|
|
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 |
|
|
|
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 |
|
|
|
126afb01a4
|
unit tests 2
|
2023-01-24 16:31:00 +01:00 |
|
|
|
c0d8888ab7
|
unit tests
|
2023-01-24 16:09:48 +01:00 |
|
|
|
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 |
|
|
|
eef00069fd
|
add all options to documentation
|
2023-01-23 20:07:57 +01:00 |
|
|
|
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 |
|
|
|
24b12024ce
|
unit test fix
|
2023-01-20 09:45:03 +01:00 |
|
|
|
593d740b84
|
documentation, file permissions
|
2023-01-19 12:54:53 +01:00 |
|
|
|
b94bc6c67b
|
adding mo fixes
|
2023-01-14 19:50:25 +01:00 |
|
|
|
ca79068604
|
Fix for adding MO's
|
2023-01-14 17:10:10 +01:00 |
|
|
|
33f269e2f4
|
contrib update
|
2023-01-12 23:16:05 +01:00 |
|
|
|
51906d6f97
|
no overwriting taxonomy when adding microorganisms
|
2023-01-12 11:33:28 +01:00 |
|
|
|
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 |
|
|
|
cf16bc7de1
|
unit tests
|
2023-01-06 13:45:20 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
e7d7b94b3e
|
no obligatory note on startup
|
2022-12-09 15:10:49 +01:00 |
|
|
|
56dad34e68
|
update prevalence with new phyla
|
2022-12-09 13:37:08 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
369e7545da
|
and yet another website fix
|
2022-10-05 10:17:53 +02:00 |
|
|
|
bc44da0e38
|
website fix
|
2022-10-05 10:07:27 +02:00 |
|
|
|
def9fc0d75
|
fix website
|
2022-10-05 09:33:21 +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 |
|
|
|
1e4eaf23f2
|
unit tests
|
2022-08-28 20:49:04 +02:00 |
|
|
|
21b4552f5a
|
unit test fix
|
2022-08-28 20:10:05 +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 |
|
|
|
4cb1db4554
|
data export
|
2022-08-27 20:51:26 +02:00 |
|
|
|
303d61b473
|
new tibble export
|
2022-08-27 20:49:37 +02:00 |
|
|
|
164886f50b
|
new workflow files
|
2022-08-26 23:25:37 +02:00 |
|
|
|
3cef2ea286
|
restore LFS
|
2022-08-26 23:21:31 +02:00 |
|
|
|
3864ab2fb8
|
Feather and Parquet files
|
2022-08-26 22:25:15 +02:00 |
|
|
|
4da32e3d40
|
set up Git LFS for large files
|
2022-08-26 14:02:08 +02:00 |
|
|
|
e05d0365a9
|
website update
|
2022-08-25 19:19:16 +02:00 |
|
|
|
5501cffbb0
|
website update
|
2022-08-25 19:18:48 +02:00 |
|
|
|
d3000a9492
|
website update
|
2022-08-25 19:16:16 +02:00 |
|
|
|
2cbce2cefa
|
website update
|
2022-08-25 19:14:07 +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 |
|
|
|
1b84564d36
|
(v1.8.1.9011) update prevalence of some genera
|
2022-06-03 12:43:25 +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 |
|
|
|
58ed15e7ac
|
(v1.8.1.9008) website update
|
2022-05-11 10:26:58 +02:00 |
|
|
|
6de5375256
|
(v1.8.1.9007) website update
|
2022-05-11 10:10:31 +02:00 |
|
|
|
859224e9d0
|
(v1.8.1.9006) added EUCAST 2022 and CLSI 2022
|
2022-05-10 21:34:30 +02:00 |
|
|
|
680e8e7a41
|
(v1.8.1.9005) as.rsi() fix for EUCAST
|
2022-05-10 17:01:37 +02:00 |
|
|
|
d4e22069bc
|
(v1.8.1.9004) fix for table() on MICs
|
2022-05-09 21:33:27 +02:00 |
|
|
|
1c891cc90c
|
(v1.8.1.9003) set_mo_source() fix
|
2022-05-09 20:36:44 +02:00 |
|
|
|
152db9d1b5
|
(v1.8.1.9002) fix for table() on MICs
|
2022-05-09 17:08:40 +02:00 |
|
|
|
4754848e96
|
(v1.8.1.9001) update unit tests, fixes #53
|
2022-04-08 11:02:45 +02:00 |
|
|
|
ccb09706e4
|
v1.8.1
|
2022-03-24 23:05:04 +01:00 |
|
|
|
7b0f1596bd
|
(v1.8.0.9010) as.mo improvement
|
2022-03-15 17:35:02 +01:00 |
|
|
|
1b0983e382
|
(v1.8.1) prerelease 1.8.1
|
2022-03-14 16:36:10 +01:00 |
|
|
|
08d387b5ce
|
(v1.8.0.9005) as.rsi() fix
|
2022-03-10 19:33:25 +01:00 |
|
|
|
ad82bb4ce0
|
(v1.8.0.9004) MIC printing in tibbles
|
2022-03-03 21:11:02 +01:00 |
|
|
|
dedbe92322
|
(v1.8.0.9003) deps update
|
2022-03-02 23:16:37 +01:00 |
|
|
|
3b2b2be5f8
|
(v1.8.0.9002) as.rsi() cleanup, more informative warnings
|
2022-03-02 15:38:55 +01:00 |
|
|
|
18e8525d10
|
(v1.8.0.9001) as.mo improvement, fixes #52
|
2022-02-26 21:58:23 +01:00 |
|
|
|
be792cc9eb
|
(v1.8.0.9000) unit tests for R 3.3
|
2022-02-01 17:08:10 +01:00 |
|
|
|
f5dcf0ad58
|
v1.8.0 as accepted by CRAN
|
2022-01-07 16:27:13 +01:00 |
|
|
|
25cef46c59
|
(v1.8.0) prerelease 1.8.0
|
2021-12-23 18:56:28 +01:00 |
|
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|
75dac113b6
|
(v1.7.1.9077) skimr support only for newer R versions
|
2021-12-23 13:38:25 +01:00 |
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|
d9274bcd0a
|
(v1.7.1.9075) assignment operator
|
2021-12-14 22:59:27 +01:00 |
|
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|
76dee66852
|
(v1.7.1.9074) as.mo() improvement, ASCII replacements for unit tests
|
2021-12-14 22:39:23 +01:00 |
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|
bd4bb1d72f
|
(v1.7.1.9073) as.rsi() fix for UTIs
|
2021-12-14 21:47:14 +01:00 |
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|
5eef01165e
|
(v1.7.1.9072) as.rsi() fix for UTIs
|
2021-12-14 12:33:29 +01:00 |
