dr. M.S. (Matthijs) Berends
c8bda784a6
unit tests
2023-06-22 14:16:25 +02:00
dr. M.S. (Matthijs) Berends
3083828e15
implement ecoffs
2023-06-22 10:07:33 +02:00
dr. M.S. (Matthijs) Berends
55b98ede4c
docs
2023-06-10 10:18:19 +02:00
dr. M.S. (Matthijs) Berends
89c447b290
Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102 , fixes #112 , fixes #113 , fixes #114 , fixes #115
2023-06-09 22:30:43 +02:00
dr. M.S. (Matthijs) Berends
9591688811
documentation update
2023-05-27 10:39:22 +02:00
dr. M.S. (Matthijs) Berends
e1966503ee
unit testing R4.3
2023-05-26 20:37:00 +02:00
dr. M.S. (Matthijs) Berends
c6135d2082
updated microorganism codes
2023-05-26 16:10:01 +02:00
dr. M.S. (Matthijs) Berends
0bcf55d3b6
improve as.mo()
2023-05-24 15:55:53 +02:00
dr. M.S. (Matthijs) Berends
3018fb87a9
icu_exclude in first_isolate(), fixes #110
2023-05-17 22:12:10 +02:00
dr. M.S. (Matthijs) Berends
8179092c57
add XPT files for SAS software
2023-05-12 10:07:55 +02:00
dr. M.S. (Matthijs) Berends
91fa73dedf
add oxygen tolerance
2023-05-11 21:56:27 +02:00
dr. M.S. (Matthijs) Berends
bf08d136a0
fix coercing NA to custom codes, fixes #107
2023-05-08 13:04:18 +02:00
dr. M.S. (Matthijs) Berends
9de19fdc49
documentation
2023-04-21 10:07:25 +02:00
dr. M.S. (Matthijs) Berends
9148a2dcf4
fix mo_rank() for 'unknown' MOs
2023-04-20 15:20:41 +02:00
dr. M.S. (Matthijs) Berends
549790c2a6
website
2023-03-20 21:59:50 +01:00
dr. M.S. (Matthijs) Berends
c28cfa3a77
fix documentation
2023-03-16 08:55:37 +01:00
dr. M.S. (Matthijs) Berends
dee675e717
Version 2.0 on CRAN
2023-03-12 14:07:45 +01:00
dr. M.S. (Matthijs) Berends
80cfc503c2
check for 2.0
2023-03-12 13:02:37 +01:00
dr. M.S. (Matthijs) Berends
9179e98e12
patient ID in first isolate
2023-03-11 17:13:19 +01:00
dr. M.S. (Matthijs) Berends
7ad8635994
documentation for 'data.table' AB selectors
2023-03-11 16:54:02 +01:00
dr. M.S. (Matthijs) Berends
45e840c02f
update NEWS
2023-03-11 14:43:31 +01:00
dr. M.S. (Matthijs) Berends
262598b8d7
support for old rsi arguments
2023-03-11 14:24:34 +01:00
dr. M.S. (Matthijs) Berends
4416394e10
website update
2023-02-26 21:26:58 +01:00
dr. M.S. (Matthijs) Berends
1d3d7d40bc
get episode unit tests
2023-02-24 19:54:56 +01:00
dr. M.S. (Matthijs) Berends
2c5a9bb622
new relative episode determination in get_episode(), fix for plotting disk/MIC values
2023-02-24 17:06:30 +01:00
dr. M.S. (Matthijs) Berends
92029c9e95
remove note
2023-02-24 10:31:36 +01:00
dr. M.S. (Matthijs) Berends
049baf0a71
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
dr. M.S. (Matthijs) Berends
a84101db08
N for only 1 AB in
2023-02-22 16:26:13 +01:00
dr. M.S. (Matthijs) Berends
551aaf6517
auto-remove missing ABs in antibiogram()
2023-02-22 16:00:52 +01:00
dr. M.S. (Matthijs) Berends
c2cfc5ef84
fix for antibiogram(), transform WHONET data set to sir
2023-02-22 15:40:05 +01:00
dr. M.S. (Matthijs) Berends
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
dr. M.S. (Matthijs) Berends
380cbec0e8
prehook
2023-02-18 14:58:02 +01:00
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
dr. M.S. (Matthijs) Berends
714a048fa9
italicise antibiogram
2023-02-17 09:42:51 +01:00
dr. M.S. (Matthijs) Berends
db2830124f
fix for using dplyr::select()
2023-02-15 19:48:34 +01:00
dr. M.S. (Matthijs) Berends
a82552dd88
fix for group selections
