40221e5244
(v1.2.0.9003) better terminal colour support
2020-06-05 13:56:05 +02:00
2c8d600914
(v1.2.0.9002) fix for joins
2020-06-03 14:33:55 +02:00
5dc4c96b7d
(v1.2.0.9001) filter_ab_class() update
2020-06-03 11:48:00 +02:00
02d07b9fb3
(v1.2.0.9000) eucast_rules() fix for tibbles
2020-06-02 16:05:56 +02:00
b44e2c9202
v1.2.0
2020-05-28 16:48:55 +02:00
d9a4b0bcaf
(v1.1.0.9021) 1st isolates update
2020-05-28 10:51:56 +02:00
86d44054f0
(v1.1.0.9020) updated taxonomy
2020-05-27 16:37:49 +02:00
ae1969b941
(v1.1.0.9019) mo_source fix
2020-05-25 01:01:14 +02:00
f5ff2e6634
(v1.1.0.9018) as.ab() update, added ab_url()
2020-05-22 20:29:55 +02:00
e467cc103e
(v1.1.0.9017) as.ab() update, added ab_url()
2020-05-22 20:15:19 +02:00
1b1e243d14
(v1.1.0.9016) small fix
2020-05-21 12:28:57 +02:00
743f9a5364
(v1.1.0.9015) new default eucast_rules
2020-05-20 12:00:17 +02:00
5216d2b520
(v1.1.0.9014) lose dependencies
2020-05-19 14:16:45 +02:00
cb1814f5ff
(v1.1.0.9013) lose dependencies
2020-05-19 13:18:01 +02:00
19703eb5d3
(v1.1.0.9012) lose dependencies
2020-05-19 12:08:49 +02:00
218fd08097
(v1.1.0.9011) lose dependencies
2020-05-18 13:59:34 +02:00
d659c9baef
(v1.1.0.9010) lose dependencies
2020-05-18 11:09:02 +02:00
bf0402a653
(v1.1.0.9009) lose dependencies
2020-05-18 10:30:53 +02:00
f68d71a5e0
(v1.1.0.9007) lose dependencies
2020-05-16 21:40:50 +02:00
29609a0e2c
(v1.1.0.9006) lose dependencies
2020-05-16 20:42:45 +02:00
df2456b91f
(v1.1.0.9005) lose dependencies
2020-05-16 20:08:21 +02:00
7f3da74b17
(v1.1.0.9004) lose dependencies
2020-05-16 13:05:47 +02:00
5bdece1f9d
(v1.1.0.9000) CI fix
2020-04-30 09:05:03 +02:00
b040185269
(v1.1.0.9000) CLSI as.rsi() fix, better vctrs support, new CI
2020-04-29 14:33:44 +02:00
c2ffbd9f95
(v1.0.1.9009) prepare for next release
2020-04-15 11:30:28 +02:00
4be54d608c
(v1.0.1.9008) RIVM abbreviations for drugs
2020-04-14 20:38:09 +02:00
cde65141d9
(v1.0.1.9007) small bugfix
2020-04-14 15:10:09 +02:00
7a6f819232
(v1.0.1.9006) added generic CLSI rules
2020-04-14 14:12:31 +02:00
d1cb7d3b6f
(v1.0.1.9005) as.mo() improvements
2020-04-13 21:09:56 +02:00
219cff403f
(v1.0.1.9004) Support dplyr 1.0.0
2020-03-14 14:05:43 +01:00
77656a676c
(v1.0.1.9002) PCA unit tests
2020-03-08 11:18:59 +01:00
9fc858f208
(v1.0.1.9001) PCA unit tests
2020-03-08 09:12:11 +01:00
fa0d9c58d9
(v1.0.1.9000) first PCA implementation
2020-03-07 21:48:21 +01:00
0d5e78b2cf
(v1.0.0.9007) small doc fix
2020-02-22 17:03:47 +01:00
ea32e9916a
(v1.0.0.9005) info printing only in interactive mode
2020-02-21 21:13:38 +01:00
47fe8b7820
(v1.0.0.9004) add example_isolaten_unclean
2020-02-21 16:05:19 +01:00
bb3728f023
(v1.0.0.9003) prepare for short update
2020-02-21 13:13:34 +01:00
6408911922
(v1.0.0.9002) fix lintr
2020-02-20 20:31:42 +01:00
bdb26f624f
(v1.0.0.9001) add uti to as.rsi()
2020-02-20 17:21:01 +01:00
c6184a0fb8
(v0.9.0.9029) add uti to as.rsi()
2020-02-20 13:19:23 +01:00
c8981a563e
(v0.9.0.9027) documentation fix
2020-02-17 15:07:25 +01:00
5e2b294351
(v0.9.0.9026) update documentation
2020-02-17 14:38:01 +01:00
11f00f8a0a
(v0.9.0.9025) update as.rsi documentation
2020-02-16 22:43:56 +01:00
c7a93af3d0
(v0.9.0.9024) global vars fix
2020-02-14 20:03:43 +01:00
9b8b02960e
