|
|
d2e8249edd
|
(v0.8.0.9004) added MDR guideline by Magiorakos et al.
|
2019-10-26 21:56:41 +02:00 |
|
|
|
00cdb498a0
|
(v0.7.1.9102) lintr
|
2019-10-11 17:21:02 +02:00 |
|
|
|
c8f6b97847
|
(v0.7.1.9100) bug_drug speed, MIC levels
|
2019-10-08 22:21:33 +02:00 |
|
|
|
f479dfce60
|
(v0.7.1.9097) mdro() examples fix
|
2019-10-07 14:57:27 +02:00 |
|
|
|
4e9c4c1b4e
|
(v0.7.1.9096) German guideline for mdro()
|
2019-10-07 14:32:06 +02:00 |
|
|
|
8bc4081b03
|
(v0.7.1.9092) as.ab() improvements
|
2019-10-04 15:36:12 +02:00 |
|
|
|
edb599ae0b
|
(v0.7.1.9091) percentage from clean pkg
|
2019-09-30 16:45:36 +02:00 |
|
|
|
99d0fe76dd
|
(v0.7.1.9088) bug_drug improvement
|
2019-09-25 15:43:22 +02:00 |
|
|
|
a8c6b8f9c4
|
(v0.7.1.9082) CI fix
|
2019-09-23 14:37:24 +02:00 |
|
|
|
64d9829030
|
(v0.7.1.9081) bug_drug fixes
|
2019-09-23 13:53:50 +02:00 |
|
|
|
66d405ff57
|
(v0.7.1.9080) new LIS codes
|
2019-09-22 17:19:59 +02:00 |
|
|
|
40e6b3e8f6
|
(v0.7.1.9077) mo codes fix
|
2019-09-20 14:18:29 +02:00 |
|
|
|
3596adb295
|
(v0.7.1.9076) mo codes
|
2019-09-20 12:33:05 +02:00 |
|
|
|
e2aa4f996b
|
(v0.7.1.9075) new microorganism codes
|
2019-09-18 15:46:09 +02:00 |
|
|
|
398c5bdc4f
|
(v0.7.1.9073) as.mo() self-learning algorithm
|
2019-09-15 22:57:30 +02:00 |
|
|
|
cd178ee569
|
(v0.7.1.9072) key_antibiotics() for foreign systems
|
2019-09-12 15:08:53 +02:00 |
|
|
|
b5d2a08401
|
(v0.7.1.9071) p_symbol()
|
2019-09-03 09:47:39 +02:00 |
|
|
|
06b6266366
|
(v0.7.1.9070) na.rm for age(), age_groups()
|
2019-09-02 15:17:41 +02:00 |
|
|
|
e2b78fa428
|
(v0.7.1.9066) bug-drug fix
|
2019-08-27 23:00:00 +02:00 |
|
|
|
248638ad91
|
(v0.7.1.9065) bug-drug fix
|
2019-08-27 22:41:09 +02:00 |
|
|
|
f3276592b7
|
(v0.7.1.9064) bug-drug fix
|
2019-08-27 19:15:04 +02:00 |
|
|
|
93be16484b
|
(v0.7.1.9063) septic_patients -> example_isolates
|
2019-08-27 16:45:42 +02:00 |
|
|
|
7a6fce4eb8
|
(v0.7.1.9062) mo/ab assignment improvements
|
2019-08-26 16:02:03 +02:00 |
|
|
|
e46cb0399f
|
(v0.7.1.9059) bug_drug_combinations
|
2019-08-25 22:53:22 +02:00 |
|
|
|
920212e815
|
(v0.7.1.9056) mo and ab subsetting
|
2019-08-14 14:57:06 +02:00 |
|
|
|
7108454ba5
|
(v0.7.1.9055) algorithm improvements
|
2019-08-13 16:15:08 +02:00 |
|
|
|
bd252a2984
|
(v0.7.1.9036) preserve ab/mo classes in subsetting
|
2019-08-12 14:48:09 +02:00 |
|
|
|
1d423cca89
|
(v0.7.1.9035) cephalosporins and unit tests
|
2019-08-11 19:07:26 +02:00 |
|
|
|
3f5828e74a
|
(v0.7.1.9034) mo.codes fix for Dracunculus spp.
