-02-08 16:06:54 +01:00
dr. M.S. (Matthijs) Berends 587e00b7be is.rsi.eligible update 2019-02-04 12:24:07 +01:00
dr. M.S. (Matthijs) Berends cd07d65734 freq and website update 2019-02-01 16:55:55 +01:00
dr. M.S. (Matthijs) Berends 0b3dc0231f freq fix 2019-01-30 16:00:55 +01:00
dr. M.S. (Matthijs) Berends 3efb54d016 freq update 2019-01-29 20:20:09 +01:00
dr. M.S. (Matthijs) Berends 6aae206320 WHONET/EARS-Net support 2019-01-29 00:06:50 +01:00
dr. M.S. (Matthijs) Berends f6336fdd89 quasiquotation for freq() 2019-01-28 11:20:32 +01:00
dr. M.S. (Matthijs) Berends e76961a66b less deps 2019-01-27 19:30:40 +01:00
dr. M.S. (Matthijs) Berends b39055c018 deprecated fix 2019-01-27 00:33:58 +01:00
dr. M.S. (Matthijs) Berends f836722269 atc_ functions 2019-01-26 23:22:56 +01:00
dr. M.S. (Matthijs) Berends f4ff98b470 WHO update, antibiotics update 2019-01-25 13:18:41 +01:00
dr. M.S. (Matthijs) Berends 46dcc7e2e8 set_mo_source 2019-01-21 15:53:01 +01:00
dr. M.S. (Matthijs) Berends c6c3088e9f select() fix for freq 2019-01-17 12:08:04 +01:00
dr. M.S. (Matthijs) Berends 046d195064 resistance predict 2019-01-15 12:45:24 +01:00
dr. M.S. (Matthijs) Berends 5aad26035c edited g.test 2019-01-12 11:06:58 +01:00
dr. M.S. (Matthijs) Berends 641d866db2 guess_ab_col, benchmarks 2019-01-11 20:37:23 +01:00
dr. M.S. (Matthijs) Berends 193a2d2863 EUCAST update, as.mo bugfix for empty vlaues 2019-01-08 16:23:45 +01:00
dr. M.S. (Matthijs) Berends bc15f660d6 guess_ab() 2019-01-06 20:23:49 +01:00
dr. M.S. (Matthijs) Berends 0205b6178d guess_mo deprecation 2019-01-06 16:40:55 +01:00
dr. M.S. (Matthijs) Berends f01d62ee5d language 2019-01-05 21:51:48 +01:00
dr. M.S. (Matthijs) Berends 6b2d464f8c big website update, licence txt update 2019-01-02 23:24:07 +01:00
dr. M.S. (Matthijs) Berends 2e4d703338 eucast rules fix, 1st isolate fix, website update 2018-12-31 01:48:53 +01:00
dr. M.S. (Matthijs) Berends 469b145d8c bye bye packrat 2018-12-30 12:00:53 +01:00
dr. M.S. (Matthijs) Berends 92a32b62a7 new website, freq updates 2018-12-29 22:24:19 +01:00
dr. M.S. (Matthijs) Berends 92d2553dfe gitlab pages 2018-12-23 21:26:21 +01:00
dr. M.S. (Matthijs) Berends 0b8084871d dplyr 0.8.0 support, fixes #7 2018-12-22 22:39:34 +01:00
dr. M.S. (Matthijs) Berends 2018d5b477 age and age_groups 2018-12-15 22:40:07 +01:00
dr. M.S. (Matthijs) Berends 81af7be36e note about portions 2018-12-14 07:23:25 +01:00
dr. M.S. (Matthijs) Berends 9478ab71be freq - decimals 2018-12-10 10:13:40 +01:00
dr. M.S. (Matthijs) Berends 8e8a9cd190 AI improvements 2018-12-07 12:04:55 +01:00
dr. M.S. (Matthijs) Berends 60fe98bbbd better as.mo handling 2018-12-06 14:36:39 +01:00
dr. M.S. (Matthijs) Berends 5cfa5bbfe3 v0.5.0 2018-11-30 16:16:04 +01:00
dr. M.S. (Matthijs) Berends 31e977937d fix for as.mo and freq 2018-11-30 12:05:59 +01:00
