 dr. M.S. (Matthijs) Berends
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2375bfdcb5
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documentation
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2023-01-07 01:51:19 +01:00 |
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dr. M.S. (Matthijs) Berends
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84ed8c32bb
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documentation
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2023-01-06 19:21:04 +01:00 |
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dr. M.S. (Matthijs) Berends
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86e28bafce
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add mo_pathogenicity
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2023-01-06 13:35:37 +01:00 |
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dr. M.S. (Matthijs) Berends
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268ec31d92
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unit tests
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2023-01-05 18:21:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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a98d0d75ea
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styler dep
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2023-01-05 14:46:44 +01:00 |
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dr. M.S. (Matthijs) Berends
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a0ee86536a
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unit tests
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2023-01-05 14:43:18 +01:00 |
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dr. M.S. (Matthijs) Berends
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77d9cf1936
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documentation
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2022-12-30 13:02:37 +01:00 |
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dr. M.S. (Matthijs) Berends
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e4ea96cbf9
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fix for R < 3.4
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2022-12-30 12:57:27 +01:00 |
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dr. M.S. (Matthijs) Berends
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1db74e86cd
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good start-up practice
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2022-12-29 16:23:57 +01:00 |
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dr. M.S. (Matthijs) Berends
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61c0bdb7af
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documentation
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2022-12-28 15:04:59 +01:00 |
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dr. M.S. (Matthijs) Berends
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ba3b237bdf
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custom mo update
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2022-12-28 14:20:10 +01:00 |
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dr. M.S. (Matthijs) Berends
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f619fb683b
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support new mo codes
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2022-12-27 15:16:15 +01:00 |
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dr. M.S. (Matthijs) Berends
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6f4bb603ec
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unit tests
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2022-12-20 22:18:50 +01:00 |
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dr. M.S. (Matthijs) Berends
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f0a2cdbf5e
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update mo algorithm
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2022-12-20 16:14:04 +01:00 |
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dr. M.S. (Matthijs) Berends
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b1b7534c78
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incorporate Bartlett et al (2022)
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2022-12-19 15:32:41 +01:00 |
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dr. M.S. (Matthijs) Berends
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23fe427cbc
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Fixes for Salmonella
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2022-12-17 14:31:33 +01:00 |
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dr. M.S. (Matthijs) Berends
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5f3a7694aa
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microorganisms update, added Salmonella groups
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2022-12-16 16:10:43 +01:00 |
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dr. M.S. (Matthijs) Berends
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8da2467209
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updated taxonomy
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2022-12-12 00:14:56 +01:00 |
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dr. M.S. (Matthijs) Berends
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eed1c14b96
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website update
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2022-12-11 11:44:29 +01:00 |
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dr. M.S. (Matthijs) Berends
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b1ead9c0fe
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doc update
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2022-12-10 10:09:57 +01:00 |
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dr. M.S. (Matthijs) Berends
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e7d7b94b3e
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no obligatory note on startup
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2022-12-09 15:10:49 +01:00 |
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dr. M.S. (Matthijs) Berends
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56dad34e68
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update prevalence with new phyla
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2022-12-09 13:37:08 +01:00 |
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dr. M.S. (Matthijs) Berends
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510140fc55
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Updated `mo_gramstain()` to reflect current taxonomy, fixes #83
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2022-12-09 10:30:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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ba51c2d92f
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add column to `as.mic()` and `as.disk()` warnings
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2022-11-28 19:39:52 +01:00 |
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dr. M.S. (Matthijs) Berends
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31fb81c382
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revised `as.rsi()`, fix for `mdro()`
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2022-11-24 20:29:00 +01:00 |
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dr. M.S. (Matthijs) Berends
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05d536ebb7