|
2019-08-09 23:45:26 +02:00 |
|
|
|
6598c5615d
|
(v0.7.1.9033) 5000 new fungi
|
2019-08-09 23:22:10 +02:00 |
|
|
|
6a349bf757
|
(v0.7.1.9032) eucast_rules() improvements
|
2019-08-09 14:28:46 +02:00 |
|
|
|
1ce4b72dd2
|
(v0.7.1.9031) include_unknown for first_isolate()
|
2019-08-08 22:39:42 +02:00 |
|
|
|
bfa92eb166
|
(v0.7.1.9028) predict update
|
2019-08-07 15:58:32 +02:00 |
|
|
|
90c874025a
|
(v0.7.1.9027) tibble printing
|
2019-08-07 15:37:39 +02:00 |
|
|
|
3a1f960f89
|
(v0.7.1.9024) eucast_rules() fix, new MOs
|
2019-08-06 14:39:22 +02:00 |
|
|
|
d6ab3896a1
|
(v0.7.1.9021) CI fix for resistance_predict
|
2019-08-04 10:48:41 +02:00 |
|
|
|
2a62c3d62a
|
(v0.7.1.9018) deps
|
2019-07-30 13:12:40 +02:00 |
|
|
|
ec0ca20dee
|
(v0.7.1.9017) deps
|
2019-07-29 21:20:26 +02:00 |
|
|
|
b7e2d7b9b8
|
(v0.7.1.9016) deps
|
2019-07-29 17:34:57 +02:00 |
|
|
|
240f03a672
|
(v0.7.1.9015) Remove freq()
|
2019-07-29 13:33:48 +02:00 |
|
|
|
b452de2fe4
|
(v0.7.1.9010) eucast informative text in verbose mode
|
2019-07-09 13:36:03 +02:00 |
|
|
|
b15d59cf03
|
(v0.7.1.9009) note for WHOCC
|
2019-07-09 11:22:46 +02:00 |
|
|
|
c57ad26c5b
|
(v0.7.1.9007) mdro update
|
2019-07-04 15:26:07 +02:00 |
|
|
|
4ff20af123
|
(v0.7.1.9006) new rsi calculations, atc class removal
|
2019-07-02 16:48:52 +02:00 |
|
|
|
156d550895
|
(v0.7.1.9005) new rsi calculations, atc class removal
|
2019-07-01 14:03:15 +02:00 |
|
|
|
65c6702b21
|
(v0.7.1.9004) atc class removal
|
2019-06-27 11:57:45 +02:00 |
|
|
|
c9156c004a
|
(v0.7.0.9013) mo_synonym fix
|
2019-06-22 14:49:12 +02:00 |
|
|
|
9c39c35f86
|
(v0.7.0.9010) mo_synonyms, plot/barplot fixes
|
2019-06-16 21:42:40 +02:00 |
|
|
|
254745061c
|
(v0.7.0.9008) T. vaginalis, rsi_df
|
2019-06-13 14:28:46 +02:00 |
|
|
|
8f674e19bb
|
(v0.7.0.9005) ab algorithm update
|
2019-06-11 14:18:25 +02:00 |
|
|
|
ec48f1d83b
|
(v0.7.0.9003) scale fix
|
2019-06-08 23:50:06 +02:00 |
|
|
|
270aa0dd33
|
v0.7.0
|
2019-06-03 17:45:22 +02:00 |
|
|
|
702da574c0
|
website update
|
2019-06-02 19:50:22 +02:00 |
|
|
|
bd73988f15
|
(v0.6.1.9053) prerelease fixes
|
2019-06-02 19:23:19 +02:00 |
|
|
|
2667fff8a7
|
(v0.6.1.9050) support staged install
|
2019-06-01 20:40:49 +02:00 |
|
|
|
a665612cb8
|
(v0.6.1.9049) data creation fix
|
2019-05-31 21:20:16 +02:00 |
|
|
|
4ed27c7e7a
|
(v0.6.1.9046) ggplot fix
|
2019-05-31 20:25:57 +02:00 |
|
|
|
f03f71eced
|
(v0.6.1.9045) age test fix
|
2019-05-31 14:40:15 +02:00 |
|
|
|
493ae2ba0c
|
(v0.6.1.9044) first_isolate fix for species
|
2019-05-31 14:25:11 +02:00 |
|
|
|
1f8ee3ec3e
|
(v0.6.1.9043) age doc fix
|
2019-05-30 08:51:38 +02:00 |
|
|
|
8b5e2b030b
|
added boxplot for (grouped) freq()
|
2019-05-29 19:56:17 +02:00 |
|
|
|
62e6f41961
|
website update
|
2019-05-29 00:36:48 +02:00 |
|
|
|
7e0e171512
|
website update
|
2019-05-23 19:39:07 +02:00 |
|
|
|
bbf8b611e3
|
doc fix
|
2019-05-23 17:35:58 +02:00 |
|
|
|
60983a1640
|
added mdr_tb()
|
2019-05-23 16:58:59 +02:00 |
|
|
|
4ca00e1868
|
speed improvement eucast_rules(), support more old MO codes
|
2019-05-20 12:00:18 +02:00 |
|
|
|
b0033dae1b
|
website update
|
2019-05-17 20:22:04 +02:00 |
|
|
|
5eda991c47
|
ab_info fix
|
2019-05-16 22:07:31 +02:00 |
|
|
|
4c3cf85a65
|
ab_info, other bug fixes
|
2019-05-16 21:20:00 +02:00 |
|
|
|
f6bf54b37d
|
documentation fix
|
2019-05-13 20:16:51 +02:00 |
|
|
|
2ea0c93e44
|
documentation fix
|
2019-05-13 16:35:48 +02:00 |
|
|
|
cc403169c6
|
first isolate missing dates fix
|
2019-05-13 14:56:23 +02:00 |
|
|
|
0dc0715dc6
|
CI tests
|
2019-05-13 12:21:57 +02:00 |
|
|
|
38a4421450
|
CI tests
|
2019-05-13 10:10:16 +02:00 |
|
|
|
fcc77164e9
|
mdro fix
|
2019-05-11 23:30:10 +02:00 |
|
|
|
68cc7ef0d0
|
new antibiotics
|
2019-05-10 16:44:59 +02:00 |
|
|
|
461eec9bac
|
cfta streptococci, codecov.yml
|
2019-04-09 14:59:17 +02:00 |
|
|
|
cffb7787d8
|
