 dr. M.S. (Matthijs) Berends
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7cda9e575b
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prepare for CRAN
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2023-10-20 14:51:48 +02:00 |
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dr. M.S. (Matthijs) Berends
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7dc96794be
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fix rounding MICs on R-devel
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2023-07-20 08:24:27 +02:00 |
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dr. M.S. (Matthijs) Berends
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7a4628b73f
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Added C. freundii complex and Y. pseudotuberculosis complex
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2023-07-14 10:49:06 +02:00 |
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dr. M.S. (Matthijs) Berends
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fd480d1a9a
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console hyperlink fix
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2023-07-14 09:50:13 +02:00 |
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dr. M.S. (Matthijs) Berends
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eff164ecb1
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indicate unique identifiers
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2023-07-12 21:26:32 +02:00 |
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dr. M.S. (Matthijs) Berends
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ea2a4652e9
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mouse-hover fixes
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2023-07-12 15:27:43 +01:00 |
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dr. M.S. (Matthijs) Berends
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e1b4f99f4f
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breakpoints fixes
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2023-07-12 15:20:04 +01:00 |
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dr. M.S. (Matthijs) Berends
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0c46f61260
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MO group fixes
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2023-07-12 15:04:48 +01:00 |
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dr. M.S. (Matthijs) Berends
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7cd9ca274c
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add strep groups to ABCG
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2023-07-12 11:41:25 +01:00 |
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dr. M.S. (Matthijs) Berends
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66eeeb4b88
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cleanup
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2023-07-11 14:29:40 +02:00 |
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dr. M.S. (Matthijs) Berends
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8df1cd8d97
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interpretation fixes
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2023-07-11 09:50:45 +02:00 |
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dr. M.S. (Matthijs) Berends
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dab20c09f6
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unit test
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2023-07-10 18:30:26 +02:00 |
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dr. M.S. (Matthijs) Berends
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1b499bf012
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fixes
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2023-07-10 17:02:28 +02:00 |
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dr. M.S. (Matthijs) Berends
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a4e2e25e3f
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reftbl in plots, speedup for as.sir() and mo_validate
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2023-07-10 16:43:46 +02:00 |
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dr. M.S. (Matthijs) Berends
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70c601ca11
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breakpoints UTI interpretation fix
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2023-07-10 13:41:52 +02:00 |
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dr. M.S. (Matthijs) Berends
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3829311dd3
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random() fix
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2023-07-08 21:00:49 +02:00 |
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dr. M.S. (Matthijs) Berends
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acb534102b
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new species groups, updated clinical breakpoints
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2023-07-08 17:30:05 +02:00 |
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dr. M.S. (Matthijs) Berends
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2d97cca6d9
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fix `reference_df` endless loop
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2023-06-26 13:52:02 +02:00 |
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dr. M.S. (Matthijs) Berends
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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 |
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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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549790c2a6
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website
|
2023-03-20 21:59:50 +01:00 |
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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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e70f2cd32c
|
knitr format
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2023-02-23 16:27:40 +01:00 |
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dr. M.S. (Matthijs) Berends
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a84101db08
|
N for only 1 AB in
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2023-02-22 16:26:13 +01:00 |