2023-02-15 17:37:49 +01:00
dr. M.S. (Matthijs) Berends
ef716f6ee3
doc fix
2023-02-15 17:16:40 +01:00
dr. M.S. (Matthijs) Berends
d4ae174c28
docs
2023-02-15 17:03:34 +01:00
dr. M.S. (Matthijs) Berends
6016547f1f
support for dplyr 1.1.0
2023-02-15 17:02:10 +01:00
dr. M.S. (Matthijs) Berends
fe41fc2e35
font size
2023-02-14 16:57:48 +01:00
dr. M.S. (Matthijs) Berends
8d37c75860
unit tests
2023-02-14 15:59:40 +01:00
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
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
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
4a54d59f70
tinytest
2023-02-06 14:36:31 +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
126afb01a4
unit tests 2
2023-01-24 16:31:00 +01:00
dr. M.S. (Matthijs) Berends
c0d8888ab7
unit tests
2023-01-24 16:09:48 +01:00
dr. M.S. (Matthijs) Berends
7b00b4f34a
unit tests
2023-01-24 14:52:15 +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. M.S. (Matthijs) Berends
24b12024ce
unit test fix
2023-01-20 09:45:03 +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
5361c0b2a0
limit GitHub runners
2023-01-05 15:41:07 +01:00
dr. M.S. (Matthijs) Berends
51c0f0814e
new setup unit tests
2023-01-05 15:03:18 +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
dr. M.S. (Matthijs) Berends
e4ea96cbf9
fix for R < 3.4
2022-12-30 12:57:27 +01:00
dr. M.S. (Matthijs) Berends
1db74e86cd
good start-up practice
2022-12-29 16:23:57 +01:00
dr. M.S. (Matthijs) Berends
ba3b237bdf
custom mo update
2022-12-28 14:20:10 +01:00
dr. M.S. (Matthijs) Berends
f0a2cdbf5e
update mo algorithm
2022-12-20 16:14:04 +01:00
dr. M.S. (Matthijs) Berends
b1b7534c78
incorporate Bartlett et al (2022)
2022-12-19 15:32:41 +01:00
dr. M.S. (Matthijs) Berends
23fe427cbc
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
dr. M.S. (Matthijs) Berends
5f3a7694aa
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
dr. M.S. (Matthijs) Berends
8da2467209
updated taxonomy
2022-12-12 00:14:56 +01:00
dr. M.S. (Matthijs) Berends
eed1c14b96
website update
2022-12-11 11:44:29 +01:00
dr. M.S. (Matthijs) Berends
e7d7b94b3e
no obligatory note on startup
2022-12-09 15:10:49 +01:00
dr. M.S. (Matthijs) Berends
56dad34e68
update prevalence with new phyla
2022-12-09 13:37:08 +01:00
dr. M.S. (Matthijs) Berends
ac55aa84de
add news
2022-12-09 11:15:11 +01:00
dr. M.S. (Matthijs) Berends
510140fc55
Updated mo_gramstain() to reflect current taxonomy, fixes #83
2022-12-09 10:30:25 +01:00
dr. M.S. (Matthijs) Berends
ba51c2d92f
add column to as.mic() and as.disk() warnings
2022-11-28 19:39:52 +01:00
dr. M.S. (Matthijs) Berends
31fb81c382
revised as.rsi(), fix for mdro()
2022-11-24 20:29:00 +01:00
dr. M.S. (Matthijs) Berends
f6862a139d
expert rules 12.0
2022-11-14 15:20:39 +01:00
dr. M.S. (Matthijs) Berends
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
dr. M.S. (Matthijs) Berends
d2ceebe376
website fix
2022-11-07 18:48:12 +01:00
dr. M.S. (Matthijs) Berends
d20caae54b
cleanup
2022-10-31 13:25:41 +01:00
dr. M.S. (Matthijs) Berends
796b972f8a
extend vctrs support
2022-10-31 11:19:06 +01:00
dr. M.S. (Matthijs) Berends
9444ed6d1d
fix antibiotics error
2022-10-30 21:05:46 +01:00
dr. M.S. (Matthijs) Berends
d40e0ef20b
completely updated antibiotics
2022-10-30 14:31:45 +01:00
dr. M.S. (Matthijs) Berends
3d9faf89cf
ATC and DDD update
2022-10-29 19:01:23 +02:00