cfta streptococci
|
2019-04-09 10:34:40 +02:00 |
|
|
|
30b559827c
|
documentation update
|
2019-04-07 22:40:02 +02:00 |
|
|
|
51fdc5d6cc
|
self-learning off
|
2019-04-06 09:38:23 +02:00 |
|
|
|
fbc9191b13
|
new EUCAST rules algorithm
|
2019-04-05 18:47:39 +02:00 |
|
|
|
b25f2d6213
|
v0.6.1
|
2019-03-28 21:33:28 +01:00 |
|
|
|
8a1d384d9c
|
ci fixes
|
2019-03-26 15:34:04 +01:00 |
|
|
|
29f444543d
|
added Becker 2019
|
2019-03-26 14:24:03 +01:00 |
|
|
|
c6a12266e7
|
DSMZ data
|
2019-03-18 14:29:41 +01:00 |
|
|
|
e18a1f1f17
|
as.mo improvement
|
2019-03-15 17:36:42 +01:00 |
|
|
|
fdffc2791b
|
memory for as.mo()
|
2019-03-15 13:57:25 +01:00 |
|
|
|
504a042fba
|
uncertainty levels, new WHONET codes
|
2019-03-12 12:19:27 +01:00 |
|
|
|
b319b89750
|
WHONET fix
|
2019-03-09 08:21:00 +01:00 |
|
|
|
0c0c6e289b
|
small as.mo fix
|
2019-03-06 14:39:02 +01:00 |
|
|
|
5c7a061a5d
|
filter_ab_class fix
|
2019-03-06 09:32:48 +01:00 |
|
|
|
74e0ae21fd
|
con WHONET, filter ab class
|
2019-03-05 22:47:42 +01:00 |
|
|
|
e835525cf6
|
unknown codes, rsi fix
|
2019-03-02 22:47:04 +01:00 |
|
|
|
c5efb272fd
|
mo_source improvement
|
2019-03-01 09:34:04 +01:00 |
|
|
|
2565b60024
|
rlang dependency, new fungi
|
2019-02-28 13:56:28 +01:00 |
|
|
|
54162522bd
|
age_groups fix
|
2019-02-27 11:36:12 +01:00 |
|
|
|
f9ded23023
|
as.mo improvement
|
2019-02-26 12:33:26 +01:00 |
|
|
|
c506d2893b
|
as.mo improvements
|
2019-02-25 15:52:32 +01:00 |
|
|
|
0ec76cfa98
|
as.mo improvement
|
2019-02-25 10:42:57 +01:00 |
|
|
|
1a6314769b
|
as.mo improvement
|
2019-02-23 16:02:31 +01:00 |
|
|
|
41ad7a22c8
|
mo_rank mo_url, added Tremellales
|
2019-02-22 22:12:10 +01:00 |
|
|
|
68a9a35ed6
|
algorithm update
|
2019-02-21 18:55:52 +01:00 |
|
|
|
c6e57ca456
|
website update
|
2019-02-20 14:18:11 +01:00 |
|
|
|
13120f465f
|
website update
|
2019-02-20 13:57:23 +01:00 |
|
|
|
8dc027309e
|
website update
|
2019-02-20 10:38:24 +01:00 |
|
|
|
fb1fc3686c
|
Catalogue of life
|
2019-02-20 00:04:48 +01:00 |
|
|
|
54f8258f8c
|
Catalogue of Life, replaces ITIS
|
2019-02-18 02:33:37 +01:00 |
|
|
|
efb2af9e3a
|
benchmarks plots
|
2019-02-14 10:23:51 +01:00 |
|
|
|
76ed26d27e
|
resistance predict update
|
2019-02-11 10:27:10 +01:00 |
|
|
|
c56b179857
|
as.rsi warning, site update
|
2019-02-09 22:16:24 +01:00 |
|
|
|
ed30312048
|
mo codes for WHONET
|
2019-02-08 16:06:54 +01:00 |
|
|
|
3d3366faf7
|
is.rsi.eligible update
|
2019-02-04 18:04:29 +01:00 |
|
|
|
587e00b7be
|
is.rsi.eligible update
|
2019-02-04 12:24:07 +01:00 |
|
|
|
0b3dc0231f
|
freq fix
|
2019-01-30 16:00:55 +01:00 |
|
|
|
3efb54d016
|
freq update
|
2019-01-29 20:20:09 +01:00 |
|
|
|
6aae206320
|
WHONET/EARS-Net support
|
2019-01-29 00:06:50 +01:00 |
|
|
|
f6336fdd89
|
quasiquotation for freq()
|
2019-01-28 11:20:32 +01:00 |
|
|
|
e76961a66b
|
less deps
|
2019-01-27 19:30:40 +01:00 |
|
|
|
a2d3ea280a
|
text updates
|
2019-01-27 13:55:23 +01:00 |
|
|
|
18b75356a9
|
re-add atc_ddd and atc_groups
|
2019-01-27 13:33:43 +01:00 |
|
|
|
6ec940bc75
|
atc_ functions
|
2019-01-27 10:53:59 +01:00 |
|
|
|
b39055c018
|
deprecated fix
|
2019-01-27 00:33:58 +01:00 |
|
|
|
f836722269
|
atc_ functions
|
2019-01-26 23:22:56 +01:00 |
|
|
|
f4ff98b470
|
WHO update, antibiotics update
|
2019-01-25 13:18:41 +01:00 |
|
|
|
46dcc7e2e8
|
set_mo_source
|
2019-01-21 15:53:01 +01:00 |
|
|
|
8db87a15e9
|
fixes
|
2019-01-15 16:38:54 +01:00 |
|
|
|
046d195064
|
resistance predict
|
2019-01-15 12:45:24 +01:00 |
|
|
|
cda7087722
|
website update
|
2019-01-12 19:31:30 +01:00 |
|
|
|
5aad26035c
|
edited g.test
|
2019-01-12 11:06:58 +01:00 |
|
|
|
641d866db2
|
guess_ab_col, benchmarks
|
2019-01-11 20:37:23 +01:00 |
|
|
|
193a2d2863
|
EUCAST update, as.mo bugfix for empty vlaues
|
2019-01-08 16:23:45 +01:00 |
|
|
|
bc15f660d6
|
guess_ab()
|
2019-01-06 20:23:49 +01:00 |
