P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity
1,424 Commits 2 Branches 28 Tags 1.6 GiB
Commit Graph

182 Commits

Author SHA1 Message Date
dr. M.S. (Matthijs) Berends 7b00b4f34a unit tests 2023-01-24 14:52:15 +01:00
dr. M.S. (Matthijs) Berends 830c67f1bf documentation, unit tests 2023-01-24 10:20:27 +01:00
Dr. Matthijs Berends 98e62c9af2
Replace RSI with SIR 2023-01-21 23:47:20 +01:00
dr. M.S. (Matthijs) Berends 24b12024ce unit test fix 2023-01-20 09:45:03 +01:00
dr. M.S. (Matthijs) Berends b94bc6c67b adding mo fixes 2023-01-14 19:50:25 +01:00
dr. M.S. (Matthijs) Berends cf16bc7de1 unit tests 2023-01-06 13:45:20 +01:00
dr. M.S. (Matthijs) Berends 86e28bafce add mo_pathogenicity 2023-01-06 13:35:37 +01:00
dr. M.S. (Matthijs) Berends 51c0f0814e new setup unit tests 2023-01-05 15:03:18 +01:00
dr. M.S. (Matthijs) Berends f619fb683b support new mo codes 2022-12-27 15:16:15 +01:00
dr. M.S. (Matthijs) Berends e493248ea5 unit test and news file 2022-12-21 09:12:53 +01:00
dr. M.S. (Matthijs) Berends 4c42a43f7d fixes 2022-12-20 22:41:39 +01:00
dr. M.S. (Matthijs) Berends 6f4bb603ec unit tests 2022-12-20 22:18:50 +01:00
dr. M.S. (Matthijs) Berends 23fe427cbc Fixes for Salmonella 2022-12-17 14:31:33 +01:00
dr. M.S. (Matthijs) Berends e7d7b94b3e no obligatory note on startup 2022-12-09 15:10:49 +01:00
dr. M.S. (Matthijs) Berends 510140fc55 Updated `mo_gramstain()` to reflect current taxonomy, fixes #83 2022-12-09 10:30:25 +01:00
dr. M.S. (Matthijs) Berends 31fb81c382 revised `as.rsi()`, fix for `mdro()` 2022-11-24 20:29:00 +01:00
dr. M.S. (Matthijs) Berends 05d536ebb7 complexes 2022-11-17 15:23:29 +01:00
Dr. Matthijs Berends 496c08d851
Implement extensive support for antiviral agents support (#77) 2022-11-13 08:46:10 +01:00
dr. M.S. (Matthijs) Berends d20caae54b cleanup 2022-10-31 13:25:41 +01:00
dr. M.S. (Matthijs) Berends 796b972f8a extend vctrs support 2022-10-31 11:19:06 +01:00
dr. M.S. (Matthijs) Berends 9444ed6d1d fix antibiotics error 2022-10-30 21:05:46 +01:00
dr. M.S. (Matthijs) Berends 3d9faf89cf ATC and DDD update 2022-10-29 19:01:23 +02:00
dr. M.S. (Matthijs) Berends 6ad7857d39 fix missing R breakpoints 2022-10-29 14:15:23 +02:00
dr. M.S. (Matthijs) Berends d10651eb26 cleanup 2022-10-22 10:20:09 +02:00
dr. M.S. (Matthijs) Berends aa2c0639d0 add confidence intervals (fixed #70), remove `combine_IR` 2022-10-20 16:08:01 +02:00
dr. M.S. (Matthijs) Berends 85e2fbe4a3 remove warnings from unit tests 2022-10-19 11:47:57 +02:00
Dr. Matthijs Berends fed3b6440f
Unit test fix 2022-10-19 08:14:38 +02:00
dr. M.S. (Matthijs) Berends f203928f7e coercion fixes 2022-10-19 06:59:36 +02:00
dr. M.S. (Matthijs) Berends e5e6d2200d fix add manual ab 2022-10-18 22:53:38 +02:00
dr. M.S. (Matthijs) Berends 76bcd3528c move object assignment to AMR_env 2022-10-14 13:02:50 +02:00
dr. M.S. (Matthijs) Berends 82e3198315 add `add_custom_antimicrobials()` 2022-10-10 20:20:39 +02:00
dr. M.S. (Matthijs) Berends 43c638d122 add `mo_current()` 2022-10-10 10:12:08 +02:00
dr. M.S. (Matthijs) Berends b9342d103e fix documentation 2022-10-06 11:33:30 +02:00
Dr. Matthijs Berends cd2acc4a29
New mo algorithm, prepare for 2.0 2022-10-05 09:12:22 +02:00
dr. M.S. (Matthijs) Berends 63fe160322 new rsi_interpretation_history 2022-09-01 15:20:57 +02:00
