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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
|
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
|
pm update, unit test fix?
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2023-02-08 13:48:06 +01:00 |
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4a54d59f70
|
tinytest
|
2023-02-06 14:36:31 +01:00 |
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75a4c1ef3e
|
fixes2
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2023-02-06 14:34:38 +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
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2023-02-06 11:57:22 +01:00 |
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4b133d4c96
|
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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126afb01a4
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unit tests 2
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2023-01-24 16:31:00 +01:00 |
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c0d8888ab7
|
unit tests
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2023-01-24 16:09:48 +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
|
documentation, unit tests
|
2023-01-24 10:20:27 +01:00 |
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eef00069fd
|
add all options to documentation
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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
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98e62c9af2
|
Replace RSI with SIR
|
2023-01-21 23:47:20 +01:00 |
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24b12024ce
|
unit test fix
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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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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 |
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84ed8c32bb
|
documentation
|
2023-01-06 19:21:04 +01:00 |
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|
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cf16bc7de1
|
unit tests
|
2023-01-06 13:45:20 +01:00 |
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|
86e28bafce
|
add mo_pathogenicity
|
2023-01-06 13:35:37 +01:00 |
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4801a6067e
|
unit tests
|
2023-01-06 11:22:02 +01:00 |
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8a0a0d4682
|
unit tests
|
2023-01-06 10:08:25 +01:00 |
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268ec31d92
|
unit tests
|
2023-01-05 18:21:48 +01:00 |
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|
5361c0b2a0
|
limit GitHub runners
|
2023-01-05 15:41:07 +01:00 |
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51c0f0814e
|
new setup unit tests
|
2023-01-05 15:03:18 +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 |
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77d9cf1936
|
documentation
|
2022-12-30 13:02:37 +01:00 |
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e4ea96cbf9
|
fix for R < 3.4
|
2022-12-30 12:57:27 +01:00 |
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|
1db74e86cd
|
good start-up practice
|
2022-12-29 16:23:57 +01:00 |
|
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|
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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|
fe09e9252b
|
custom mo update
|
2022-12-27 16:03:03 +01:00 |
|
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|
f619fb683b
|
support new mo codes
|
2022-12-27 15:16:15 +01:00 |
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|
e493248ea5
|
unit test and news file
|
2022-12-21 09:12:53 +01:00 |
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4c42a43f7d
|
fixes
|
2022-12-20 22:41:39 +01:00 |
|
|
|
6f4bb603ec
|
unit tests
|
2022-12-20 22:18:50 +01:00 |
|
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|
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 |
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|
|
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 |
|
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|
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 |
|
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|
ac55aa84de
|
add news
|
2022-12-09 11:15:11 +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 |
|
|
|
8d1679bab3
|
website update
|
2022-11-12 09:44:36 +01:00 |
|
|
|
af205e2705
|
update collabs
|
2022-11-10 22:07:35 +01:00 |
|
|
|
d2ceebe376
|
website fix
|
2022-11-07 18:48:12 +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 |
|
|
|
fa620f8ebd
|
fix export of lists in antibiotics and antivirals
|
2022-10-29 16:17:48 +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 |
|
|
|
bfca21bd3f
|
precommit update
|
2022-10-21 19:31:46 +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 |
|
Dr. Matthijs Berends
|
fed3b6440f
|
Unit test fix
|
2022-10-19 08:14:38 +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 |
|
|
|
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 |
|
|
|
3deeedc4b6
|
website fix
|
2022-10-10 20:21:41 +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 |
|