|
|
|
2c798547bf
|
language
|
2019-01-05 21:40:04 +01:00 |
|
|
|
6652f7d82b
|
fix warnings
|
2019-01-04 09:49:42 +01:00 |
|
|
|
80ea555663
|
guess_ab
|
2019-01-03 23:56:19 +01:00 |
|
|
|
6b2d464f8c
|
big website update, licence txt update
|
2019-01-02 23:24:07 +01:00 |
|
|
|
68baf058cd
|
website update
|
2018-12-31 10:35:26 +01:00 |
|
|
|
92a32b62a7
|
new website, freq updates
|
2018-12-29 22:24:19 +01:00 |
|
|
|
0b8084871d
|
dplyr 0.8.0 support, fixes #7
|
2018-12-22 22:39:34 +01:00 |
|
|
|
b937662a97
|
limits for scale_y_percent - Licence update
|
2018-12-16 22:45:12 +01:00 |
|
|
|
1ed0cc9bfd
|
age_groups fix
|
2018-12-16 11:40:54 +01:00 |
|
|
|
2018d5b477
|
age and age_groups
|
2018-12-15 22:40:07 +01:00 |
|
|
|
7e5fe75a17
|
small text fixes
|
2018-12-14 07:48:12 +01:00 |
|
|
|
81af7be36e
|
note about portions
|
2018-12-14 07:23:25 +01:00 |
|
|
|
01a6d56334
|
add kingdom to mo_taxonomy
|
2018-12-10 21:47:25 +01:00 |
|
|
|
5ab7eb07bc
|
keyab automatic
|
2018-12-10 15:14:29 +01:00 |
|
|
|
9478ab71be
|
freq - decimals
|
2018-12-10 10:13:40 +01:00 |
|
|
|
8e8a9cd190
|
AI improvements
|
2018-12-07 12:04:55 +01:00 |
|
|
|
60fe98bbbd
|
better as.mo handling
|
2018-12-06 14:36:39 +01:00 |
|
|
|
9ddf6dc530
|
support A. species for as.mo, cleanup
|
2018-11-24 20:25:09 +01:00 |
|
|
|
a8132922af
|
unit test read.4d, unselecting freq cols
|
2018-11-19 13:00:22 +01:00 |
|
|
|
83c7da85ab
|
unit tests
|
2018-11-16 22:28:55 +01:00 |
|
|
|
d22b7f00da
|
unit tests
|
2018-11-16 22:22:42 +01:00 |
|
|
|
4fcc2b409a
|
MDRO update
|
2018-11-16 20:50:50 +01:00 |
|
|
|
fab64e6728
|
read.4D improvements
|
2018-11-15 12:42:35 +01:00 |
|
|
|
6b0f4ffbd4
|
new kingdom
|
2018-11-09 13:11:54 +01:00 |
|
|
|
84e08f516a
|
grouping var for freq
|
2018-11-06 16:41:59 +01:00 |
|
|
|
d15bb2ab3f
|
read_4D
|
2018-11-05 15:30:49 +01:00 |
|
|
|
d07e9b904e
|
new function get_locale
|
2018-11-05 13:20:32 +01:00 |
|
|
|
e601fd259a
|
test syntax fix
|
2018-11-01 20:50:10 +01:00 |
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5476fecc73
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eucast update
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2018-11-01 20:23:33 +01:00 |
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f7687557c9
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eucast updates
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2018-11-01 17:06:08 +01:00 |
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9cd4ab928a
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speed improvement as.mo, freq title
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2018-10-31 12:10:49 +01:00 |
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1bf8dc2983
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as.mo speedup: assigned to namespace
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2018-10-29 17:26:17 +01:00 |
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707aa20a37
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fixes
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2018-10-23 14:59:36 +02:00 |
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7997de6a6d
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mdro and 1st isolate improvements
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2018-10-23 11:15:05 +02:00 |
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c2a93b46db
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breaks param, tidyr dep change, freq markdown
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2018-10-22 12:32:59 +02:00 |
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ec15b82fd6
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param header for freq
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2018-10-19 21:52:08 +02:00 |
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86b03577a7
