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d2ceebe376
|
website fix
|
2022-11-07 18:48:12 +01:00 |
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2d90218305
|
documentation fix
|
2022-11-05 12:06:40 +01:00 |
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8dc94a9eda
|
documentation fix
|
2022-11-05 09:31:19 +01:00 |
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|
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3b652983b7
|
documentation fix
|
2022-11-05 08:18:06 +01:00 |
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d20caae54b
|
cleanup
|
2022-10-31 13:25:41 +01:00 |
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796b972f8a
|
extend vctrs support
|
2022-10-31 11:19:06 +01:00 |
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|
9444ed6d1d
|
fix antibiotics error
|
2022-10-30 21:05:46 +01:00 |
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|
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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fa620f8ebd
|
fix export of lists in antibiotics and antivirals
|
2022-10-29 16:17:48 +02:00 |
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|
afdc48db1e
|
fix txt export of microorganisms
|
2022-10-29 16:08:18 +02:00 |
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6ad7857d39
|
fix missing R breakpoints
|
2022-10-29 14:15:23 +02:00 |
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|
c2801ba7a1
|
new rsi_translation
|
2022-10-22 22:00:15 +02:00 |
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|
d10651eb26
|
cleanup
|
2022-10-22 10:20:09 +02:00 |
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d0b54f640c
|
Update contributors list
|
2022-10-21 21:56:54 +02:00 |
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bfca21bd3f
|
precommit update
|
2022-10-21 19:31:46 +02:00 |
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faca6d608a
|
mean AMR distance
|
2022-10-21 16:02:14 +02:00 |
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178ab5e5ff
|
mean AMR distance
|
2022-10-21 15:59:31 +02:00 |
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4bebba3610
|
fix for scoped dplyr verbs
|
2022-10-21 15:13:19 +02:00 |
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aa2c0639d0
|
add confidence intervals (fixed #70), remove combine_IR
|
2022-10-20 16:08:01 +02:00 |
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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 |
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f203928f7e
|
coercion fixes
|
2022-10-19 06:59:36 +02:00 |
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3fc39198d0
|
unit test fix
|
2022-10-18 23:03:16 +02:00 |
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e5e6d2200d
|
fix add manual ab
|
2022-10-18 22:53:38 +02:00 |
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ad68b50ecd
|
custom ab fix
|
2022-10-15 15:20:13 +02:00 |
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|
76bcd3528c
|
move object assignment to AMR_env
|
2022-10-14 13:02:50 +02:00 |
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|
|
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 |
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33227a5d90
|
support ab selectors for manual AB codes
|
2022-10-11 10:49:55 +02:00 |
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57d66cd9d0
|
doc fix
|
2022-10-10 21:38:39 +02:00 |
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955f9d7020
|
documentation fix
|
2022-10-10 21:03:39 +02:00 |
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3deeedc4b6
|
website fix
|
2022-10-10 20:21:41 +02:00 |
|
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82e3198315
|
add add_custom_antimicrobials()
|
2022-10-10 20:20:39 +02:00 |
|
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4fe90092c7
|
fix for NA in as.ab()
|
2022-10-10 15:44:59 +02:00 |
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43c638d122
|
add mo_current()
|
2022-10-10 10:12:08 +02:00 |
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b753b84128
|
fix for mo type translation
|
2022-10-06 12:11:51 +02:00 |
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b9342d103e
|
fix documentation
|
2022-10-06 11:33:30 +02:00 |
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369e7545da
|
and yet another website fix
|
2022-10-05 10:17:53 +02:00 |
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bc44da0e38
|
website fix
|
2022-10-05 10:07:27 +02:00 |
|
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|
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 |
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|
63fe160322
|
new rsi_interpretation_history
|
2022-09-01 15:20:57 +02:00 |
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|