dr. M.S. (Matthijs) Berends 9ddf6dc530 support A. species for as.mo, cleanup 2018-11-24 20:25:09 +01:00
dr. M.S. (Matthijs) Berends a8132922af unit test read.4d, unselecting freq cols 2018-11-19 13:00:22 +01:00
dr. M.S. (Matthijs) Berends 4fcc2b409a MDRO update 2018-11-16 20:50:50 +01:00
dr. M.S. (Matthijs) Berends fab64e6728 read.4D improvements 2018-11-15 12:42:35 +01:00
dr. M.S. (Matthijs) Berends 6b0f4ffbd4 new kingdom 2018-11-09 13:11:54 +01:00
dr. M.S. (Matthijs) Berends d07e9b904e new function get_locale 2018-11-05 13:20:32 +01:00
dr. M.S. (Matthijs) Berends 5476fecc73 eucast update 2018-11-01 20:23:33 +01:00
dr. M.S. (Matthijs) Berends 9cd4ab928a speed improvement as.mo, freq title 2018-10-31 12:10:49 +01:00
dr. M.S. (Matthijs) Berends 1bf8dc2983 as.mo speedup: assigned to namespace 2018-10-29 17:26:17 +01:00
dr. M.S. (Matthijs) Berends 87757748bd switch to gitlab 2018-10-23 16:49:40 +02:00
dr. M.S. (Matthijs) Berends 299c5bea43 na freq, removed factors 2018-10-23 09:42:26 +02:00
dr. M.S. (Matthijs) Berends c2a93b46db breaks param, tidyr dep change, freq markdown 2018-10-22 12:32:59 +02:00
dr. M.S. (Matthijs) Berends 86b03577a7 fix for as.mo, added also_single_tested 2018-10-19 13:53:31 +02:00
dr. M.S. (Matthijs) Berends 693f64bdbf new EUCAST rules: clinical breakpoints 2018-10-17 17:32:34 +02:00
dr. M.S. (Matthijs) Berends d5a41de711 parameter combine_IR 2018-10-16 09:59:31 +02:00
dr. M.S. (Matthijs) Berends 5b5b95a47b count_all and some fixes 2018-10-12 16:35:18 +02:00
dr. M.S. (Matthijs) Berends 95c9fdc552 CRAN fixes for release 0.4.0 
https://cran.r-project.org/web/checks/check_results_AMR.html
 2018-10-09 13:53:33 +02:00
dr. M.S. (Matthijs) Berends c7c57f4042 0.4.0, just published on CRAN 2018-10-01 19:36:42 +02:00
dr. M.S. (Matthijs) Berends 3119a221e5 authors from ITIS, diff for freq 2018-10-01 11:39:43 +02:00
dr. M.S. (Matthijs) Berends 768fe17324 removed clipboard functions as it violated CRAN policies 2018-09-28 16:05:18 +02:00
dr. M.S. (Matthijs) Berends 2b0080995e speed improvement for as.mo, more old taxonomic names 2018-09-27 23:23:48 +02:00
dr. M.S. (Matthijs) Berends 9c566585b0 first inclusion of ITIS data 2018-09-24 23:33:29 +02:00
dr. M.S. (Matthijs) Berends db14781593 add labels_rsi_count 2018-09-16 22:11:17 +02:00
dr. M.S. (Matthijs) Berends 26f5be0033 support for portuguese, language determination based on system 2018-09-08 16:06:47 +02:00
dr. M.S. (Matthijs) Berends b388e3fee7 Support for German and Spanish microorganism properties, cleanup 2018-09-04 11:33:30 +02:00
dr. M.S. (Matthijs) Berends 75fe4d401f new MOs, cleanup 2018-09-01 21:19:46 +02:00
dr. M.S. (Matthijs) Berends 5965d3c794 replaced bactid by mo 2018-08-31 13:36:19 +02:00
dr. M.S. (Matthijs) Berends 029157b3be 163 new trade names, added ab_tradenames 2018-08-29 12:27:37 +02:00
dr. M.S. (Matthijs) Berends 972fc4f6c7 ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid 2018-08-28 13:51:13 +02:00
