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bf08d136a0
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fix coercing NA to custom codes, fixes #107
|
2023-05-08 13:04:18 +02:00 |
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9148a2dcf4
|
fix mo_rank() for 'unknown' MOs
|
2023-04-20 15:20:41 +02:00 |
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cabffb22fd
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anaerobic codes
|
2023-04-17 11:26:19 +02:00 |
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1a02d302d4
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Fix translatable strings
|
2023-04-15 09:32:13 +02:00 |
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ed70f95380
|
Fix clinical breakpoints
|
2023-04-14 23:14:34 +02:00 |
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147f9112e9
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Fix some WHONET codes
|
2023-04-14 11:12:26 +02:00 |
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549790c2a6
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website
|
2023-03-20 21:59:50 +01:00 |
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c28cfa3a77
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fix documentation
|
2023-03-16 08:55:37 +01:00 |
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dd7cc86485
|
help page %like%
|
2023-03-14 19:49:50 +01:00 |
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80cfc503c2
|
check for 2.0
|
2023-03-12 13:02:37 +01:00 |
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9179e98e12
|
patient ID in first isolate
|
2023-03-11 17:13:19 +01:00 |
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7ad8635994
|
documentation for 'data.table' AB selectors
|
2023-03-11 16:54:02 +01:00 |
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45e840c02f
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update NEWS
|
2023-03-11 14:43:31 +01:00 |
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262598b8d7
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support for old rsi arguments
|
2023-03-11 14:24:34 +01:00 |
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4416394e10
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website update
|
2023-02-26 21:26:58 +01:00 |
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1d3d7d40bc
|
get episode unit tests
|
2023-02-24 19:54:56 +01:00 |
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2c5a9bb622
|
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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551aaf6517
|
auto-remove missing ABs in antibiogram()
|
2023-02-22 16:00:52 +01:00 |
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c2cfc5ef84
|
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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8d902410f9
|
unit tests
|
2023-02-18 14:56:06 +01:00 |
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8dcf101a9c
|
website
|
2023-02-18 13:08:08 +01:00 |
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ba255ddb00
|
website
|
2023-02-18 11:57:17 +01:00 |
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e890360986
|
website syntax update
|
2023-02-17 11:39:00 +01:00 |
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714a048fa9
|
italicise antibiogram
|
2023-02-17 09:42:51 +01:00 |
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db2830124f
|
fix for using dplyr::select()
|
2023-02-15 19:48:34 +01:00 |
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a82552dd88
|
fix for group selections
|
2023-02-15 17:37:49 +01:00 |
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ef716f6ee3
|
doc fix
|
2023-02-15 17:16:40 +01:00 |
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6016547f1f
|
support for dplyr 1.1.0
|
2023-02-15 17:02:10 +01:00 |
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a4cd38c433
|
fix for R < 3.2, expect_warning() on hold
|
2023-02-14 10:41:01 +01:00 |
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3396236eef
|
unit test fixes
|
2023-02-13 16:56:25 +01:00 |
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b6d2b1398d
|
Fix for antibiogram() in R <=3.4
|
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
|
add include_screening to as.sir()
|
2023-02-12 15:09:54 +01:00 |
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c740967cf2
|
fix for binding rows
|
2023-02-12 11:20:14 +01:00 |
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c51fb24363
|
pm_bind_rows
|
2023-02-11 22:28:48 +01:00 |
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b146de6d7f
|
fix for bind_rows2, added 4 langs
|
2023-02-11 21:57:12 +01:00 |
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2007c3eef3
|
bind_rows
|
2023-02-10 17:09:48 +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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822e9de82c
|
pm update, unit test fix?