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complexes
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2022-11-17 15:23:29 +01:00 |
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dr. M.S. (Matthijs) Berends
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f6862a139d
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expert rules 12.0
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2022-11-14 15:20:39 +01:00 |
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dr. M.S. (Matthijs) Berends
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7ca44fb756
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cleanup and new intro logo
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2022-11-13 13:44:25 +01:00 |
Dr. Matthijs Berends
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496c08d851
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Implement extensive support for antiviral agents support (#77)
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2022-11-13 08:46:10 +01:00 |
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dr. M.S. (Matthijs) Berends
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2d90218305
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documentation fix
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2022-11-05 12:06:40 +01:00 |
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dr. M.S. (Matthijs) Berends
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8dc94a9eda
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documentation fix
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2022-11-05 09:31:19 +01:00 |
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dr. M.S. (Matthijs) Berends
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3b652983b7
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documentation fix
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2022-11-05 08:18:06 +01:00 |
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dr. M.S. (Matthijs) Berends
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d20caae54b
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cleanup
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2022-10-31 13:25:41 +01:00 |
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dr. M.S. (Matthijs) Berends
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796b972f8a
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extend vctrs support
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2022-10-31 11:19:06 +01:00 |
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dr. M.S. (Matthijs) Berends
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9444ed6d1d
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fix antibiotics error
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2022-10-30 21:05:46 +01:00 |
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dr. M.S. (Matthijs) Berends
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d40e0ef20b
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completely updated `antibiotics`
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2022-10-30 14:31:45 +01:00 |
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dr. M.S. (Matthijs) Berends
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3d9faf89cf
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ATC and DDD update
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2022-10-29 19:01:23 +02:00 |
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dr. M.S. (Matthijs) Berends
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afdc48db1e
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fix txt export of microorganisms
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2022-10-29 16:08:18 +02:00 |
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dr. M.S. (Matthijs) Berends
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6ad7857d39
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fix missing R breakpoints
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2022-10-29 14:15:23 +02:00 |
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dr. M.S. (Matthijs) Berends
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c2801ba7a1
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new rsi_translation
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2022-10-22 22:00:15 +02:00 |
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dr. M.S. (Matthijs) Berends
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d10651eb26
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cleanup
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2022-10-22 10:20:09 +02:00 |
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dr. M.S. (Matthijs) Berends
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d0b54f640c
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Update contributors list
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2022-10-21 21:56:54 +02:00 |
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dr. M.S. (Matthijs) Berends
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faca6d608a
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mean AMR distance
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2022-10-21 16:02:14 +02:00 |
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dr. M.S. (Matthijs) Berends
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178ab5e5ff
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mean AMR distance
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2022-10-21 15:59:31 +02:00 |
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dr. M.S. (Matthijs) Berends
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4bebba3610
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fix for scoped dplyr verbs
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2022-10-21 15:13:19 +02:00 |
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dr. M.S. (Matthijs) Berends
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aa2c0639d0
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add confidence intervals (fixed #70), remove `combine_IR`
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2022-10-20 16:08:01 +02:00 |
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dr. M.S. (Matthijs) Berends
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85e2fbe4a3
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remove warnings from unit tests
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2022-10-19 11:47:57 +02:00 |
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dr. M.S. (Matthijs) Berends
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f203928f7e
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coercion fixes
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2022-10-19 06:59:36 +02:00 |
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dr. M.S. (Matthijs) Berends
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3fc39198d0
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unit test fix
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2022-10-18 23:03:16 +02:00 |
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dr. M.S. (Matthijs) Berends
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e5e6d2200d
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fix add manual ab
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2022-10-18 22:53:38 +02:00 |
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dr. M.S. (Matthijs) Berends
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ad68b50ecd
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custom ab fix