dr. M.S. (Matthijs) Berends 2acdb1981c atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00
dr. M.S. (Matthijs) Berends a100d07da6 removed ratio, better rsi_calc, update for freq 2018-08-24 11:08:20 +02:00
dr. M.S. (Matthijs) Berends 0c0e538ef4 dependencies 2018-08-23 22:05:17 +02:00
dr. M.S. (Matthijs) Berends 8ab93b6688 unit tests 2018-08-23 01:01:50 +02:00
dr. M.S. (Matthijs) Berends da5379c881 quasiquotation, alpha for geom_rsi 2018-08-23 00:40:36 +02:00
dr. M.S. (Matthijs) Berends 3e87c8f409 count_* functions 2018-08-22 00:02:26 +02:00
dr. M.S. (Matthijs) Berends 6bab01948e v0.3.0 2018-08-14 13:25:24 +02:00
dr. M.S. (Matthijs) Berends e5193c7749 AppVeyor 2018-08-13 23:05:53 +02:00
dr. M.S. (Matthijs) Berends dba06c3295 abname improvement, small fixes 2018-08-13 11:00:53 +02:00
dr. M.S. (Matthijs) Berends e5d32cafe0 new unit tests for ggplot, small fixes 2018-08-12 17:44:06 +02:00
dr. M.S. (Matthijs) Berends 1ba7d883fe new ggplot enhancement 2018-08-11 21:30:00 +02:00
dr. M.S. (Matthijs) Berends 53fa198e35 new portion functions 2018-08-10 15:01:05 +02:00
dr. M.S. (Matthijs) Berends ae2433a020 rsi family for resistance analysis 2018-08-03 14:49:29 +02:00
dr. M.S. (Matthijs) Berends bd9bcfef78 thesis advisors 2018-08-03 09:59:39 +02:00
dr. M.S. (Matthijs) Berends 6262315527 Becker classification 
Lancefield classification
Added Lancefield groups to `microorganisms` data set
 2018-08-02 13:15:45 +02:00
dr. M.S. (Matthijs) Berends edd2dd09dc rsi for freq 2018-08-01 22:37:28 +02:00
dr. M.S. (Matthijs) Berends 211e3bae14 remove reshape2 dependency 2018-07-30 01:18:40 +02:00
dr. M.S. (Matthijs) Berends feab1cad6b small fixes 2018-07-28 09:34:03 +02:00
dr. M.S. (Matthijs) Berends 498e88b5cf improvement for forecasting resistance 2018-07-26 16:30:42 +02:00
dr. M.S. (Matthijs) Berends d9e204031d update to septic_patients, speed improvements 2018-07-25 14:17:04 +02:00
dr. M.S. (Matthijs) Berends 8421638b60 new class bactid 2018-07-23 14:14:03 +02:00
dr. M.S. (Matthijs) Berends 9920ac8a5c fix for keyab, more examples 2018-07-23 10:35:39 +02:00
dr. M.S. (Matthijs) Berends ad662d7bab new col names for `key_antibiotics` 2018-07-19 15:11:23 +02:00
dr. M.S. (Matthijs) Berends 5cb9c541f8 new algorithm key abs 2018-07-17 13:02:05 +02:00
dr. M.S. (Matthijs) Berends a5a4354651 speed improvements 2018-07-17 10:32:26 +02:00
dr. M.S. (Matthijs) Berends 715a7630ca support format.freq 2018-07-16 16:41:48 +02:00
dr. M.S. (Matthijs) Berends 6eaf33baf3 speed improvements 2018-07-15 22:56:41 +02:00
dr. M.S. (Matthijs) Berends 8240959f38 support older mac release 2018-07-13 19:40:50 +02:00
dr. M.S. (Matthijs) Berends b6655f6454 Welcome C++! 2018-07-13 17:23:46 +02:00
dr. M.S. (Matthijs) Berends a28289562a remove print function, out of scope 2018-07-11 20:12:19 +02:00