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fix for as.mo, added also_single_tested
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2018-10-19 13:53:31 +02:00 |
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b464dd524a
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new verbose
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2018-10-19 00:17:03 +02:00 |
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0ef91be3ac
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param rules for EUCAST
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2018-10-18 12:10:10 +02:00 |
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693f64bdbf
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new EUCAST rules: clinical breakpoints
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2018-10-17 17:32:34 +02:00 |
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d5a41de711
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parameter combine_IR
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2018-10-16 09:59:31 +02:00 |
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5b5b95a47b
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count_all and some fixes
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2018-10-12 16:35:18 +02:00 |
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95c9fdc552
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CRAN fixes for release 0.4.0
https://cran.r-project.org/web/checks/check_results_AMR.html
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2018-10-09 13:53:33 +02:00 |
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ed17db0263
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renamed year columns to ref
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2018-10-01 14:44:40 +02:00 |
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3119a221e5
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authors from ITIS, diff for freq
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2018-10-01 11:39:43 +02:00 |
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92c9cc2608
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diff for freq, fix for mo_shortname
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2018-09-29 21:54:32 +02:00 |
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a6aa9e95fb
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completed old taxonomic names
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2018-09-28 20:13:13 +02:00 |
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768fe17324
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removed clipboard functions as it violated CRAN policies
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2018-09-28 16:05:18 +02:00 |
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2b0080995e
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speed improvement for as.mo, more old taxonomic names
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2018-09-27 23:23:48 +02:00 |
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450992baea
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new: 1680 old taxonomic names
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2018-09-25 16:44:40 +02:00 |
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9c566585b0
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first inclusion of ITIS data
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2018-09-24 23:33:29 +02:00 |
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5d80cef338
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added taxonomic data from ITIS
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2018-09-17 20:53:32 +02:00 |
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db14781593