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2022-10-15 15:20:13 +02:00 |
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Dr. Matthijs Berends
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85ed7ea5f0
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more robust install check
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2022-10-14 15:45:20 +02:00 |
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dr. M.S. (Matthijs) Berends
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76bcd3528c
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move object assignment to AMR_env
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2022-10-14 13:02:50 +02:00 |
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dr. M.S. (Matthijs) Berends
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dfae4c7e7d
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fast-forward from pull
Merge branch 'main' of https://github.com/msberends/AMR into main
# Conflicts:
# DESCRIPTION
# R/add_custom_antimicrobials.R
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2022-10-11 10:53:51 +02:00 |
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dr. M.S. (Matthijs) Berends
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33227a5d90
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support ab selectors for manual AB codes
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2022-10-11 10:49:55 +02:00 |
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dr. M.S. (Matthijs) Berends
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57d66cd9d0
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doc fix
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2022-10-10 21:38:39 +02:00 |
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dr. M.S. (Matthijs) Berends
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955f9d7020
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documentation fix
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2022-10-10 21:03:39 +02:00 |
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dr. M.S. (Matthijs) Berends
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82e3198315
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add `add_custom_antimicrobials()`
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2022-10-10 20:20:39 +02:00 |
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dr. M.S. (Matthijs) Berends
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4fe90092c7
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fix for `NA` in `as.ab()`
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2022-10-10 15:44:59 +02:00 |
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dr. M.S. (Matthijs) Berends
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43c638d122
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add `mo_current()`
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2022-10-10 10:12:08 +02:00 |
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dr. M.S. (Matthijs) Berends
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b753b84128
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fix for mo type translation
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2022-10-06 12:11:51 +02:00 |
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dr. M.S. (Matthijs) Berends
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b9342d103e
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fix documentation
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2022-10-06 11:33:30 +02:00 |
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Dr. Matthijs Berends
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cd2acc4a29
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New mo algorithm, prepare for 2.0
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2022-10-05 09:12:22 +02:00 |
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dr. M.S. (Matthijs) Berends
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63fe160322
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new rsi_interpretation_history
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2022-09-01 15:20:57 +02:00 |
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dr. M.S. (Matthijs) Berends
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3fca703fbf
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new AMR distance function
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2022-08-30 21:48:02 +02:00 |
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dr. M.S. (Matthijs) Berends
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fbd5d32541
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small fixes
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2022-08-29 09:35:36 +02:00 |
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dr. M.S. (Matthijs) Berends
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e7af5fc716
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fix AMR vignette
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2022-08-28 22:38:08 +02:00 |
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dr. M.S. (Matthijs) Berends
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2ed5f13880
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Fixes #57
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2022-08-28 21:13:26 +02:00 |
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dr. M.S. (Matthijs) Berends
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c44ddf272f
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fix for R <= 3.3
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2022-08-28 19:34:04 +02:00 |
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dr. M.S. (Matthijs) Berends
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71db246d5c
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unit test fix
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2022-08-28 19:17:12 +02:00 |
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dr. M.S. (Matthijs) Berends
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f781998904
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amoxicillin interpretation fix
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2022-08-28 11:17:53 +02:00 |
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dr. M.S. (Matthijs) Berends
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4d050aef7c
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styled, unit test fix
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2022-08-28 10:31:50 +02:00 |
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dr. M.S. (Matthijs) Berends
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303d61b473
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new tibble export
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2022-08-27 20:49:37 +02:00 |
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dr. M.S. (Matthijs) Berends
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3864ab2fb8
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Feather and Parquet files
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2022-08-26 22:25:15 +02:00 |
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dr. M.S. (Matthijs) Berends
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bdbc112f99
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website update
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2022-08-21 17:22:34 +02:00 |
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dr. M.S. (Matthijs) Berends