3fca703fbf
|
new AMR distance function
|
2022-08-30 21:48:02 +02:00 |
|
|
|
fbd5d32541
|
small fixes
|
2022-08-29 09:35:36 +02:00 |
|
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|
e7af5fc716
|
fix AMR vignette
|
2022-08-28 22:38:08 +02:00 |
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|
2ed5f13880
|
Fixes #57
|
2022-08-28 21:13:26 +02:00 |
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1e4eaf23f2
|
unit tests
|
2022-08-28 20:49:04 +02:00 |
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21b4552f5a
|
unit test fix
|
2022-08-28 20:10:05 +02:00 |
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c44ddf272f
|
fix for R <= 3.3
|
2022-08-28 19:34:04 +02:00 |
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71db246d5c
|
unit test fix
|
2022-08-28 19:17:12 +02:00 |
|
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f781998904
|
amoxicillin interpretation fix
|
2022-08-28 11:17:53 +02:00 |
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4d050aef7c
|
styled, unit test fix
|
2022-08-28 10:31:50 +02:00 |
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4cb1db4554
|
data export
|
2022-08-27 20:51:26 +02:00 |
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303d61b473
|
new tibble export
|
2022-08-27 20:49:37 +02:00 |
|
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164886f50b
|
new workflow files
|
2022-08-26 23:25:37 +02:00 |
|
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3cef2ea286
|
restore LFS
|
2022-08-26 23:21:31 +02:00 |
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3864ab2fb8
|
Feather and Parquet files
|
2022-08-26 22:25:15 +02:00 |
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4da32e3d40
|
set up Git LFS for large files
|
2022-08-26 14:02:08 +02:00 |
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e05d0365a9
|
website update
|
2022-08-25 19:19:16 +02:00 |
|
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5501cffbb0
|
website update
|
2022-08-25 19:18:48 +02:00 |
|
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|
d3000a9492
|
website update
|
2022-08-25 19:16:16 +02:00 |
|
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|
2cbce2cefa
|
website update
|
2022-08-25 19:14:07 +02:00 |
|
|
|
bdbc112f99
|
website update
|
2022-08-21 17:22:34 +02:00 |
|
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d6676e9443
|
disk documentation fix
|
2022-08-21 16:52:09 +02:00 |
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952d16de33
|
new, automated website
|
2022-08-21 16:37:20 +02:00 |
|
|
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7226b70c3d
|
update languages
|
2022-08-20 20:17:14 +02:00 |
|
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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 |
|
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7f981e7778
|
(v1.8.1.9013) add Toxoplasma
|
2022-06-10 13:15:23 +02:00 |
|
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|
b84d647cac
|
(v1.8.1.9012) update prevalence of some genera
|
2022-06-03 13:28:55 +02:00 |
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1b84564d36
|
(v1.8.1.9011) update prevalence of some genera
|
2022-06-03 12:43:25 +02:00 |
|
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|
70a07bad39
|
(v1.8.1.9010) random when pkg not loaded
|
2022-05-16 12:52:50 +02:00 |
|
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2c5bc73ed6
|
(v1.8.1.9009) random when pkg not loaded
|
2022-05-16 09:29:46 +02:00 |
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58ed15e7ac
|
(v1.8.1.9008) website update
|
2022-05-11 10:26:58 +02:00 |
|
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|
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 |
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1b0983e382
|
(v1.8.1) prerelease 1.8.1
|
2022-03-14 16:36:10 +01:00 |
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08d387b5ce
|
(v1.8.0.9005) as.rsi() fix
|
2022-03-10 19:33:25 +01:00 |
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|
ad82bb4ce0
|
(v1.8.0.9004) MIC printing in tibbles
|
2022-03-03 21:11:02 +01:00 |
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dedbe92322
|
(v1.8.0.9003) deps update
|
2022-03-02 23:16:37 +01:00 |
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|
3b2b2be5f8
|
(v1.8.0.9002) as.rsi() cleanup, more informative warnings
|
2022-03-02 15:38:55 +01:00 |
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|
18e8525d10
|
(v1.8.0.9001) as.mo improvement, fixes #52
|
2022-02-26 21:58:23 +01:00 |
|
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|
be792cc9eb
|
(v1.8.0.9000) unit tests for R 3.3
|
2022-02-01 17:08:10 +01:00 |
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f5dcf0ad58
|