dr. M.S. (Matthijs) Berends e3e10c2e88 fix for macOS and older tidyr versions 2018-07-11 12:34:02 +02:00
dr. M.S. (Matthijs) Berends eca406b18b travis build fails for macos 2018-07-11 11:46:06 +02:00
dr. M.S. (Matthijs) Berends f63414d519 new g.test, extra unit tests 2018-07-10 12:27:07 +02:00
dr. M.S. (Matthijs) Berends fc30d3fb13 freq: support for table 2018-07-09 14:02:58 +02:00
dr. M.S. (Matthijs) Berends 14b990d769 kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00
dr. M.S. (Matthijs) Berends 34ee0247ac addins and small improvements to microorganisms dataset 2018-07-04 17:20:03 +02:00
dr. M.S. (Matthijs) Berends 2ca01e2d8d remove rlang dependency 2018-07-01 22:23:34 +02:00
dr. M.S. (Matthijs) Berends 965fe8681b rlang dep for Travis/macOS 2018-07-01 21:50:34 +02:00
dr. M.S. (Matthijs) Berends 3527894b49 new g.test() and edited freq() 2018-07-01 21:40:37 +02:00
dr. M.S. (Matthijs) Berends 6ee713cec1 move tbl_parse_guess 2018-06-29 08:56:03 +02:00
dr. M.S. (Matthijs) Berends 649a8025aa add clipboard functions again 2018-06-27 15:54:56 +02:00
dr. M.S. (Matthijs) Berends a9bd5472d0 top_freq 2018-06-20 14:47:37 +02:00
dr. M.S. (Matthijs) Berends bdc860e29c atc_groups 2018-06-19 10:05:38 +02:00
dr. M.S. (Matthijs) Berends 0a5898b17d fix for printing tibbles, improve guess_bactid 2018-06-08 12:06:54 +02:00
dr. M.S. (Matthijs) Berends efdf5a3dc5 prevent dplyr:row_number warning 2018-05-31 14:19:25 +02:00
dr. M.S. (Matthijs) Berends 5593aee19e edit as.rsi algor. 2018-05-30 23:02:16 +02:00
uscloud dcc26dd942 Update freq function 2018-05-22 16:34:22 +02:00
dr. M.S. (Matthijs) Berends f05e7178cb added vignette of freq 2018-05-09 11:44:46 +02:00
dr. M.S. (Matthijs) Berends c0fc82c794 Added function `n_rsi` 2018-05-02 14:56:25 +02:00
dr. M.S. (Matthijs) Berends 8fe70d5652 Fix Latex PDF error 2018-04-30 16:24:11 +02:00
dr. M.S. (Matthijs) Berends 970e3ed7f1 EUCAST rules for MDRO 2018-04-25 15:33:58 +02:00
dr. M.S. (Matthijs) Berends 82fec5cc51 Try to support older R versions 2018-04-19 14:10:57 +02:00
dr. M.S. (Matthijs) Berends e7396b8f39 Try to support older R versions 2018-04-19 12:50:23 +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 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 c182a9673d fix clipboard on linux 2018-04-02 11:11:21 +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
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 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 04fc3573ec
add barplots 2018-03-13 14:34:10 +01:00
dr. M.S. (Matthijs) Berends be51a95448
rename columns 2018-02-26 10:53:54 +01:00
dr. M.S. (Matthijs) Berends 3f859210d5
new date for push test 2018-02-22 22:04:22 +01:00
dr. M.S. (Matthijs) Berends d8da8daf9a
First CRAN submission edits 2018-02-22 20:48:48 +01:00
dr. M.S. (Matthijs) Berends 62304dc23f
first commit 2018-02-21 11:52:31 +01:00