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d6676e9443
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disk documentation fix
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2022-08-21 16:52:09 +02:00 |
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dr. M.S. (Matthijs) Berends
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952d16de33
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new, automated website
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2022-08-21 16:37:20 +02:00 |
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dr. M.S. (Matthijs) Berends
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7226b70c3d
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update languages
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2022-08-20 20:17:14 +02:00 |
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dr. M.S. (Matthijs) Berends
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3f2f60ab77
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language updates
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2022-08-19 12:33:14 +02:00 |
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dr. M.S. (Matthijs) Berends
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ab97268f4c
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(v1.8.1.9014) add Toxoplasma
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2022-08-12 23:27:15 +02:00 |
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dr. M.S. (Matthijs) Berends
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7f981e7778
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(v1.8.1.9013) add Toxoplasma
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2022-06-10 13:15:23 +02:00 |
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dr. M.S. (Matthijs) Berends
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b84d647cac
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(v1.8.1.9012) update prevalence of some genera
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2022-06-03 13:28:55 +02:00 |
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dr. M.S. (Matthijs) Berends
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70a07bad39
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(v1.8.1.9010) random when pkg not loaded
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2022-05-16 12:52:50 +02:00 |
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dr. M.S. (Matthijs) Berends
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2c5bc73ed6
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(v1.8.1.9009) random when pkg not loaded
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2022-05-16 09:29:46 +02:00 |
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dr. M.S. (Matthijs) Berends
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6de5375256
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(v1.8.1.9007) website update
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2022-05-11 10:10:31 +02:00 |
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dr. M.S. (Matthijs) Berends
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859224e9d0
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(v1.8.1.9006) added EUCAST 2022 and CLSI 2022
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2022-05-10 21:34:30 +02:00 |
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dr. M.S. (Matthijs) Berends
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680e8e7a41
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(v1.8.1.9005) as.rsi() fix for EUCAST
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2022-05-10 17:01:37 +02:00 |
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dr. M.S. (Matthijs) Berends
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d4e22069bc
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(v1.8.1.9004) fix for table() on MICs
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2022-05-09 21:33:27 +02:00 |
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dr. M.S. (Matthijs) Berends
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1c891cc90c
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(v1.8.1.9003) set_mo_source() fix
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2022-05-09 20:36:44 +02:00 |
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dr. M.S. (Matthijs) Berends
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152db9d1b5
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(v1.8.1.9002) fix for table() on MICs
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2022-05-09 17:08:40 +02:00 |
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dr. M.S. (Matthijs) Berends
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4754848e96
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(v1.8.1.9001) update unit tests, fixes #53
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2022-04-08 11:02:45 +02:00 |
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dr. M.S. (Matthijs) Berends
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ccb09706e4
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v1.8.1
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2022-03-24 23:05:04 +01:00 |
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dr. M.S. (Matthijs) Berends
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7b0f1596bd
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(v1.8.0.9010) as.mo improvement
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2022-03-15 17:35:02 +01:00 |
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dr. M.S. (Matthijs) Berends
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1b0983e382
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(v1.8.1) prerelease 1.8.1
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2022-03-14 16:36:10 +01:00 |
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dr. M.S. (Matthijs) Berends
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08d387b5ce
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(v1.8.0.9005) as.rsi() fix
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2022-03-10 19:33:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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ad82bb4ce0
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(v1.8.0.9004) MIC printing in tibbles
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2022-03-03 21:11:02 +01:00 |
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dr. M.S. (Matthijs) Berends
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3b2b2be5f8
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(v1.8.0.9002) as.rsi() cleanup, more informative warnings
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2022-03-02 15:38:55 +01:00 |
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dr. M.S. (Matthijs) Berends
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18e8525d10
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(v1.8.0.9001) as.mo improvement, fixes #52
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2022-02-26 21:58:23 +01:00 |
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dr. M.S. (Matthijs) Berends
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f5dcf0ad58
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v1.8.0 as accepted by CRAN
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2022-01-07 16:27:13 +01:00 |
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dr. M.S. (Matthijs) Berends
|
25cef46c59
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(v1.8.0) prerelease 1.8.0