v1.8.0 as accepted by CRAN
|
2022-01-07 16:27:13 +01:00 |
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|
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 |
|
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|
0cbf8f48b6
|
(v1.7.1.9071) rsi disk fix
|
2021-12-13 11:57:34 +01:00 |
|
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|
578e7dfee9
|
(v1.7.1.9070) Better WHONET support
|
2021-12-13 10:18:28 +01:00 |
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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
|
(v1.7.1.9066) mdro EUCAST v3.3
|
2021-12-11 15:29:30 +01:00 |
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e0a2634f14
|
(v1.7.1.9065) unit tests
|
2021-12-11 15:13:44 +01:00 |
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|
77ba4318ea
|
(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
|
2021-12-11 13:41:31 +01:00 |
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|
e18c49ed93
|
(v1.7.1.9063) not_intrinsic_resistant
|
2021-12-09 10:48:25 +01:00 |
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e63defe324
|
(v1.7.1.9062) website update
|
2021-12-06 11:12:30 +01:00 |
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1fa3fc6af2
|
(v1.7.1.9061) bugfix set_ab_names
|
2021-12-05 23:21:59 +01:00 |
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75965124ef
|
(v1.7.1.9060) bugfix set_ab_names
|
2021-12-05 23:11:10 +01:00 |
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|
b747036deb
|
(v1.7.1.9059) bugfix set_ab_names
|
2021-12-05 22:59:06 +01:00 |
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7965468ccd
|
(v1.7.1.9058) vars selection for set_ab_names()
|
2021-12-05 22:06:45 +01:00 |
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|
3abe61fd61
|
(v1.7.1.9057) NAs in get_episode()
|
2021-12-02 13:32:14 +01:00 |
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5375f75829
|
(v1.7.1.9056) unit tests
|
2021-11-29 11:55:18 +01:00 |
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c8698347cb
|
(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers
|
2021-11-29 10:38:38 +01:00 |
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|
|
694cf5ba77
|
(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
|
2021-11-28 23:01:26 +01:00 |
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|
|
9a2c431e16
|
(v1.7.1.9053) fortify() methods
|
2021-11-01 13:51:13 +01:00 |
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91149d6d35
|
(v1.7.1.9052) eucast-update
|
2021-10-06 16:22:36 +02:00 |
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|
|
37e6e35ec4
|
(v1.7.1.9051) updated taxonomy, updated git branch name
|
2021-10-06 13:23:57 +02:00 |
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|
8f5e5a3fc2
|
(v1.7.1.9050) fix for as.mo
|
2021-10-05 14:00:35 +02:00 |
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2bcf28281d
|
(v1.7.1.9049) unit tests
|
2021-10-05 09:58:08 +02:00 |
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d1b16ce641
|
(v1.7.1.9048) unit tests
|
2021-10-04 10:22:10 +02:00 |
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9b97233be2
|
(v1.7.1.9046) unit tests
|
2021-10-03 13:50:52 +02:00 |
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b0c84cce9c
|
(v1.7.1.9045) unit tests
|
2021-09-29 20:24:02 +02:00 |
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557ce74fd7
|
(v1.7.1.9044) unit tests
|
2021-09-29 20:13:52 +02:00 |
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45f597cac5
|
(v1.7.1.9043) unit tests
|
2021-09-29 20:10:44 +02:00 |
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e8d3ce05d7
|
(v1.7.1.9041) new GH actions, branches rename
|
2021-09-29 16:36:03 +02:00 |
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93a4734b44
|
(v1.7.1.9040) Support for Danish
|
2021-09-29 12:12:35 +02:00 |
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5f433d6e5c
|
(v1.7.1.9039) reinitiate all units tests
|
2021-09-03 13:08:36 +02:00 |
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81a1a432bd
|
(v1.7.1.9038) dplyr grouping fix on windows?
|
2021-09-01 16:52:55 +02:00 |
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bcab74fb6d
|
(v1.7.1.9037) dplyr grouping fix on windows?
|
2021-08-31 17:06:44 +02:00 |
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|
953dfac9e5
|
(v1.7.1.9036) dplyr grouping fix on windows?
|
2021-08-30 16:49:46 +02:00 |
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986bd826ee
|
(v1.7.1.9035) dplyr grouping fix on windows?
|
2021-08-30 15:43:12 +02:00 |
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|
af23f91e5c
|
website update
|
2021-08-30 15:07:18 +02:00 |
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1daa117e9f
|
(v1.7.1.9033) dplyr grouping fix on windows?