|
2023-02-08 13:48:06 +01:00 |
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75a4c1ef3e
|
fixes2
|
2023-02-06 14:34:38 +01:00 |
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f7dd890b79
|
fixes
|
2023-02-06 12:38:52 +01:00 |
|
|
|
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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89a577805f
|
prelim fix for g.test
|
2023-01-30 12:26:48 +01:00 |
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7b00b4f34a
|
unit tests
|
2023-01-24 14:52:15 +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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|
24b12024ce
|
unit test fix
|
2023-01-20 09:45:03 +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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51906d6f97
|
no overwriting taxonomy when adding microorganisms
|
2023-01-12 11:33:28 +01:00 |
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|
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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 |
|
|
|
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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a0ee86536a
|
unit tests
|
2023-01-05 14:43:18 +01:00 |
|
|
|
77d9cf1936
|
documentation
|
2022-12-30 13:02:37 +01:00 |
|
|
|
e4ea96cbf9
|
fix for R < 3.4
|
2022-12-30 12:57:27 +01:00 |
|
|
|
1db74e86cd
|
good start-up practice
|
2022-12-29 16:23:57 +01:00 |
|
|
|
61c0bdb7af
|
documentation
|
2022-12-28 15:04:59 +01:00 |
|
|
|
ba3b237bdf
|
custom mo update
|
2022-12-28 14:20:10 +01:00 |
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|
f619fb683b
|
support new mo codes
|
2022-12-27 15:16:15 +01:00 |
|
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|
6f4bb603ec
|
unit tests
|
2022-12-20 22:18:50 +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 |
|
|
|
e7d7b94b3e
|
no obligatory note on startup
|
2022-12-09 15:10:49 +01:00 |
|
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|
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 |
|
|
|
ba51c2d92f
|
add column to as.mic() and as.disk() warnings
|
2022-11-28 19:39:52 +01:00 |
|
|
|
31fb81c382
|
revised as.rsi(), fix for mdro()
|
2022-11-24 20:29:00 +01:00 |
|
|
|
05d536ebb7
|
complexes
|
2022-11-17 15:23:29 +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 |
|
|
|
d20caae54b
|
cleanup
|
2022-10-31 13:25:41 +01:00 |
|
|
|
796b972f8a
|
extend vctrs support
|
2022-10-31 11:19:06 +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 |
|
|
|
3d9faf89cf
|
ATC and DDD update
|
2022-10-29 19:01:23 +02:00 |
|
|
|
afdc48db1e
|
fix txt export of microorganisms
|
2022-10-29 16:08:18 +02:00 |
|
|
|
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 |
|
|
|
d10651eb26
|
cleanup
|
2022-10-22 10:20:09 +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 |
|
|
|
f203928f7e
|
coercion fixes
|
2022-10-19 06:59:36 +02:00 |
|
|
|
3fc39198d0
|
unit test fix
|
2022-10-18 23:03:16 +02:00 |
|
|
|
e5e6d2200d
|
fix add manual ab
|
2022-10-18 22:53:38 +02:00 |
|
|
|
ad68b50ecd
|
custom ab fix
|
2022-10-15 15:20:13 +02:00 |
|
Dr. Matthijs Berends
|
85ed7ea5f0
|
more robust install check
|
2022-10-14 15:45:20 +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 |
|
|
|
955f9d7020
|
documentation fix
|
2022-10-10 21:03:39 +02:00 |
|
|
|
82e3198315
|
add add_custom_antimicrobials()
|
2022-10-10 20:20:39 +02:00 |
|
|
|
4fe90092c7
|
fix for NA in as.ab()
|
2022-10-10 15:44:59 +02:00 |
|
|
|
43c638d122
|
add mo_current()
|
2022-10-10 10:12:08 +02:00 |
|
|
|
b753b84128
|
fix for mo type translation
|
2022-10-06 12:11:51 +02:00 |
|
|
|
b9342d103e
|
fix documentation
|
2022-10-06 11:33:30 +02:00 |
|
Dr. Matthijs Berends
|
cd2acc4a29
|
New mo algorithm, prepare for 2.0
|
2022-10-05 09:12:22 +02:00 |
|
|
|
63fe160322
|
new rsi_interpretation_history
|
2022-09-01 15:20:57 +02:00 |
|
|
|
3fca703fbf
|
new AMR distance function
|
2022-08-30 21:48:02 +02:00 |
|
|
|
fbd5d32541
|
small fixes
|
2022-08-29 09:35:36 +02:00 |
|
|
|
e7af5fc716
|
fix AMR vignette
|
2022-08-28 22:38:08 +02:00 |
|
|
|
2ed5f13880
|
Fixes #57
|
2022-08-28 21:13:26 +02:00 |
|
|
|
c44ddf272f
|
fix for R <= 3.3
|
2022-08-28 19:34:04 +02:00 |
|
|
|
71db246d5c
|
unit test fix
|
2022-08-28 19:17:12 +02:00 |
|
|
|
f781998904
|
amoxicillin interpretation fix
|
2022-08-28 11:17:53 +02:00 |
|
|
|
4d050aef7c
|
styled, unit test fix
|
2022-08-28 10:31:50 +02:00 |
|
|
|
303d61b473
|
new tibble export
|
2022-08-27 20:49:37 +02:00 |
|
|
|
3864ab2fb8
|
Feather and Parquet files
|
2022-08-26 22:25:15 +02:00 |
|
|
|
bdbc112f99
|
website update
|
2022-08-21 17:22:34 +02:00 |
|
|
|
d6676e9443
|
disk documentation fix
|
2022-08-21 16:52:09 +02:00 |
|
|
|
952d16de33
|
new, automated website
|
2022-08-21 16:37:20 +02:00 |
|
|
|
7226b70c3d
|
update languages
|
2022-08-20 20:17:14 +02:00 |
|
|
|
3f2f60ab77
|
language updates
|
2022-08-19 12:33:14 +02:00 |
|
|
|
ab97268f4c
|
(v1.8.1.9014) add Toxoplasma
|
2022-08-12 23:27:15 +02:00 |
|
|
|
7f981e7778
|
(v1.8.1.9013) add Toxoplasma
|
2022-06-10 13:15:23 +02:00 |
|
|
|
b84d647cac
|
(v1.8.1.9012) update prevalence of some genera
|
2022-06-03 13:28:55 +02:00 |
|
|
|
70a07bad39
|
(v1.8.1.9010) random when pkg not loaded
|
2022-05-16 12:52:50 +02:00 |
|
|
|
2c5bc73ed6
|
(v1.8.1.9009) random when pkg not loaded
|
2022-05-16 09:29:46 +02:00 |
|