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2021-12-23 18:56:28 +01:00 |
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dr. M.S. (Matthijs) Berends
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75dac113b6
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(v1.7.1.9077) skimr support only for newer R versions
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2021-12-23 13:38:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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d9274bcd0a
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(v1.7.1.9075) assignment operator
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2021-12-14 22:59:27 +01:00 |
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dr. M.S. (Matthijs) Berends
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76dee66852
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(v1.7.1.9074) as.mo() improvement, ASCII replacements for unit tests
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2021-12-14 22:39:23 +01:00 |
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dr. M.S. (Matthijs) Berends
|
bd4bb1d72f
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(v1.7.1.9073) as.rsi() fix for UTIs
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2021-12-14 21:47:14 +01:00 |
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dr. M.S. (Matthijs) Berends
|
5eef01165e
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(v1.7.1.9072) as.rsi() fix for UTIs
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2021-12-14 12:33:29 +01:00 |
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dr. M.S. (Matthijs) Berends
|
0cbf8f48b6
|
(v1.7.1.9071) rsi disk fix
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2021-12-13 11:57:34 +01:00 |
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dr. M.S. (Matthijs) Berends
|
578e7dfee9
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(v1.7.1.9070) Better WHONET support
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2021-12-13 10:18:28 +01:00 |
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dr. M.S. (Matthijs) Berends
|
f90e27c1b0
|
(v1.7.1.9069) CLSI 2021 support
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2021-12-12 11:36:58 +01:00 |
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dr. M.S. (Matthijs) Berends
|
1e66a3daf3
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(v1.7.1.9068) new logo, unit tests
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2021-12-12 11:07:02 +01:00 |
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dr. M.S. (Matthijs) Berends
|
56f1ce328a
|
(v1.7.1.9067) Support for Swedish and Russian
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2021-12-12 09:42:03 +01:00 |
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dr. M.S. (Matthijs) Berends
|
5b5f70a103
|
(v1.7.1.9066) mdro EUCAST v3.3
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2021-12-11 15:29:30 +01:00 |
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dr. M.S. (Matthijs) Berends
|
e0a2634f14
|
(v1.7.1.9065) unit tests
|
2021-12-11 15:13:44 +01:00 |
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dr. M.S. (Matthijs) Berends
|
77ba4318ea
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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
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2021-12-11 13:41:31 +01:00 |
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dr. M.S. (Matthijs) Berends
|
e18c49ed93
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(v1.7.1.9063) not_intrinsic_resistant
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2021-12-09 10:48:25 +01:00 |
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dr. M.S. (Matthijs) Berends
|
1fa3fc6af2
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(v1.7.1.9061) bugfix set_ab_names
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2021-12-05 23:21:59 +01:00 |
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dr. M.S. (Matthijs) Berends
|
75965124ef
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(v1.7.1.9060) bugfix set_ab_names
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2021-12-05 23:11:10 +01:00 |
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dr. M.S. (Matthijs) Berends
|
b747036deb
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(v1.7.1.9059) bugfix set_ab_names
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2021-12-05 22:59:06 +01:00 |
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dr. M.S. (Matthijs) Berends
|
7965468ccd
|
(v1.7.1.9058) vars selection for set_ab_names()
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2021-12-05 22:06:45 +01:00 |
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dr. M.S. (Matthijs) Berends
|
3abe61fd61
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(v1.7.1.9057) NAs in get_episode()
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2021-12-02 13:32:14 +01:00 |
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dr. M.S. (Matthijs) Berends
|
5375f75829
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(v1.7.1.9056) unit tests
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2021-11-29 11:55:18 +01:00 |
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dr. M.S. (Matthijs) Berends
|
c8698347cb
|
(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers
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2021-11-29 10:38:38 +01:00 |
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dr. M.S. (Matthijs) Berends
|
694cf5ba77
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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
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2021-11-28 23:01:26 +01:00 |
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dr. M.S. (Matthijs) Berends
|
9a2c431e16
|
(v1.7.1.9053) fortify() methods
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2021-11-01 13:51:13 +01:00 |
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dr. M.S. (Matthijs) Berends
|
91149d6d35
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(v1.7.1.9052) eucast-update
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2021-10-06 16:22:36 +02:00 |
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dr. M.S. (Matthijs) Berends
|
37e6e35ec4
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(v1.7.1.9051) updated taxonomy, updated git branch name
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2021-10-06 13:23:57 +02:00 |
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dr. M.S. (Matthijs) Berends
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8f5e5a3fc2
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(v1.7.1.9050) fix for as.mo
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2021-10-05 14:00:35 +02:00 |
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dr. M.S. (Matthijs) Berends
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2bcf28281d
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(v1.7.1.9049) unit tests
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2021-10-05 09:58:08 +02:00 |
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dr. M.S. (Matthijs) Berends
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93a4734b44
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(v1.7.1.9040) Support for Danish
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2021-09-29 12:12:35 +02:00 |
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dr. M.S. (Matthijs) Berends
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81a1a432bd
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(v1.7.1.9038) dplyr grouping fix on windows?