|
2021-08-30 15:01:32 +02:00 |
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6ca6a3f6df
|
(v1.7.1.9032) dplyr grouping fix on windows?
|
2021-08-30 14:17:27 +02:00 |
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e6ce25162e
|
(v1.7.1.9031) dplyr grouping fix on windows?
|
2021-08-30 14:07:46 +02:00 |
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|
d6a916d70b
|
(v1.7.1.9030) unit test
|
2021-08-29 23:50:45 +02:00 |
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f0a4d29fe0
|
(v1.7.1.9029) unit test fix
|
2021-08-21 10:20:05 +02:00 |
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e4de7f5055
|
(v1.7.1.9028) fix unit test
|
2021-08-20 00:08:31 +02:00 |
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41f35c73cd
|
(v1.7.1.9027) fix unit test
|
2021-08-19 23:56:18 +02:00 |
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2ab21b7af3
|
(v1.7.1.9026) updated DDDs
|
2021-08-19 23:43:02 +02:00 |
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1b62bab007
|
(v1.7.1.9025) unit tests
|
2021-08-18 23:19:38 +02:00 |
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a44283f998
|
(v1.7.1.9024) unit tests
|
2021-08-17 14:34:11 +02:00 |
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a2d249962f
|
(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47
|
2021-08-16 21:54:34 +02:00 |
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4e1efd902c
|
(v1.7.1.9022) rely on vctrs for ab selectors
|
2021-07-23 21:42:11 +02:00 |
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0ec81cc12e
|
(v1.7.1.9021) autoplot generics
|
2021-07-12 22:12:28 +02:00 |
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6838f03bde
|
(v1.7.1.9020) autoplot generics
|
2021-07-12 20:24:49 +02:00 |
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fc946564d1
|
(v1.7.1.9019) Morganella MIC in EUCAST 2021
|
2021-07-12 12:28:41 +02:00 |
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5ccb330b42
|
(v1.7.1.9018) translation fix
|
2021-07-11 13:20:45 +02:00 |
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39d97ab53b
|
(v1.7.1.9017) ab selector error
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2021-07-08 23:05:45 +02:00 |
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b228eb1536
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(v1.7.1.9016) only_treatable ab selectors
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2021-07-08 22:23:28 +02:00 |
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625a6fb304
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(v1.7.1.9015) removed S3 taxonomic_name again
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2021-07-07 20:34:05 +02:00 |
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ad10693a1a
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(v1.7.1.9014) rep() for S3 classes
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2021-07-06 16:35:14 +02:00 |
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16b4c74d44
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(v1.7.1.9013) temp fix for ggplot2 bug #4511
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2021-07-04 22:10:46 +02:00 |
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350dbe6a11
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(v1.7.1.9012) update unit tests
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2021-07-04 20:25:30 +02:00 |
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5b5741f681
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(v1.7.1.9011) subsetting taxonomy fix
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2021-07-04 15:26:50 +02:00 |
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3bd50710e8
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(v1.7.1.9010) fix for count_* and proportion_*
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2021-07-04 12:00:41 +02:00 |
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3e26929838
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(v1.7.1.9009) fix for ab class selectors
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2021-07-03 21:56:53 +02:00 |
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c8491d07f8
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(v1.7.1.9008) unit tests
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2021-06-23 10:19:38 +02:00 |
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95050ee3e0
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(v1.7.1.9007) Updated antibiotics dataset, fixes #41
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2021-06-23 10:03:17 +02:00 |
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1dc9d237f6
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(v1.7.1.9006) unit tests
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2021-06-22 13:09:41 +02:00 |
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d04e83f494
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(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1
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2021-06-22 12:16:42 +02:00 |
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c44d9392ca
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(v1.7.1.9004) more extensive unit tests
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2021-06-15 10:51:04 +02:00 |
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556bf0014d
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(v1.7.1.9003) unit test
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2021-06-14 22:37:05 +02:00 |
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99be4c7e7e
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(v1.7.1.9002) ab class selectors update
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2021-06-14 22:04:04 +02:00 |
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683a0e748a
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(v1.7.1.9001) unit tests
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2021-06-05 15:12:01 +02:00 |
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1908e7cc7a
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(v1.7.1.9000) ab_class update, unit tests
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2021-06-04 21:07:55 +02:00 |
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7e70403efb
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(v1.7.1) New CRAN release
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2021-06-03 15:19:21 +02:00 |
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279376fccb
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(v1.7.0.9002) old MO codes
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2021-06-01 16:36:33 +02:00 |
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bef0f42f66
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(v1.7.0.9001) CLSI 2020 guideline
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2021-06-01 15:33:06 +02:00 |