|
|
|
0cbf8f48b6
|
(v1.7.1.9071) rsi disk fix
|
2021-12-13 11:57:34 +01:00 |
|
|
|
578e7dfee9
|
(v1.7.1.9070) Better WHONET support
|
2021-12-13 10:18:28 +01:00 |
|
|
|
f90e27c1b0
|
(v1.7.1.9069) CLSI 2021 support
|
2021-12-12 11:36:58 +01:00 |
|
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|
1e66a3daf3
|
(v1.7.1.9068) new logo, unit tests
|
2021-12-12 11:07:02 +01:00 |
|
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|
56f1ce328a
|
(v1.7.1.9067) Support for Swedish and Russian
|
2021-12-12 09:42:03 +01:00 |
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|
5b5f70a103
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(v1.7.1.9066) mdro EUCAST v3.3
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2021-12-11 15:29:30 +01:00 |
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e0a2634f14
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(v1.7.1.9065) unit tests
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2021-12-11 15:13:44 +01:00 |
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77ba4318ea
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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
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2021-12-11 13:41:31 +01:00 |
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e18c49ed93
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(v1.7.1.9063) not_intrinsic_resistant
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2021-12-09 10:48:25 +01:00 |
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e63defe324
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(v1.7.1.9062) website update
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2021-12-06 11:12:30 +01:00 |
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1fa3fc6af2
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(v1.7.1.9061) bugfix set_ab_names
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2021-12-05 23:21:59 +01:00 |
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75965124ef
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(v1.7.1.9060) bugfix set_ab_names
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2021-12-05 23:11:10 +01:00 |
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b747036deb
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(v1.7.1.9059) bugfix set_ab_names
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2021-12-05 22:59:06 +01:00 |
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7965468ccd
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(v1.7.1.9058) vars selection for set_ab_names()
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2021-12-05 22:06:45 +01:00 |
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3abe61fd61
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(v1.7.1.9057) NAs in get_episode()
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2021-12-02 13:32:14 +01:00 |
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5375f75829
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(v1.7.1.9056) unit tests
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2021-11-29 11:55:18 +01:00 |
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c8698347cb
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(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers
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2021-11-29 10:38:38 +01:00 |
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694cf5ba77
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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
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2021-11-28 23:01:26 +01:00 |
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9a2c431e16
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(v1.7.1.9053) fortify() methods
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2021-11-01 13:51:13 +01:00 |
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91149d6d35
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(v1.7.1.9052) eucast-update
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2021-10-06 16:22:36 +02:00 |
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37e6e35ec4
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(v1.7.1.9051) updated taxonomy, updated git branch name
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2021-10-06 13:23:57 +02:00 |
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8f5e5a3fc2
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(v1.7.1.9050) fix for as.mo
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2021-10-05 14:00:35 +02:00 |
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2bcf28281d
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(v1.7.1.9049) unit tests
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2021-10-05 09:58:08 +02:00 |
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d1b16ce641