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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
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c2cfc5ef84
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fix for `antibiogram()`, transform `WHONET` data set to `sir`
|
2023-02-22 15:40:05 +01:00 |
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dr. M.S. (Matthijs) Berends
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dad25302f2
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make `rsi` work in more cases, documentation update
|
2023-02-22 14:38:57 +01:00 |
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dr. M.S. (Matthijs) Berends
|
8d902410f9
|
unit tests
|
2023-02-18 14:56:06 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
8dcf101a9c
|
website
|
2023-02-18 13:08:08 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
ba255ddb00
|
website
|
2023-02-18 11:57:17 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
e890360986
|
website syntax update
|
2023-02-17 11:39:00 +01:00 |
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dr. M.S. (Matthijs) Berends
|
714a048fa9
|
italicise antibiogram
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2023-02-17 09:42:51 +01:00 |
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dr. M.S. (Matthijs) Berends
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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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dr. M.S. (Matthijs) Berends
|
a82552dd88
|
fix for group selections
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2023-02-15 17:37:49 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
ef716f6ee3
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doc fix
|
2023-02-15 17:16:40 +01:00 |
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dr. M.S. (Matthijs) Berends
|
6016547f1f
|
support for dplyr 1.1.0
|
2023-02-15 17:02:10 +01:00 |
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dr. M.S. (Matthijs) Berends
|
a4cd38c433
|
fix for R < 3.2, `expect_warning()` on hold
|
2023-02-14 10:41:01 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
3396236eef
|
unit test fixes
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2023-02-13 16:56:25 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
b6d2b1398d
|
Fix for `antibiogram()` in R <=3.4
|
2023-02-13 10:21:43 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
45a9697c84
|
unit tests
|
2023-02-12 17:10:48 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
68abb00c59
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add include_screening to `as.sir()`
|
2023-02-12 15:09:54 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
c740967cf2
|
fix for binding rows
|
2023-02-12 11:20:14 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
c51fb24363
|
pm_bind_rows
|
2023-02-11 22:28:48 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
b146de6d7f
|
fix for bind_rows2, added 4 langs
|
2023-02-11 21:57:12 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
2007c3eef3
|
bind_rows
|
2023-02-10 17:09:48 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
03294c7901
|
fix for Salmonella group A, unit tests
|
2023-02-10 16:47:25 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
bc434db835
|
bring back `antibiogram()`, without deps
|
2023-02-10 16:18:00 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
70a7ba0206
|
fix first isolate
|
2023-02-10 13:13:17 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
1a0dc4bf46
|
revert back to pre-antibiogram
|
2023-02-09 13:07:39 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
aa48c6bf53
|
pm fixes
|
2023-02-08 16:51:41 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
822e9de82c
|
pm update, unit test fix?
|
2023-02-08 13:48:06 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
75a4c1ef3e
|
fixes2
|
2023-02-06 14:34:38 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
f7dd890b79
|
fixes
|
2023-02-06 12:38:52 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
9e99e66f01
|
use dplyr where available, new `antibiogram()` for WISCA, fixed Salmonella Typhi/Paratyphi
|
2023-02-06 11:57:22 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
4b133d4c96
|
unit tests
|
2023-01-30 17:24:03 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
89a577805f
|
prelim fix for g.test
|
2023-01-30 12:26:48 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
7b00b4f34a
|
unit tests
|
2023-01-24 14:52:15 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
830c67f1bf
|
documentation, unit tests
|
2023-01-24 10:20:27 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
eef00069fd
|
add all options to documentation
|
2023-01-23 20:07:57 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
19fd0ef121
|
sort sir history
|
2023-01-23 15:01:21 +01:00 |
|
Dr. Matthijs Berends
|
98e62c9af2
|
Replace RSI with SIR
|
2023-01-21 23:47:20 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
24b12024ce
|
unit test fix
|
2023-01-20 09:45:03 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
593d740b84
|
documentation, file permissions
|
2023-01-19 12:54:53 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
b94bc6c67b
|
adding mo fixes
|
2023-01-14 19:50:25 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
ca79068604
|
Fix for adding MO's
|
2023-01-14 17:10:10 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
33f269e2f4
|
contrib update
|
2023-01-12 23:16:05 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
51906d6f97
|
no overwriting taxonomy when adding microorganisms
|
2023-01-12 11:33:28 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
1029aa2fdc
|
algorithm improvement
|
2023-01-07 14:53:14 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
08fe5a88c0
|
documentation
|
2023-01-07 01:54:46 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
2375bfdcb5
|
documentation
|
2023-01-07 01:51:19 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
84ed8c32bb
|
documentation
|
2023-01-06 19:21:04 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
86e28bafce
|
add mo_pathogenicity
|
2023-01-06 13:35:37 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
268ec31d92
|
unit tests
|
2023-01-05 18:21:48 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
a98d0d75ea
|
styler dep
|
2023-01-05 14:46:44 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
a0ee86536a
|
unit tests
|
2023-01-05 14:43:18 +01:00 |
|
dr. M.S. (Matthijs) Berends
|
77d9cf1936
|
documentation
|
2022-12-30 13:02:37 +01:00 |