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AMR
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Author SHA1 Message Date
dr. M.S. (Matthijs) Berends 4b133d4c96 unit tests 2023-01-30 17:24:03 +01:00
dr. M.S. (Matthijs) Berends 89a577805f prelim fix for g.test 2023-01-30 12:26:48 +01:00
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. M.S. (Matthijs) Berends eef00069fd add all options to documentation 2023-01-23 20:07:57 +01:00
dr. M.S. (Matthijs) Berends 19fd0ef121 sort sir history 2023-01-23 15:01:21 +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 593d740b84 documentation, file permissions 2023-01-19 12:54:53 +01:00
dr. M.S. (Matthijs) Berends b94bc6c67b adding mo fixes 2023-01-14 19:50:25 +01:00
dr. M.S. (Matthijs) Berends ca79068604 Fix for adding MO's 2023-01-14 17:10:10 +01:00
dr. M.S. (Matthijs) Berends 33f269e2f4 contrib update 2023-01-12 23:16:05 +01:00
dr. M.S. (Matthijs) Berends 51906d6f97 no overwriting taxonomy when adding microorganisms 2023-01-12 11:33:28 +01:00
dr. M.S. (Matthijs) Berends 1029aa2fdc algorithm improvement 2023-01-07 14:53:14 +01:00
dr. M.S. (Matthijs) Berends 08fe5a88c0 documentation 2023-01-07 01:54:46 +01:00
dr. M.S. (Matthijs) Berends 2375bfdcb5 documentation 2023-01-07 01:51:19 +01:00
dr. M.S. (Matthijs) Berends 84ed8c32bb documentation 2023-01-06 19:21:04 +01:00
dr. M.S. (Matthijs) Berends 86e28bafce add mo_pathogenicity 2023-01-06 13:35:37 +01:00
dr. M.S. (Matthijs) Berends 268ec31d92 unit tests 2023-01-05 18:21:48 +01:00
dr. M.S. (Matthijs) Berends a98d0d75ea styler dep 2023-01-05 14:46:44 +01:00
dr. M.S. (Matthijs) Berends a0ee86536a unit tests 2023-01-05 14:43:18 +01:00
dr. M.S. (Matthijs) Berends 77d9cf1936 documentation 2022-12-30 13:02:37 +01:00
dr. M.S. (Matthijs) Berends e4ea96cbf9 fix for R < 3.4 2022-12-30 12:57:27 +01:00
dr. M.S. (Matthijs) Berends 1db74e86cd good start-up practice 2022-12-29 16:23:57 +01:00
dr. M.S. (Matthijs) Berends 61c0bdb7af documentation 2022-12-28 15:04:59 +01:00
dr. M.S. (Matthijs) Berends ba3b237bdf custom mo update 2022-12-28 14:20:10 +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 6f4bb603ec unit tests 2022-12-20 22:18:50 +01:00
dr. M.S. (Matthijs) Berends f0a2cdbf5e update mo algorithm 2022-12-20 16:14:04 +01:00
dr. M.S. (Matthijs) Berends b1b7534c78 incorporate Bartlett et al (2022) 2022-12-19 15:32:41 +01:00
dr. M.S. (Matthijs) Berends 23fe427cbc Fixes for Salmonella 2022-12-17 14:31:33 +01:00
dr. M.S. (Matthijs) Berends 5f3a7694aa microorganisms update, added Salmonella groups 2022-12-16 16:10:43 +01:00
dr. M.S. (Matthijs) Berends 8da2467209 updated taxonomy 2022-12-12 00:14:56 +01:00
dr. M.S. (Matthijs) Berends eed1c14b96 website update 2022-12-11 11:44:29 +01:00
dr. M.S. (Matthijs) Berends b1ead9c0fe doc update 2022-12-10 10:09:57 +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 56dad34e68 update prevalence with new phyla 2022-12-09 13:37:08 +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 ba51c2d92f add column to `as.mic()` and `as.disk()` warnings 2022-11-28 19:39:52 +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. M.S. (Matthijs) Berends f6862a139d expert rules 12.0 2022-11-14 15:20:39 +01:00
dr. M.S. (Matthijs) Berends 7ca44fb756 cleanup and new intro logo 2022-11-13 13:44:25 +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 2d90218305 documentation fix 2022-11-05 12:06:40 +01:00
dr. M.S. (Matthijs) Berends 8dc94a9eda documentation fix 2022-11-05 09:31:19 +01:00