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f406319503
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(v1.7.0.9000) package size
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2021-05-30 22:14:38 +02:00 |
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41d279daa1
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(v1.7.0) v1.7.0
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2021-05-26 11:10:34 +02:00 |
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ac73a8d849
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v1.7.0
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2021-05-24 15:29:17 +02:00 |
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e5599bc694
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(v1.6.0.9065) unit tests
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2021-05-24 11:01:32 +02:00 |
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4fbf9e1720
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(v1.6.0.9064) prepare new release
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2021-05-24 09:34:08 +02:00 |
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a13fd98e8b
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(v1.6.0.9063) prepare new release
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2021-05-24 09:00:11 +02:00 |
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06302d296a
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(v1.6.0.9062) code consistency
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2021-05-24 00:06:28 +02:00 |
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07939b1a14
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(v1.6.0.9061) age() update
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2021-05-23 23:11:16 +02:00 |
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fa2f5214b9
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(v1.6.0.9060) unit tests
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2021-05-22 10:05:59 +02:00 |
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0b1f59edec
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(v1.6.0.9058) unit tests
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2021-05-22 08:58:51 +02:00 |
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65a8b58aa6
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(v1.6.0.9056) support codecov again
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2021-05-21 20:30:48 +02:00 |
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b210f1327c
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(v1.6.0.9055) support codecov again
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2021-05-21 20:20:51 +02:00 |
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fecc5d183c
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(v1.6.0.9054) unit tests
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2021-05-20 15:06:08 +02:00 |
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69a656abc0
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(v1.6.0.9053) unit tests
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2021-05-20 13:42:17 +02:00 |
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4a2a48b7c1
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(v1.6.0.9052) unit tests
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2021-05-20 11:42:39 +02:00 |
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04ef5b28e7
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(v1.6.0.9050) printing NA in custom_eucast_rules()
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2021-05-20 10:10:40 +02:00 |
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9a2879cba9
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(v1.6.0.9049) unit tests
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2021-05-20 00:07:27 +02:00 |
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2413efd5c1
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(v1.6.0.9048) ab selectors overhaul
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2021-05-19 22:55:42 +02:00 |
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6920c0be41
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(v1.6.0.9047) filter_ab_class() fixes
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2021-05-18 11:29:31 +02:00 |
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cfb7df823e
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(v1.6.0.9044) betalactams() selector
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2021-05-18 00:53:04 +02:00 |
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be49131ed7
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(v1.6.0.9043) translation update
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2021-05-17 19:43:01 +02:00 |
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83fec69a03
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(v1.6.0.9042) translation update
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2021-05-17 11:26:12 +02:00 |
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916df6e90c
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(v1.6.0.9041) filter_ab_class() fix
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2021-05-16 10:50:00 +02:00 |
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00496e45b7
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(v1.6.0.9040) unit tests
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2021-05-16 09:25:36 +02:00 |
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6c3ab19e3a
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(v1.6.0.9038) unit tests
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2021-05-15 23:47:36 +02:00 |
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3619c1327c
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(v1.6.0.9037) unit tests
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2021-05-15 23:36:02 +02:00 |
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73fb0374c3
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(v1.6.0.9036) unit tests
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2021-05-15 23:25:10 +02:00 |
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229e1bb407
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(v1.6.0.9035) unit tests
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2021-05-15 22:55:12 +02:00 |
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86736ab9a7
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(v1.6.0.9032) unit tests
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2021-05-15 21:54:56 +02:00 |
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d8c91d5876
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(v1.6.0.9031) tinytest unit tests
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2021-05-15 21:36:22 +02:00 |
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