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2021-09-01 16:52:55 +02:00 |
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dr. M.S. (Matthijs) Berends
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bcab74fb6d
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(v1.7.1.9037) dplyr grouping fix on windows?
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2021-08-31 17:06:44 +02:00 |
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dr. M.S. (Matthijs) Berends
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986bd826ee
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(v1.7.1.9035) dplyr grouping fix on windows?
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2021-08-30 15:43:12 +02:00 |
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dr. M.S. (Matthijs) Berends
|
1daa117e9f
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(v1.7.1.9033) dplyr grouping fix on windows?
|
2021-08-30 15:01:32 +02:00 |
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dr. M.S. (Matthijs) Berends
|
6ca6a3f6df
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(v1.7.1.9032) dplyr grouping fix on windows?
|
2021-08-30 14:17:27 +02:00 |
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dr. M.S. (Matthijs) Berends
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e6ce25162e
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(v1.7.1.9031) dplyr grouping fix on windows?
|
2021-08-30 14:07:46 +02:00 |
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dr. M.S. (Matthijs) Berends
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d6a916d70b
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(v1.7.1.9030) unit test
|
2021-08-29 23:50:45 +02:00 |
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dr. M.S. (Matthijs) Berends
|
2ab21b7af3
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(v1.7.1.9026) updated DDDs
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2021-08-19 23:43:02 +02:00 |
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dr. M.S. (Matthijs) Berends
|
1b62bab007
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(v1.7.1.9025) unit tests
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2021-08-18 23:19:38 +02:00 |
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dr. M.S. (Matthijs) Berends
|
a44283f998
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(v1.7.1.9024) unit tests
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2021-08-17 14:34:11 +02:00 |
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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
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2021-08-16 21:54:34 +02:00 |
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dr. M.S. (Matthijs) Berends
|
4e1efd902c
|
(v1.7.1.9022) rely on vctrs for ab selectors
|
2021-07-23 21:42:11 +02:00 |
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dr. M.S. (Matthijs) Berends
|
0ec81cc12e
|
(v1.7.1.9021) autoplot generics
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2021-07-12 22:12:28 +02:00 |
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dr. M.S. (Matthijs) Berends
|
6838f03bde
|
(v1.7.1.9020) autoplot generics
|
2021-07-12 20:24:49 +02:00 |
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dr. M.S. (Matthijs) Berends
|
fc946564d1
|
(v1.7.1.9019) Morganella MIC in EUCAST 2021
|
2021-07-12 12:28:41 +02:00 |
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dr. M.S. (Matthijs) Berends
|
5ccb330b42
|
(v1.7.1.9018) translation fix
|
2021-07-11 13:20:45 +02:00 |
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dr. M.S. (Matthijs) Berends
|
39d97ab53b
|
(v1.7.1.9017) ab selector error
|
2021-07-08 23:05:45 +02:00 |
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dr. M.S. (Matthijs) Berends
|
b228eb1536
|
(v1.7.1.9016) only_treatable ab selectors
|
2021-07-08 22:23:28 +02:00 |
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dr. M.S. (Matthijs) Berends
|
625a6fb304
|
(v1.7.1.9015) removed S3 taxonomic_name again
|
2021-07-07 20:34:05 +02:00 |
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dr. M.S. (Matthijs) Berends
|
ad10693a1a
|
(v1.7.1.9014) rep() for S3 classes
|
2021-07-06 16:35:14 +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 |
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dr. M.S. (Matthijs) Berends
|
5b5741f681
|
(v1.7.1.9011) subsetting taxonomy fix
|
2021-07-04 15:26:50 +02:00 |