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add labels_rsi_count
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2018-09-16 22:11:17 +02:00 |
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b792a2754e
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added prevalence column and alterted as.mo algorith to use it, added ab_name as alias
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2018-09-16 16:43:29 +02:00 |
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d049ec9e69
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ggplot2_rsi fix
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2018-09-13 14:48:34 +02:00 |
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cb0d74a4f0
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support for French and Italian, added quote to freq
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2018-09-10 15:45:25 +02:00 |
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b83e6a9380
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algoritm improvement, removed all Catabacter except for C. hongkongensis
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2018-09-10 11:40:54 +02:00 |
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4816419f0c
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AI improvements for microorganisms
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2018-09-09 12:11:44 +02:00 |
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26f5be0033
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support for portuguese, language determination based on system
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2018-09-08 16:06:47 +02:00 |
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de36b0be23
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fix for empty values in mo_property
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2018-09-05 12:21:27 +02:00 |
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e39a9a8b05
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added mo_shortname
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2018-09-05 10:51:46 +02:00 |
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790bd1622d
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added vanA to vanE positive Enterococci
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2018-09-05 09:49:19 +02:00 |
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b388e3fee7
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Support for German and Spanish microorganism properties, cleanup
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2018-09-04 11:33:30 +02:00 |
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75fe4d401f
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new MOs, cleanup
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2018-09-01 21:19:46 +02:00 |
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5965d3c794
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replaced bactid by mo
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2018-08-31 13:36:19 +02:00 |
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98ff131680
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support for older versions of ggplot2
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2018-08-29 16:39:28 +02:00 |
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d654444c8e
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re added nrow
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2018-08-29 16:35:32 +02:00 |
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d9e68e0a50
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ggplot_rsi example update, more unit tests
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2018-08-29 16:25:57 +02:00 |
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