dr. M.S. (Matthijs) Berends 3fca703fbf new AMR distance function 2022-08-30 21:48:02 +02:00
dr. M.S. (Matthijs) Berends c44ddf272f fix for R <= 3.3 2022-08-28 19:34:04 +02:00
dr. M.S. (Matthijs) Berends 71db246d5c unit test fix 2022-08-28 19:17:12 +02:00
dr. M.S. (Matthijs) Berends 4d050aef7c styled, unit test fix 2022-08-28 10:31:50 +02:00
dr. M.S. (Matthijs) Berends 303d61b473 new tibble export 2022-08-27 20:49:37 +02:00
dr. M.S. (Matthijs) Berends 7226b70c3d update languages 2022-08-20 20:17:14 +02:00
dr. M.S. (Matthijs) Berends 680e8e7a41 (v1.8.1.9005) as.rsi() fix for EUCAST 2022-05-10 17:01:37 +02:00
dr. M.S. (Matthijs) Berends d4e22069bc (v1.8.1.9004) fix for table() on MICs 2022-05-09 21:33:27 +02:00
dr. M.S. (Matthijs) Berends 1c891cc90c (v1.8.1.9003) set_mo_source() fix 2022-05-09 20:36:44 +02:00
dr. M.S. (Matthijs) Berends 7b0f1596bd (v1.8.0.9010) as.mo improvement 2022-03-15 17:35:02 +01:00
dr. M.S. (Matthijs) Berends 3b2b2be5f8 (v1.8.0.9002) as.rsi() cleanup, more informative warnings 2022-03-02 15:38:55 +01:00
dr. M.S. (Matthijs) Berends be792cc9eb (v1.8.0.9000) unit tests for R 3.3 2022-02-01 17:08:10 +01:00
dr. M.S. (Matthijs) Berends 25cef46c59 (v1.8.0) prerelease 1.8.0 2021-12-23 18:56:28 +01:00
dr. M.S. (Matthijs) Berends 3f4ff260d2 unit test 2021-12-23 15:36:54 +01:00
dr. M.S. (Matthijs) Berends 75dac113b6 (v1.7.1.9077) skimr support only for newer R versions 2021-12-23 13:38:25 +01:00
dr. M.S. (Matthijs) Berends 76dee66852 (v1.7.1.9074) as.mo() improvement, ASCII replacements for unit tests 2021-12-14 22:39:23 +01:00
dr. M.S. (Matthijs) Berends bd4bb1d72f (v1.7.1.9073) as.rsi() fix for UTIs 2021-12-14 21:47:14 +01:00
dr. M.S. (Matthijs) Berends 0cbf8f48b6 (v1.7.1.9071) rsi disk fix 2021-12-13 11:57:34 +01:00
dr. M.S. (Matthijs) Berends 578e7dfee9 (v1.7.1.9070) Better WHONET support 2021-12-13 10:18:28 +01:00
dr. M.S. (Matthijs) Berends 1e66a3daf3 (v1.7.1.9068) new logo, unit tests 2021-12-12 11:07:02 +01:00
dr. M.S. (Matthijs) Berends 56f1ce328a (v1.7.1.9067) Support for Swedish and Russian 2021-12-12 09:42:03 +01:00
dr. M.S. (Matthijs) Berends e0a2634f14 (v1.7.1.9065) unit tests 2021-12-11 15:13:44 +01:00
dr. M.S. (Matthijs) Berends e18c49ed93 (v1.7.1.9063) not_intrinsic_resistant 2021-12-09 10:48:25 +01:00
dr. M.S. (Matthijs) Berends 1fa3fc6af2 (v1.7.1.9061) bugfix set_ab_names 2021-12-05 23:21:59 +01:00
dr. M.S. (Matthijs) Berends 7965468ccd (v1.7.1.9058) vars selection for set_ab_names() 2021-12-05 22:06:45 +01:00
dr. M.S. (Matthijs) Berends 5375f75829 (v1.7.1.9056) unit tests 2021-11-29 11:55:18 +01:00
dr. M.S. (Matthijs) Berends 694cf5ba77 (v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup 2021-11-28 23:01:26 +01:00
dr. M.S. (Matthijs) Berends 37e6e35ec4 (v1.7.1.9051) updated taxonomy, updated git branch name 2021-10-06 13:23:57 +02:00
dr. M.S. (Matthijs) Berends 2bcf28281d (v1.7.1.9049) unit tests 2021-10-05 09:58:08 +02:00
dr. M.S. (Matthijs) Berends d1b16ce641 (v1.7.1.9048) unit tests 2021-10-04 10:22:10 +02:00
dr. M.S. (Matthijs) Berends 93a4734b44 (v1.7.1.9040) Support for Danish 2021-09-29 12:12:35 +02:00
dr. M.S. (Matthijs) Berends 5f433d6e5c (v1.7.1.9039) reinitiate all units tests 2021-09-03 13:08:36 +02:00
dr. M.S. (Matthijs) Berends bcab74fb6d (v1.7.1.9037) dplyr grouping fix on windows? 2021-08-31 17:06:44 +02:00