(v0.9.0.9023) EUCAST 2020 guidelines
2020-02-14 19:54:13 +01:00
5a98e6b777
(v0.9.0.9022) inheritance fix
2020-02-10 14:18:15 +01:00
b4356a299c
(v0.9.0.9021) inheritance fix
2020-02-10 12:25:02 +01:00
c7a76ba713
(v0.9.0.9020) as.mo() improvement
2020-02-09 22:04:29 +01:00
4e1c16c5a5
(v0.9.0.9019) website update
2020-02-01 15:09:36 +01:00
f152ab9a48
(v0.9.0.9018) Remove mo_history
2020-01-31 23:27:38 +01:00
1b80773c22
(v0.9.0.9017) documentation fix
2020-01-27 19:30:26 +01:00
a13c62e6e8
(v0.9.0.9016) Support SNOMED codes
2020-01-27 19:14:23 +01:00
9a3891efe4
(v0.9.0.9014) Machine reading guidelines
2020-01-27 11:05:39 +01:00
423d1d3c41
(v0.9.0.9013) Support for LOINC codes
2020-01-26 20:38:54 +01:00
449d9bde35
(v0.9.0.9012) Support for LOINC codes
2020-01-26 20:20:00 +01:00
64f5ceef03
(v0.9.0.9009) antibiotics data set update
2020-01-08 11:30:33 +01:00
ced1a7b7fa
(v0.9.0.9008) Happy new year! Add lifecycles
2020-01-05 17:22:09 +01:00
db5dfff0ca
(v0.9.0.9006) added CITATION file
2019-12-22 11:43:38 +01:00
ba3ce77f02
(v0.9.0.9005) as.mo for G. species
2019-12-21 10:56:06 +01:00
2db2a2458a
(v0.9.0.9003) as.mo() speedup for fullnames
2019-12-20 15:05:58 +01:00
a7e538e562
(v0.9.0) website fixes
2019-11-30 13:31:12 +01:00
56ce9bf665
(v0.9.0) website fixes
2019-11-30 12:01:50 +01:00
bb2ed55842
(v0.9.0) v0.9.0
2019-11-29 19:43:23 +01:00
9feef53bde
(v0.8.0.9037) complete documentation rewrite
2019-11-28 23:00:37 +01:00
c5f00f4a9f
(v0.8.0.9036) complete documentation rewrite
2019-11-28 22:32:17 +01:00
7c28b392b1
(v0.8.0.9035) add more mo codes
2019-11-24 22:48:56 +01:00
e53cc4990c
(v0.8.0.9034) add cid to antivirals
2019-11-23 12:39:57 +01:00
267320f15f
(v0.8.0.9033) antivirals data set, cleanup
2019-11-18 12:10:47 +01:00
67f3f4387b
(v0.8.0.9032) fix regex error
2019-11-15 16:50:46 +01:00
09e2730b53
(v0.8.0.9031) as.mo() improvements
2019-11-15 15:25:03 +01:00
248b45da71
(v0.8.0.9030) depend on tidyr >= 1.0.0
2019-11-11 10:46:39 +01:00
d22834c5b8
(v0.8.0.9029) cleanup
2019-11-10 15:50:18 +01:00
54b6322056
(v0.8.0.9028) examples fix
2019-11-10 13:17:20 +01:00
59ededa8dc
(v0.8.0.9027) adding susceptibility() and resistance()
2019-11-10 12:16:56 +01:00
ef640add2d
(v0.8.0.9021) update vignettes
2019-11-09 11:33:22 +01:00
e2d05cb1b0
(v0.8.0.9017) keywords update
2019-11-06 14:43:23 +01:00
a1fd2cd98a
(v0.8.0.9014) unit test update
2019-11-05 22:23:45 +01:00
2560aa1a53
(v0.8.0.9013) unit test update
2019-11-05 21:52:58 +01:00
5345d2759a
(v0.8.0.9012) mdro improvement
2019-11-05 11:28:52 +01:00
fe606e287b
(v0.8.0.9011) col guess update
2019-11-04 12:08:08 +01:00
9060233953
(v0.8.0.9010) mdro bug fix
2019-11-04 11:35:34 +01:00
0bb531f3e0
(v0.8.0.9009) unit test
2019-11-03 22:41:29 +01:00
29e448883d
(v0.8.0.9008) new verbose mode for MDROs
2019-11-03 22:24:42 +01:00
09c4b04cd0
(v0.8.0.9007) Enterobacterales order
2019-10-30 23:02:50 +01:00
7ff2ad8188
(v0.8.0.9006) small typos
2019-10-27 00:31:59 +02:00
412077a6f2
(v0.8.0.9005) fix unit tests
2019-10-26 22:21:26 +02:00
d2e8249edd
(v0.8.0.9004) added MDR guideline by Magiorakos et al.
2019-10-26 21:56:41 +02:00
c01dc8a5b7
(v0.8.0.9003) printing fix for AB columns
2019-10-23 15:44:11 +02:00
3e5ab53209
