 dr. M.S. (Matthijs) Berends
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3396236eef
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unit test fixes
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2023-02-13 16:56:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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b6d2b1398d
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Fix for `antibiogram()` in R <=3.4
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2023-02-13 10:21:43 +01:00 |
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dr. M.S. (Matthijs) Berends
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45a9697c84
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unit tests
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2023-02-12 17:10:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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68abb00c59
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add include_screening to `as.sir()`
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2023-02-12 15:09:54 +01:00 |
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dr. M.S. (Matthijs) Berends
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c740967cf2
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fix for binding rows
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2023-02-12 11:20:14 +01:00 |
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dr. M.S. (Matthijs) Berends
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c51fb24363
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pm_bind_rows
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2023-02-11 22:28:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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b146de6d7f
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fix for bind_rows2, added 4 langs
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2023-02-11 21:57:12 +01:00 |
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dr. M.S. (Matthijs) Berends
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2007c3eef3
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bind_rows
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2023-02-10 17:09:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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03294c7901
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fix for Salmonella group A, unit tests
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2023-02-10 16:47:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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bc434db835
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bring back `antibiogram()`, without deps
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2023-02-10 16:18:00 +01:00 |
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dr. M.S. (Matthijs) Berends
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70a7ba0206
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fix first isolate
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2023-02-10 13:13:17 +01:00 |
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dr. M.S. (Matthijs) Berends
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1a0dc4bf46
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revert back to pre-antibiogram
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2023-02-09 13:07:39 +01:00 |
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dr. M.S. (Matthijs) Berends
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aa48c6bf53
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pm fixes
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2023-02-08 16:51:41 +01:00 |
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dr. M.S. (Matthijs) Berends
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822e9de82c
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pm update, unit test fix?
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2023-02-08 13:48:06 +01:00 |
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dr. M.S. (Matthijs) Berends
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75a4c1ef3e
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fixes2
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2023-02-06 14:34:38 +01:00 |
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dr. M.S. (Matthijs) Berends
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f7dd890b79
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fixes
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2023-02-06 12:38:52 +01:00 |
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dr. M.S. (Matthijs) Berends
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9e99e66f01
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use dplyr where available, new `antibiogram()` for WISCA, fixed Salmonella Typhi/Paratyphi
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2023-02-06 11:57:22 +01:00 |
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dr. M.S. (Matthijs) Berends
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4b133d4c96
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unit tests
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2023-01-30 17:24:03 +01:00 |
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dr. M.S. (Matthijs) Berends
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89a577805f
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prelim fix for g.test
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2023-01-30 12:26:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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7b00b4f34a
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unit tests
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2023-01-24 14:52:15 +01:00 |
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dr. M.S. (Matthijs) Berends
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830c67f1bf
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documentation, unit tests
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2023-01-24 10:20:27 +01:00 |
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dr. M.S. (Matthijs) Berends
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eef00069fd
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add all options to documentation
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2023-01-23 20:07:57 +01:00 |
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dr. M.S. (Matthijs) Berends
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19fd0ef121
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sort sir history
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2023-01-23 15:01:21 +01:00 |
Dr. Matthijs Berends
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98e62c9af2
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Replace RSI with SIR
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2023-01-21 23:47:20 +01:00 |
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dr. M.S. (Matthijs) Berends
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24b12024ce
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unit test fix
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2023-01-20 09:45:03 +01:00 |
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dr. M.S. (Matthijs) Berends
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593d740b84
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documentation, file permissions
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2023-01-19 12:54:53 +01:00 |
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dr. M.S. (Matthijs) Berends
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b94bc6c67b
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adding mo fixes
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2023-01-14 19:50:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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ca79068604
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Fix for adding MO's
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2023-01-14 17:10:10 +01:00 |
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dr. M.S. (Matthijs) Berends
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33f269e2f4
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contrib update
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2023-01-12 23:16:05 +01:00 |
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dr. M.S. (Matthijs) Berends
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51906d6f97
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no overwriting taxonomy when adding microorganisms
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2023-01-12 11:33:28 +01:00 |
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dr. M.S. (Matthijs) Berends
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1029aa2fdc
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algorithm improvement
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2023-01-07 14:53:14 +01:00 |
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dr. M.S. (Matthijs) Berends
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08fe5a88c0
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documentation
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2023-01-07 01:54:46 +01:00 |
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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 |
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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
|
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
|
ad68b50ecd
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
b753b84128
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fix for mo type translation
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2022-10-06 12:11:51 +02:00 |
|
dr. M.S. (Matthijs) Berends
|
b9342d103e
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fix documentation
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2022-10-06 11:33:30 +02:00 |
|
Dr. Matthijs Berends
|
cd2acc4a29
|
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
|
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
|
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
|
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
|
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
|
2ed5f13880
|
Fixes #57
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2022-08-28 21:13:26 +02:00 |