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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 20:06:12 +01:00
Commit Graph

612 Commits

Author SHA1 Message Date
f7dd890b79 fixes 2023-02-06 12:38:52 +01:00
9e99e66f01 use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
4b133d4c96 unit tests 2023-01-30 17:24:03 +01:00
830c67f1bf documentation, unit tests 2023-01-24 10:20:27 +01:00
eef00069fd add all options to documentation 2023-01-23 20:07:57 +01:00
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
593d740b84 documentation, file permissions 2023-01-19 12:54:53 +01:00
b94bc6c67b adding mo fixes 2023-01-14 19:50:25 +01:00
ca79068604 Fix for adding MO's 2023-01-14 17:10:10 +01:00
33f269e2f4 contrib update 2023-01-12 23:16:05 +01:00
1029aa2fdc algorithm improvement 2023-01-07 14:53:14 +01:00
08fe5a88c0 documentation 2023-01-07 01:54:46 +01:00
2375bfdcb5 documentation 2023-01-07 01:51:19 +01:00
84ed8c32bb documentation 2023-01-06 19:21:04 +01:00
86e28bafce add mo_pathogenicity 2023-01-06 13:35:37 +01:00
268ec31d92 unit tests 2023-01-05 18:21:48 +01:00
a98d0d75ea styler dep 2023-01-05 14:46:44 +01:00
77d9cf1936 documentation 2022-12-30 13:02:37 +01:00
61c0bdb7af documentation 2022-12-28 15:04:59 +01:00
ba3b237bdf custom mo update 2022-12-28 14:20:10 +01:00
f619fb683b support new mo codes 2022-12-27 15:16:15 +01:00
f0a2cdbf5e update mo algorithm 2022-12-20 16:14:04 +01:00
b1b7534c78 incorporate Bartlett et al (2022) 2022-12-19 15:32:41 +01:00
23fe427cbc Fixes for Salmonella 2022-12-17 14:31:33 +01:00
5f3a7694aa microorganisms update, added Salmonella groups 2022-12-16 16:10:43 +01:00
8da2467209 updated taxonomy 2022-12-12 00:14:56 +01:00
eed1c14b96 website update 2022-12-11 11:44:29 +01:00
b1ead9c0fe doc update 2022-12-10 10:09:57 +01:00
56dad34e68 update prevalence with new phyla 2022-12-09 13:37:08 +01:00
510140fc55 Updated mo_gramstain() to reflect current taxonomy, fixes #83 2022-12-09 10:30:25 +01:00
31fb81c382 revised as.rsi(), fix for mdro() 2022-11-24 20:29:00 +01:00
f6862a139d expert rules 12.0 2022-11-14 15:20:39 +01:00
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
2d90218305 documentation fix 2022-11-05 12:06:40 +01:00
8dc94a9eda documentation fix 2022-11-05 09:31:19 +01:00
3b652983b7 documentation fix 2022-11-05 08:18:06 +01:00
9444ed6d1d fix antibiotics error 2022-10-30 21:05:46 +01:00
d40e0ef20b completely updated antibiotics 2022-10-30 14:31:45 +01:00
3d9faf89cf ATC and DDD update 2022-10-29 19:01:23 +02:00
6ad7857d39 fix missing R breakpoints 2022-10-29 14:15:23 +02:00
c2801ba7a1 new rsi_translation 2022-10-22 22:00:15 +02:00
d0b54f640c Update contributors list 2022-10-21 21:56:54 +02:00
faca6d608a mean AMR distance 2022-10-21 16:02:14 +02:00
178ab5e5ff mean AMR distance 2022-10-21 15:59:31 +02:00
4bebba3610 fix for scoped dplyr verbs 2022-10-21 15:13:19 +02:00
aa2c0639d0 add confidence intervals (fixed #70), remove combine_IR 2022-10-20 16:08:01 +02:00
85e2fbe4a3 remove warnings from unit tests 2022-10-19 11:47:57 +02:00
ad68b50ecd custom ab fix 2022-10-15 15:20:13 +02:00