(v0.8.0.9002) eucast_rules() fix for S. maltophilia
2019-10-23 14:48:25 +02:00
666126cd5e
(v0.8.0.9001) guideline text on as.rsi()
2019-10-21 14:12:28 +02:00
10e6b225e7
(v0.7.1.9107) v0.8.0
2019-10-15 14:35:23 +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
683d226fd3
Update guess_ab_col.R
2019-10-08 08:02:19 +00:00
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
1e260d85c8
(v0.7.1.9095) get_column_abx() fix
2019-10-06 22:19:26 +02:00
3d5692219e
(v0.7.1.9094) get_column_abx() improvement
2019-10-06 21:44:08 +02:00
b6653a620a
(v0.7.1.9093) as.ab() fix
2019-10-06 21:07:38 +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
b39e7feae6
(v0.7.1.9090) factor levels of mdr_tb
2019-09-26 21:58:06 +02:00
b9f01d686e
(v0.7.1.9089) eucast file update
2019-09-25 22:37:40 +02:00
99d0fe76dd
(v0.7.1.9088) bug_drug improvement
2019-09-25 15:43:22 +02:00
04cd0d25db
(v0.7.1.9087) small fix
2019-09-23 23:09:50 +02:00
38336d7408
(v0.7.1.9086) small fix
2019-09-23 23:00:18 +02:00
ad5f211a8f
(v0.7.1.9085) Salmonella fix
2019-09-23 21:24:37 +02:00
76dc948067
(v0.7.1.9084) CI fix
2019-09-23 20:55:54 +02:00
8ce252fbc5
(v0.7.1.9083) LIS code improvement
2019-09-23 17:32:05 +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
57b0bd92a0
(v0.7.1.9079) small fixes
2019-09-22 12:41:45 +02:00
46b61e9a70
(v0.7.1.9078) unit tests
2019-09-20 14:50:02 +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
f553a08a7b
(v0.7.1.9074) CI updates
2019-09-16 12:00:56 +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
c7be72f0ce
(v0.7.1.9069) documentation update
2019-09-01 13:16:57 +02:00
88ee1b7268
(v0.7.1.9068) gramstain to freq()
2019-08-30 14:50:56 +02:00
34a82d091e
(v0.7.1.9067) honor info
2019-08-28 17:12:48 +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
13d4fef801
(v0.7.1.9061) mo_property improvement
2019-08-26 10:03:37 +02:00
05dcb43660
(v0.7.1.9060) globals
2019-08-25 23:25:12 +02:00
e46cb0399f
(v0.7.1.9059) bug_drug_combinations
2019-08-25 22:53:22 +02:00
7c069145ac
(v0.7.1.9058) as.mo() improvement
2019-08-20 11:40:54 +02:00
04d49a62af
(v0.7.1.9057) get_column_abx() improvement
2019-08-15 17:09:27 +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
5f2733349e
(v0.7.1.9038) mo algorithm inprovements
2019-08-12 19:07:15 +02:00
c44c5e3913
(v0.7.1.9037) CI and global env fix
2019-08-12 15:34:49 +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
22a206ffd8
(v0.7.1.9030) eucast_rules() fix
2019-08-08 15:52:07 +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
96b334d7cc
website update
2019-08-06 14:46:30 +02:00
3a1f960f89
(v0.7.1.9024) eucast_rules() fix, new MOs
2019-08-06 14:39:22 +02:00
85b62aaf8f
(v0.7.1.9023) wrong percentage in as.mo()
2019-08-04 17:41:12 +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
9ac5a34b36
(v0.7.1.9014) MO codes update
2019-07-16 16:14:11 +02:00
c652c6913f
(v0.7.1.9013) guess_mo_ab speed improvement
2019-07-11 13:39:18 +02:00
68230d0712
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +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
453c159eac
0.7.1
2019-06-23 14:49:17 +02:00
c9156c004a
(v0.7.0.9013) mo_synonym fix
2019-06-22 14:49:12 +02:00
7094c1f459
website update
2019-06-16 22:14:43 +02:00
9c39c35f86