dr. M.S. (Matthijs) Berends 3b652983b7 documentation fix 2022-11-05 08:18:06 +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 d40e0ef20b completely updated `antibiotics` 2022-10-30 14:31:45 +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 afdc48db1e fix txt export of microorganisms 2022-10-29 16:08:18 +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 c2801ba7a1 new rsi_translation 2022-10-22 22:00:15 +02:00
dr. M.S. (Matthijs) Berends d10651eb26 cleanup 2022-10-22 10:20:09 +02:00
dr. M.S. (Matthijs) Berends d0b54f640c Update contributors list 2022-10-21 21:56:54 +02:00
dr. M.S. (Matthijs) Berends faca6d608a mean AMR distance 2022-10-21 16:02:14 +02:00
dr. M.S. (Matthijs) Berends 178ab5e5ff mean AMR distance 2022-10-21 15:59:31 +02:00
dr. M.S. (Matthijs) Berends 4bebba3610 fix for scoped dplyr verbs 2022-10-21 15:13:19 +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. M.S. (Matthijs) Berends f203928f7e coercion fixes 2022-10-19 06:59:36 +02:00
dr. M.S. (Matthijs) Berends 3fc39198d0 unit test fix 2022-10-18 23:03:16 +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 ad68b50ecd custom ab fix 2022-10-15 15:20:13 +02:00
Dr. Matthijs Berends 85ed7ea5f0
more robust install check 2022-10-14 15:45:20 +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 dfae4c7e7d fast-forward from pull 
Merge branch 'main' of https://github.com/msberends/AMR into main

# Conflicts:
#	DESCRIPTION
#	R/add_custom_antimicrobials.R
 2022-10-11 10:53:51 +02:00
dr. M.S. (Matthijs) Berends 33227a5d90 support ab selectors for manual AB codes 2022-10-11 10:49:55 +02:00
dr. M.S. (Matthijs) Berends 57d66cd9d0 doc fix 2022-10-10 21:38:39 +02:00
dr. M.S. (Matthijs) Berends 955f9d7020 documentation fix 2022-10-10 21:03:39 +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 4fe90092c7 fix for `NA` in `as.ab()` 2022-10-10 15:44:59 +02:00
dr. M.S. (Matthijs) Berends 43c638d122 add `mo_current()` 2022-10-10 10:12:08 +02:00
dr. M.S. (Matthijs) Berends b753b84128 fix for mo type translation 2022-10-06 12:11:51 +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 fbd5d32541 small fixes 2022-08-29 09:35:36 +02:00
dr. M.S. (Matthijs) Berends e7af5fc716 fix AMR vignette 2022-08-28 22:38:08 +02:00
dr. M.S. (Matthijs) Berends 2ed5f13880 Fixes #57 2022-08-28 21:13:26 +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 f781998904 amoxicillin interpretation fix 2022-08-28 11:17:53 +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 3864ab2fb8 Feather and Parquet files 2022-08-26 22:25:15 +02:00
dr. M.S. (Matthijs) Berends bdbc112f99 website update 2022-08-21 17:22:34 +02:00
dr. M.S. (Matthijs) Berends d6676e9443 disk documentation fix 2022-08-21 16:52:09 +02:00
dr. M.S. (Matthijs) Berends 952d16de33 new, automated website 2022-08-21 16:37:20 +02:00
dr. M.S. (Matthijs) Berends 7226b70c3d update languages 2022-08-20 20:17:14 +02:00
dr. M.S. (Matthijs) Berends 3f2f60ab77 language updates 2022-08-19 12:33:14 +02:00
dr. M.S. (Matthijs) Berends ab97268f4c (v1.8.1.9014) add Toxoplasma 2022-08-12 23:27:15 +02:00
dr. M.S. (Matthijs) Berends 7f981e7778 (v1.8.1.9013) add Toxoplasma 2022-06-10 13:15:23 +02:00
dr. M.S. (Matthijs) Berends b84d647cac (v1.8.1.9012) update prevalence of some genera 2022-06-03 13:28:55 +02:00
dr. M.S. (Matthijs) Berends 70a07bad39 (v1.8.1.9010) random when pkg not loaded 2022-05-16 12:52:50 +02:00
dr. M.S. (Matthijs) Berends 2c5bc73ed6 (v1.8.1.9009) random when pkg not loaded 2022-05-16 09:29:46 +02:00
dr. M.S. (Matthijs) Berends 6de5375256 (v1.8.1.9007) website update 2022-05-11 10:10:31 +02:00