Commit Graph

320 Commits

Author SHA1 Message Date
dr. M.S. (Matthijs) Berends 7f344836ea (v2.1.1.9064) unit tests 2024-07-16 15:55:58 +02:00
dr. M.S. (Matthijs) Berends 640888f408 (v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update 2024-07-16 14:53:17 +02:00
dr. M.S. (Matthijs) Berends 9bf7584d58 (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
dr. M.S. (Matthijs) Berends 0d8a91db49 rename pre-commit hook to pre-commit checks (no-check) 2024-04-23 10:55:48 +02:00
dr. M.S. (Matthijs) Berends 7be4dabbc0 support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
dr. M.S. (Matthijs) Berends ea2a4652e9 mouse-hover fixes 2023-07-12 15:27:43 +01:00
dr. M.S. (Matthijs) Berends 0c46f61260 MO group fixes 2023-07-12 15:04:48 +01:00
dr. M.S. (Matthijs) Berends 66eeeb4b88 cleanup 2023-07-11 14:29:40 +02:00
dr. M.S. (Matthijs) Berends a4e2e25e3f reftbl in plots, speedup for as.sir() and mo_validate 2023-07-10 16:43:46 +02:00
dr. M.S. (Matthijs) Berends 70c601ca11 breakpoints UTI interpretation fix 2023-07-10 13:41:52 +02:00
dr. M.S. (Matthijs) Berends acb534102b new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
dr. M.S. (Matthijs) Berends 2d97cca6d9 fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
dr. M.S. (Matthijs) Berends 1d9ee39cc7 fix for mo codes 2023-06-22 15:24:18 +02:00
Dr. Matthijs Berends f065945d7b
Update clinical breakpoints and fix some `as.mo()` bugs (#117)
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
dr. M.S. (Matthijs) Berends 9591688811 documentation update 2023-05-27 10:39:22 +02:00
dr. M.S. (Matthijs) Berends 766db4e21f as.mo fix 2023-05-26 19:20:21 +02:00
dr. M.S. (Matthijs) Berends c6135d2082 updated microorganism codes 2023-05-26 16:10:01 +02:00
dr. M.S. (Matthijs) Berends 0bcf55d3b6 improve `as.mo()` 2023-05-24 15:55:53 +02:00
dr. M.S. (Matthijs) Berends 91fa73dedf add oxygen tolerance 2023-05-11 21:56:27 +02:00
dr. M.S. (Matthijs) Berends bf08d136a0 fix coercing `NA` to custom codes, fixes #107 2023-05-08 13:04:18 +02:00
dr. M.S. (Matthijs) Berends cabffb22fd anaerobic codes 2023-04-17 11:26:19 +02:00
dr. M.S. (Matthijs) Berends 1a02d302d4 Fix translatable strings 2023-04-15 09:32:13 +02:00
dr. M.S. (Matthijs) Berends 147f9112e9 Fix some WHONET codes 2023-04-14 11:12:26 +02:00
dr. M.S. (Matthijs) Berends 80cfc503c2 check for 2.0 2023-03-12 13:02:37 +01:00
dr. M.S. (Matthijs) Berends 262598b8d7 support for old rsi arguments 2023-03-11 14:24:34 +01:00
dr. M.S. (Matthijs) Berends 4416394e10 website update 2023-02-26 21:26:58 +01:00
dr. M.S. (Matthijs) Berends dad25302f2 make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
dr. M.S. (Matthijs) Berends 45a9697c84 unit tests 2023-02-12 17:10:48 +01:00
dr. M.S. (Matthijs) Berends c740967cf2 fix for binding rows 2023-02-12 11:20:14 +01:00
dr. M.S. (Matthijs) Berends c51fb24363 pm_bind_rows 2023-02-11 22:28:48 +01:00
dr. M.S. (Matthijs) Berends 2007c3eef3 bind_rows 2023-02-10 17:09:48 +01:00
dr. M.S. (Matthijs) Berends 03294c7901 fix for Salmonella group A, unit tests 2023-02-10 16:47:25 +01:00
dr. M.S. (Matthijs) Berends bc434db835 bring back `antibiogram()`, without deps 2023-02-10 16:18:00 +01:00
dr. M.S. (Matthijs) Berends 1a0dc4bf46 revert back to pre-antibiogram 2023-02-09 13:07:39 +01:00
dr. M.S. (Matthijs) Berends 9e99e66f01 use dplyr where available, new `antibiogram()` for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
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 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 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 1029aa2fdc algorithm improvement 2023-01-07 14:53:14 +01:00
dr. M.S. (Matthijs) Berends 2375bfdcb5 documentation 2023-01-07 01:51:19 +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 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