dr. M.S. (Matthijs) Berends 953dfac9e5 (v1.7.1.9036) dplyr grouping fix on windows? 2021-08-30 16:49:46 +02:00
dr. M.S. (Matthijs) Berends 986bd826ee (v1.7.1.9035) dplyr grouping fix on windows? 2021-08-30 15:43:12 +02:00
dr. M.S. (Matthijs) Berends 1daa117e9f (v1.7.1.9033) dplyr grouping fix on windows? 2021-08-30 15:01:32 +02:00
dr. M.S. (Matthijs) Berends e6ce25162e (v1.7.1.9031) dplyr grouping fix on windows? 2021-08-30 14:07:46 +02:00
dr. M.S. (Matthijs) Berends d6a916d70b (v1.7.1.9030) unit test 2021-08-29 23:50:45 +02:00
dr. M.S. (Matthijs) Berends e4de7f5055 (v1.7.1.9028) fix unit test 2021-08-20 00:08:31 +02:00
dr. M.S. (Matthijs) Berends 41f35c73cd (v1.7.1.9027) fix unit test 2021-08-19 23:56:18 +02:00
dr. M.S. (Matthijs) Berends 2ab21b7af3 (v1.7.1.9026) updated DDDs 2021-08-19 23:43:02 +02:00
dr. M.S. (Matthijs) Berends 1b62bab007 (v1.7.1.9025) unit tests 2021-08-18 23:19:38 +02:00
dr. M.S. (Matthijs) Berends a2d249962f (v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47 2021-08-16 21:54:34 +02:00
dr. M.S. (Matthijs) Berends 4e1efd902c (v1.7.1.9022) rely on vctrs for ab selectors 2021-07-23 21:42:11 +02:00
dr. M.S. (Matthijs) Berends 6838f03bde (v1.7.1.9020) autoplot generics 2021-07-12 20:24:49 +02:00
dr. M.S. (Matthijs) Berends 5ccb330b42 (v1.7.1.9018) translation fix 2021-07-11 13:20:45 +02:00
dr. M.S. (Matthijs) Berends b228eb1536 (v1.7.1.9016) only_treatable ab selectors 2021-07-08 22:23:28 +02:00
dr. M.S. (Matthijs) Berends 625a6fb304 (v1.7.1.9015) removed S3 taxonomic_name again 2021-07-07 20:34:05 +02:00
dr. M.S. (Matthijs) Berends 16b4c74d44 (v1.7.1.9013) temp fix for ggplot2 bug #4511 2021-07-04 22:10:46 +02:00
dr. M.S. (Matthijs) Berends 350dbe6a11 (v1.7.1.9012) update unit tests 2021-07-04 20:25:30 +02:00
dr. M.S. (Matthijs) Berends c8491d07f8 (v1.7.1.9008) unit tests 2021-06-23 10:19:38 +02:00
dr. M.S. (Matthijs) Berends 95050ee3e0 (v1.7.1.9007) Updated antibiotics dataset, fixes #41 2021-06-23 10:03:17 +02:00
dr. M.S. (Matthijs) Berends d04e83f494 (v1.7.1.9005) ab class selectors for R-3.0 and R-3.1 2021-06-22 12:16:42 +02:00
dr. M.S. (Matthijs) Berends 99be4c7e7e (v1.7.1.9002) ab class selectors update 2021-06-14 22:04:04 +02:00
dr. M.S. (Matthijs) Berends 1908e7cc7a (v1.7.1.9000) ab_class update, unit tests 2021-06-04 21:07:55 +02:00
dr. M.S. (Matthijs) Berends 279376fccb (v1.7.0.9002) old MO codes 2021-06-01 16:36:33 +02:00
dr. M.S. (Matthijs) Berends f406319503 (v1.7.0.9000) package size 2021-05-30 22:14:38 +02:00
dr. M.S. (Matthijs) Berends f1d9b489c5 (v1.7.0) unit tests 2021-05-26 14:04:12 +02:00
dr. M.S. (Matthijs) Berends 55457d0ab6 v1.7.0 2021-05-25 10:00:11 +02:00
dr. M.S. (Matthijs) Berends ac73a8d849 v1.7.0 2021-05-24 15:29:17 +02:00
dr. M.S. (Matthijs) Berends e5599bc694 (v1.6.0.9065) unit tests 2021-05-24 11:01:32 +02:00
dr. M.S. (Matthijs) Berends 06302d296a (v1.6.0.9062) code consistency 2021-05-24 00:06:28 +02:00
dr. M.S. (Matthijs) Berends b210f1327c (v1.6.0.9055) support codecov again 2021-05-21 20:20:51 +02:00
dr. M.S. (Matthijs) Berends fecc5d183c (v1.6.0.9054) unit tests 2021-05-20 15:06:08 +02:00
dr. M.S. (Matthijs) Berends 04ef5b28e7 (v1.6.0.9050) printing NA in custom_eucast_rules() 2021-05-20 10:10:40 +02:00