(v0.7.0.9010) mo_synonyms, plot/barplot fixes
2019-06-16 21:42:40 +02:00
980be2b22d
(v0.7.0.9009) global note
2019-06-13 16:40:35 +02:00
254745061c
(v0.7.0.9008) T. vaginalis, rsi_df
2019-06-13 14:28:46 +02:00
699e87ab4a
(v0.7.0.9007) renamed notes fix
2019-06-12 16:08:20 +02:00
44ab53128e
(v0.7.0.9006) ab algorithm fix for ATC codes
2019-06-11 15:31:32 +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
f50d3a5ba1
(v0.7.0.9002) scale fix
2019-06-08 15:00:28 +02:00
f02679fb63
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
270aa0dd33
v0.7.0
2019-06-03 17:45:22 +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
0a6580b4eb
(v0.6.1.9047) ggplot fix
2019-05-31 20:48:22 +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
27380fa021
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
7e0e171512
website update
2019-05-23 19:39:07 +02:00
3688fcaabf
doc fix
2019-05-23 17:59:43 +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
07d26cd485
faster determination of abx
2019-05-20 19:12:41 +02:00
6eb08a2ea3
new git flow to repository
2019-05-20 14:16:53 +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
c3ae6b7699
freq fix
2019-05-17 09:09:18 +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
73f1ee1159
freq/age fix
2019-04-11 00:54:48 +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
56d4b4719f
ci for devel and freq fix
2019-03-29 21:45:46 +01:00
7dca9791a2
v0.6.1
2019-03-28 22:30:19 +01:00
713290a9a6
v0.6.1
2019-03-28 22:05:03 +01:00
b25f2d6213
v0.6.1
2019-03-28 21:33:28 +01:00
8a1d384d9c
ci fixes
2019-03-26 15:34:04 +01:00
afd12d5486
ci fixes
2019-03-26 14:42:56 +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
b561de462a
global var
2019-03-15 20:15:56 +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
cf3bdb54c7
global var fix
2019-02-27 19:02:47 +01:00
95c49fdf79
global var fix
2019-02-27 17:39:39 +01:00
642f6571fe
as.mo fix
2019-02-27 14:22:07 +01:00
54162522bd
age_groups fix
2019-02-27 11:36:12 +01:00
4ba2ff68e0
language fix
2019-02-26 13:02:04 +01:00
f9ded23023
as.mo improvement
2019-02-26 12:33:26 +01:00
f25a4b3679
as.mo improvements
2019-02-25 16:07:21 +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
e65d1a3036
as.mo improvement
2019-02-23 21:49:02 +01:00
f16a152d06
as.mo improvements
2019-02-23 18:08:28 +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
6c542268be
unit tests
2019-02-21 23:32:30 +01:00
68a9a35ed6
algorithm update
2019-02-21 18:55:52 +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
ae44b185e6
fix freq length calculation
2019-02-13 17:14:59 +01:00
30ff770c93
freq update
2019-02-12 15:38:31 +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
cd07d65734
freq and website update
2019-02-01 16:55:55 +01:00
d75ec01f92
website update
2019-01-30 19:52:58 +01:00
0b3dc0231f
freq fix
2019-01-30 16:00:55 +01:00
e6489483c7
website update
2019-01-29 20:38:45 +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
63e343d555
deps fix
2019-01-27 20:49:11 +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
5493e1f05d
website update
2019-01-25 20:47:57 +01:00
f4ff98b470
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
9529d097b6
as.mo
2019-01-21 21:24:40 +01:00
46dcc7e2e8
