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1d9ee39cc7
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fix for mo codes
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2023-06-22 15:24:18 +02:00 |
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Dr. Matthijs Berends
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f065945d7b
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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
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2023-06-22 15:10:59 +02:00 |
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9591688811
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documentation update
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2023-05-27 10:39:22 +02:00 |
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e1966503ee
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unit testing R4.3
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2023-05-26 20:37:00 +02:00 |
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766db4e21f
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as.mo fix
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2023-05-26 19:20:21 +02:00 |
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c6135d2082
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updated microorganism codes
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2023-05-26 16:10:01 +02:00 |
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0bcf55d3b6
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improve as.mo()
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2023-05-24 15:55:53 +02:00 |
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3018fb87a9
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icu_exclude in first_isolate(), fixes #110
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2023-05-17 22:12:10 +02:00 |
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91fa73dedf
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add oxygen tolerance
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2023-05-11 21:56:27 +02:00 |
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bf08d136a0
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fix coercing NA to custom codes, fixes #107
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2023-05-08 13:04:18 +02:00 |
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9148a2dcf4
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fix mo_rank() for 'unknown' MOs
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2023-04-20 15:20:41 +02:00 |
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cabffb22fd
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anaerobic codes
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2023-04-17 11:26:19 +02:00 |
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1a02d302d4
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Fix translatable strings
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2023-04-15 09:32:13 +02:00 |
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ed70f95380
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Fix clinical breakpoints
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2023-04-14 23:14:34 +02:00 |
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147f9112e9
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Fix some WHONET codes
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2023-04-14 11:12:26 +02:00 |
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549790c2a6
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website
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2023-03-20 21:59:50 +01:00 |
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c28cfa3a77
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fix documentation
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2023-03-16 08:55:37 +01:00 |
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dd7cc86485
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help page %like%
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2023-03-14 19:49:50 +01:00 |
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80cfc503c2
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check for 2.0
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2023-03-12 13:02:37 +01:00 |
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9179e98e12
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patient ID in first isolate
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2023-03-11 17:13:19 +01:00 |
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7ad8635994
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documentation for 'data.table' AB selectors
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2023-03-11 16:54:02 +01:00 |
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45e840c02f
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update NEWS
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2023-03-11 14:43:31 +01:00 |
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262598b8d7
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support for old rsi arguments
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2023-03-11 14:24:34 +01:00 |
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4416394e10
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website update
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2023-02-26 21:26:58 +01:00 |
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1d3d7d40bc
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get episode unit tests
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2023-02-24 19:54:56 +01:00 |
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2c5a9bb622
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new relative episode determination in get_episode(), fix for plotting disk/MIC values
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2023-02-24 17:06:30 +01:00 |
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92029c9e95
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remove note
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2023-02-24 10:31:36 +01:00 |
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049baf0a71
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fix for antibiograms on R < 3.5
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2023-02-24 09:43:10 +01:00 |
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e70f2cd32c
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knitr format
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2023-02-23 16:27:40 +01:00 |
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a84101db08
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N for only 1 AB in
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2023-02-22 16:26:13 +01:00 |
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551aaf6517
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auto-remove missing ABs in antibiogram()
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2023-02-22 16:00:52 +01:00 |
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c2cfc5ef84
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fix for antibiogram(), transform WHONET data set to sir
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2023-02-22 15:40:05 +01:00 |
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dad25302f2
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make rsi work in more cases, documentation update
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2023-02-22 14:38:57 +01:00 |
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8d902410f9
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unit tests
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2023-02-18 14:56:06 +01:00 |
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8dcf101a9c
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website
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2023-02-18 13:08:08 +01:00 |
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ba255ddb00
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website
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2023-02-18 11:57:17 +01:00 |
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e890360986
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website syntax update
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2023-02-17 11:39:00 +01:00 |
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714a048fa9
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italicise antibiogram
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2023-02-17 09:42:51 +01:00 |
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db2830124f
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fix for using dplyr::select()
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2023-02-15 19:48:34 +01:00 |
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a82552dd88
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fix for group selections
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2023-02-15 17:37:49 +01:00 |
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ef716f6ee3
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doc fix
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2023-02-15 17:16:40 +01:00 |
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6016547f1f
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support for dplyr 1.1.0
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2023-02-15 17:02:10 +01:00 |
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a4cd38c433
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fix for R < 3.2, expect_warning() on hold
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2023-02-14 10:41:01 +01:00 |
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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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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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45a9697c84
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unit tests
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2023-02-12 17:10:48 +01:00 |
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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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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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c51fb24363
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pm_bind_rows
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2023-02-11 22:28:48 +01:00 |
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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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2007c3eef3
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bind_rows
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2023-02-10 17:09:48 +01:00 |
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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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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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70a7ba0206
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fix first isolate
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2023-02-10 13:13:17 +01:00 |
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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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aa48c6bf53
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pm fixes
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2023-02-08 16:51:41 +01:00 |
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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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75a4c1ef3e
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fixes2
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2023-02-06 14:34:38 +01:00 |
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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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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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4b133d4c96
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unit tests
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2023-01-30 17:24:03 +01:00 |
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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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7b00b4f34a
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unit tests
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2023-01-24 14:52:15 +01:00 |
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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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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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19fd0ef121
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sort sir history
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2023-01-23 15:01:21 +01:00 |
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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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24b12024ce
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unit test fix
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2023-01-20 09:45:03 +01:00 |
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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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b94bc6c67b
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adding mo fixes
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2023-01-14 19:50:25 +01:00 |
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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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33f269e2f4
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contrib update
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2023-01-12 23:16:05 +01:00 |
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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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1029aa2fdc
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algorithm improvement
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2023-01-07 14:53:14 +01:00 |
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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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2375bfdcb5
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documentation
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2023-01-07 01:51:19 +01:00 |
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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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86e28bafce
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add mo_pathogenicity
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2023-01-06 13:35:37 +01:00 |
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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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a98d0d75ea
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styler dep
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2023-01-05 14:46:44 +01:00 |
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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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77d9cf1936
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documentation
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2022-12-30 13:02:37 +01:00 |
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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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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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61c0bdb7af
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documentation
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2022-12-28 15:04:59 +01:00 |
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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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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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6f4bb603ec
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unit tests
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2022-12-20 22:18:50 +01:00 |
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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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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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23fe427cbc
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Fixes for Salmonella
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2022-12-17 14:31:33 +01:00 |
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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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8da2467209
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updated taxonomy
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2022-12-12 00:14:56 +01:00 |
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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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b1ead9c0fe
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doc update
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2022-12-10 10:09:57 +01:00 |
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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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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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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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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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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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