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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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dab20c09f6
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unit test
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2023-07-10 18:30:26 +02:00 |
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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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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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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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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. Matthijs Berends
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f065945d7b
|
Update clinical breakpoints and fix some as.mo() bugs (#117)
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
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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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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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02322ac2ee
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Fix PK/PD breakpoints
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2023-04-19 00:31:31 +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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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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1d3d7d40bc
|
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
|
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
|
2023-02-24 09:43:10 +01:00 |
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e70f2cd32c
|
knitr format
|
2023-02-23 16:27:40 +01:00 |
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a84101db08
|
N for only 1 AB in
|
2023-02-22 16:26:13 +01:00 |
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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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dad25302f2
|
make rsi work in more cases, documentation update
|
2023-02-22 14:38:57 +01:00 |
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e890360986
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website syntax update
|
2023-02-17 11:39:00 +01:00 |
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714a048fa9
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italicise antibiogram
|
2023-02-17 09:42:51 +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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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
|
unit tests
|
2023-02-12 17:10:48 +01:00 |
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68abb00c59
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add include_screening to as.sir()
|
2023-02-12 15:09:54 +01:00 |
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b146de6d7f
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fix for bind_rows2, added 4 langs
|
2023-02-11 21:57:12 +01:00 |
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03294c7901
|
fix for Salmonella group A, unit tests
|
2023-02-10 16:47:25 +01:00 |
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bc434db835
|
bring back antibiogram(), without deps
|
2023-02-10 16:18:00 +01:00 |
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70a7ba0206
|
fix first isolate
|
2023-02-10 13:13:17 +01:00 |
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1a0dc4bf46
|
revert back to pre-antibiogram
|
2023-02-09 13:07:39 +01:00 |
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aa48c6bf53
|
pm fixes
|
2023-02-08 16:51:41 +01:00 |
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f7dd890b79
|
fixes
|
2023-02-06 12:38:52 +01:00 |
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9e99e66f01
|
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
|
2023-02-06 11:57:22 +01:00 |
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4b133d4c96
|
unit tests
|
2023-01-30 17:24:03 +01:00 |
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830c67f1bf
|
documentation, unit tests
|
2023-01-24 10:20:27 +01:00 |
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eef00069fd
|
add all options to documentation
|
2023-01-23 20:07:57 +01:00 |