set_mo_source
2019-01-21 15:53:01 +01:00
c6c3088e9f
select() fix for freq
2019-01-17 12:08:04 +01:00
1ee710c861
resistance predict
2019-01-15 16:51:49 +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
3661df7365
direct warning if failing as.mo
2019-01-12 16:45:20 +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
0205b6178d
guess_mo deprecation
2019-01-06 16:40:55 +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
2e4d703338
eucast rules fix, 1st isolate fix, website update
2018-12-31 01:48:53 +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
bd5f46d734
age_groups fix
2018-12-16 09:50:14 +01:00
2018d5b477
age and age_groups
2018-12-15 22:40:07 +01:00
ecebc60bfd
C stack error fix
2018-12-14 11:44:15 +01:00
857f565db0
reorganised notes and warnings
2018-12-14 10:52:20 +01:00
dec4947103
freq header fix for NAs
2018-12-14 10:08:51 +01:00
e4737d3add
date transformation fix for tibbles
2018-12-14 09:31:53 +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
74a7f4453b
small CI fix
2018-12-06 16:07:06 +01:00
60fe98bbbd
better as.mo handling
2018-12-06 14:36:39 +01:00
31e977937d
fix for as.mo and freq
2018-11-30 12:05:59 +01:00
9ddf6dc530
support A. species for as.mo, cleanup
2018-11-24 20:25:09 +01:00
63ba4b2980
small error in freq
2018-11-19 13:06:07 +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
373e0cb32f
unit test fail
2018-11-16 21:57:55 +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
5cb8f3cf72
get_locale improvement
2018-11-12 15:07:43 +01:00
6b0f4ffbd4
new kingdom
2018-11-09 13:11:54 +01:00
9be5e0318b
freq: fix na.rm in groups
2018-11-08 16:10:03 +01:00
84e08f516a
grouping var for freq
2018-11-06 16:41:59 +01:00
ee664f2a4c
small fix
2018-11-05 15:36:07 +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
d0bc05e5b1
speed improvement is.rsi.eligible
2018-11-02 14:55:29 +01:00
40a159e78d
more unit tests
2018-11-02 10:27:57 +01:00
e601fd259a
test syntax fix
2018-11-01 20:50:10 +01:00
5476fecc73
eucast update
2018-11-01 20:23:33 +01:00
f7687557c9
eucast updates
2018-11-01 17:06:08 +01:00
9cd4ab928a
speed improvement as.mo, freq title
2018-10-31 12:10:49 +01:00
1bf8dc2983
as.mo speedup: assigned to namespace
2018-10-29 17:26:17 +01:00
707aa20a37
fixes
2018-10-23 14:59:36 +02:00
7997de6a6d
mdro and 1st isolate improvements
2018-10-23 11:15:05 +02:00
299c5bea43
na freq, removed factors
2018-10-23 09:42:26 +02:00
9c56257da1
freq - print title bold in markdown
2018-10-22 13:06:54 +02:00
c2a93b46db
breaks param, tidyr dep change, freq markdown
2018-10-22 12:32:59 +02:00
ec15b82fd6
param header for freq
2018-10-19 21:52:08 +02:00
86b03577a7
fix for as.mo, added also_single_tested
2018-10-19 13:53:31 +02:00
032c0d51ef
better verbose in EUCAST
2018-10-19 00:57:10 +02:00
b464dd524a
new verbose
2018-10-19 00:17:03 +02:00
0ef91be3ac
param rules for EUCAST
2018-10-18 12:10:10 +02:00
693f64bdbf
new EUCAST rules: clinical breakpoints
2018-10-17 17:32:34 +02:00
d5a41de711
parameter combine_IR
2018-10-16 09:59:31 +02:00
5b5b95a47b
count_all and some fixes
2018-10-12 16:35:18 +02:00
e7d937d36e
update NEWS
2018-10-10 10:50:19 +02:00
67521394f6
more unit tests
2018-10-09 15:41:44 +02:00
95c9fdc552
CRAN fixes for release 0.4.0
...