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(v1.7.1.9048) unit tests
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2021-10-04 10:22:10 +02:00 |
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9b97233be2
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(v1.7.1.9046) unit tests
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2021-10-03 13:50:52 +02:00 |
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b0c84cce9c
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(v1.7.1.9045) unit tests
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2021-09-29 20:24:02 +02:00 |
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557ce74fd7
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(v1.7.1.9044) unit tests
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2021-09-29 20:13:52 +02:00 |
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45f597cac5
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(v1.7.1.9043) unit tests
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2021-09-29 20:10:44 +02:00 |
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e8d3ce05d7
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(v1.7.1.9041) new GH actions, branches rename
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2021-09-29 16:36:03 +02:00 |
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93a4734b44
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(v1.7.1.9040) Support for Danish
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2021-09-29 12:12:35 +02:00 |
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5f433d6e5c
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(v1.7.1.9039) reinitiate all units tests
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2021-09-03 13:08:36 +02:00 |
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81a1a432bd
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(v1.7.1.9038) dplyr grouping fix on windows?
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2021-09-01 16:52:55 +02:00 |
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bcab74fb6d
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(v1.7.1.9037) dplyr grouping fix on windows?
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2021-08-31 17:06:44 +02:00 |
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953dfac9e5
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(v1.7.1.9036) dplyr grouping fix on windows?
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2021-08-30 16:49:46 +02:00 |
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986bd826ee
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(v1.7.1.9035) dplyr grouping fix on windows?
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2021-08-30 15:43:12 +02:00 |
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af23f91e5c
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website update
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2021-08-30 15:07:18 +02:00 |
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1daa117e9f
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(v1.7.1.9033) dplyr grouping fix on windows?
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2021-08-30 15:01:32 +02:00 |
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6ca6a3f6df
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(v1.7.1.9032) dplyr grouping fix on windows?
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2021-08-30 14:17:27 +02:00 |
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e6ce25162e
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(v1.7.1.9031) dplyr grouping fix on windows?
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2021-08-30 14:07:46 +02:00 |
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d6a916d70b
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(v1.7.1.9030) unit test
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2021-08-29 23:50:45 +02:00 |
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f0a4d29fe0
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(v1.7.1.9029) unit test fix
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2021-08-21 10:20:05 +02:00 |
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e4de7f5055
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(v1.7.1.9028) fix unit test
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2021-08-20 00:08:31 +02:00 |
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41f35c73cd
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(v1.7.1.9027) fix unit test
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2021-08-19 23:56:18 +02:00 |
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2ab21b7af3
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(v1.7.1.9026) updated DDDs
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2021-08-19 23:43:02 +02:00 |
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