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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 |
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593d740b84
|
documentation, file permissions
|
2023-01-19 12:54:53 +01:00 |
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b94bc6c67b
|
adding mo fixes
|
2023-01-14 19:50:25 +01:00 |
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ca79068604
|
Fix for adding MO's
|
2023-01-14 17:10:10 +01:00 |
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33f269e2f4
|
contrib update
|
2023-01-12 23:16:05 +01:00 |
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1029aa2fdc
|
algorithm improvement
|
2023-01-07 14:53:14 +01:00 |
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08fe5a88c0
|
documentation
|
2023-01-07 01:54:46 +01:00 |
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2375bfdcb5
|
documentation
|
2023-01-07 01:51:19 +01:00 |
|
|
|
84ed8c32bb
|
documentation
|
2023-01-06 19:21:04 +01:00 |
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|
|
86e28bafce
|
add mo_pathogenicity
|
2023-01-06 13:35:37 +01:00 |
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|
268ec31d92
|
unit tests
|
2023-01-05 18:21:48 +01:00 |
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|
|
a98d0d75ea
|
styler dep
|
2023-01-05 14:46:44 +01:00 |
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|
77d9cf1936
|
documentation
|
2022-12-30 13:02:37 +01:00 |
|
|
|
61c0bdb7af
|
documentation
|
2022-12-28 15:04:59 +01:00 |
|
|
|
ba3b237bdf
|
custom mo update
|
2022-12-28 14:20:10 +01:00 |
|
|
|
f619fb683b
|
support new mo codes
|
2022-12-27 15:16:15 +01:00 |
|
|
|
f0a2cdbf5e
|
update mo algorithm
|
2022-12-20 16:14:04 +01:00 |
|
|
|
b1b7534c78
|
incorporate Bartlett et al (2022)
|
2022-12-19 15:32:41 +01:00 |
|
|
|
23fe427cbc
|
Fixes for Salmonella
|
2022-12-17 14:31:33 +01:00 |
|
|
|
5f3a7694aa
|
microorganisms update, added Salmonella groups
|
2022-12-16 16:10:43 +01:00 |
|
|
|
8da2467209
|
updated taxonomy
|
2022-12-12 00:14:56 +01:00 |
|
|
|
eed1c14b96
|
website update
|
2022-12-11 11:44:29 +01:00 |
|
|
|
b1ead9c0fe
|
doc update
|
2022-12-10 10:09:57 +01:00 |
|
|
|
56dad34e68
|
update prevalence with new phyla
|
2022-12-09 13:37:08 +01:00 |
|
|
|
510140fc55
|
Updated mo_gramstain() to reflect current taxonomy, fixes #83
|
2022-12-09 10:30:25 +01:00 |
|
|
|
31fb81c382
|
revised as.rsi(), fix for mdro()
|
2022-11-24 20:29:00 +01:00 |
|
|
|
f6862a139d
|
expert rules 12.0
|
2022-11-14 15:20:39 +01:00 |
|
|
|
7ca44fb756
|
cleanup and new intro logo
|
2022-11-13 13:44:25 +01:00 |
|
Dr. Matthijs Berends
|
496c08d851
|
Implement extensive support for antiviral agents support (#77)
|
2022-11-13 08:46:10 +01:00 |
|
|
|
2d90218305
|
documentation fix
|
2022-11-05 12:06:40 +01:00 |
|
|
|
8dc94a9eda
|
documentation fix
|
2022-11-05 09:31:19 +01:00 |
|
|
|
3b652983b7
|
documentation fix
|
2022-11-05 08:18:06 +01:00 |
|
|
|
9444ed6d1d
|
fix antibiotics error
|
2022-10-30 21:05:46 +01:00 |
|
|
|
d40e0ef20b
|
completely updated antibiotics
|
2022-10-30 14:31:45 +01:00 |
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|
3d9faf89cf
|
ATC and DDD update
|
2022-10-29 19:01:23 +02:00 |
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|
|
6ad7857d39
|
fix missing R breakpoints
|
2022-10-29 14:15:23 +02:00 |
|
|
|
c2801ba7a1
|
new rsi_translation
|
2022-10-22 22:00:15 +02:00 |
|
|
|
d0b54f640c
|
Update contributors list
|
2022-10-21 21:56:54 +02:00 |
|
|
|
faca6d608a
|
mean AMR distance
|
2022-10-21 16:02:14 +02:00 |
|
|
|
178ab5e5ff
|
mean AMR distance
|
2022-10-21 15:59:31 +02:00 |
|
|
|
4bebba3610
|
fix for scoped dplyr verbs
|
2022-10-21 15:13:19 +02:00 |
|
|
|
aa2c0639d0
|
add confidence intervals (fixed #70), remove combine_IR
|
2022-10-20 16:08:01 +02:00 |
|
|
|
85e2fbe4a3
|
remove warnings from unit tests
|
2022-10-19 11:47:57 +02:00 |
|
|
|
ad68b50ecd
|
custom ab fix
|
2022-10-15 15:20:13 +02:00 |
|
|
|
76bcd3528c
|
move object assignment to AMR_env
|
2022-10-14 13:02:50 +02:00 |
|
|
|
dfae4c7e7d
|
fast-forward from pull
Merge branch 'main' of https://github.com/msberends/AMR into main
# Conflicts:
# DESCRIPTION
# R/add_custom_antimicrobials.R
|
2022-10-11 10:53:51 +02:00 |
|
|
|
33227a5d90
|
support ab selectors for manual AB codes
|
2022-10-11 10:49:55 +02:00 |
|
|
|
57d66cd9d0
|
doc fix
|
2022-10-10 21:38:39 +02:00 |
|