https://cran.r-project.org/web/checks/check_results_AMR.html
2018-10-09 13:53:33 +02:00
6d761436f7
benchmarks on readme and speed improvement for direct mo codes
2018-10-01 16:26:02 +02:00
ed17db0263
renamed year columns to ref
2018-10-01 14:44:40 +02:00
3119a221e5
authors from ITIS, diff for freq
2018-10-01 11:39:43 +02:00
92c9cc2608
diff for freq, fix for mo_shortname
2018-09-29 21:54:32 +02:00
a6aa9e95fb
completed old taxonomic names
2018-09-28 20:13:13 +02:00
768fe17324
removed clipboard functions as it violated CRAN policies
2018-09-28 16:05:18 +02:00
2b0080995e
speed improvement for as.mo, more old taxonomic names
2018-09-27 23:23:48 +02:00
450992baea
new: 1680 old taxonomic names
2018-09-25 16:44:40 +02:00
9c566585b0
first inclusion of ITIS data
2018-09-24 23:33:29 +02:00
5d80cef338
added taxonomic data from ITIS
2018-09-17 20:53:32 +02:00
7680e4edd8
add shortest and longest to freq for characters
2018-09-17 09:42:09 +02:00
db14781593
add labels_rsi_count
2018-09-16 22:11:17 +02:00
b792a2754e
added prevalence column and alterted as.mo algorith to use it, added ab_name as alias
2018-09-16 16:43:29 +02:00
b0ca49d68d
small improvement for is.rsi.eligible, more unit tests
2018-09-14 11:54:01 +02:00
cf5711fb0b
algorithm improvement
2018-09-14 10:31:21 +02:00
d049ec9e69
ggplot2_rsi fix
2018-09-13 14:48:34 +02:00
cb0d74a4f0
support for French and Italian, added quote to freq
2018-09-10 15:45:25 +02:00
b83e6a9380
algoritm improvement, removed all Catabacter except for C. hongkongensis
2018-09-10 11:40:54 +02:00
4816419f0c
AI improvements for microorganisms
2018-09-09 12:11:44 +02:00
936198372e
translate CoNS
2018-09-08 16:24:12 +02:00
26f5be0033
support for portuguese, language determination based on system
2018-09-08 16:06:47 +02:00
c5073f2fd1
small fix for microorganisms data set
2018-09-06 16:50:03 +02:00
de36b0be23
fix for empty values in mo_property
2018-09-05 12:21:27 +02:00
e39a9a8b05
added mo_shortname
2018-09-05 10:51:46 +02:00
790bd1622d
added vanA to vanE positive Enterococci
2018-09-05 09:49:19 +02:00
b388e3fee7
Support for German and Spanish microorganism properties, cleanup
2018-09-04 11:33:30 +02:00
e25dd0e282
fix for joins
2018-09-03 10:04:49 +02:00
75fe4d401f
new MOs, cleanup
2018-09-01 21:19:46 +02:00
5965d3c794
replaced bactid by mo
2018-08-31 13:36:19 +02:00
98ff131680
support for older versions of ggplot2
2018-08-29 16:39:28 +02:00
d654444c8e
re added nrow
2018-08-29 16:35:32 +02:00
d9e68e0a50
ggplot_rsi example update, more unit tests
2018-08-29 16:25:57 +02:00
029157b3be
163 new trade names, added ab_tradenames
2018-08-29 12:27:37 +02:00
972fc4f6c7
ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid
2018-08-28 13:51:13 +02:00
2acdb1981c
atc and bactid functions, readme update
2018-08-25 22:01:14 +02:00
baaf4cc3e1
few extra tests
2018-08-24 14:18:38 +02:00
a100d07da6
removed ratio, better rsi_calc, update for freq
2018-08-24 11:08:20 +02:00
febd0ca885
geom_rsi - any parameter
2018-08-23 21:27:15 +02:00
da5379c881
quasiquotation, alpha for geom_rsi
2018-08-23 00:40:36 +02:00
3e87c8f409
count_* functions
2018-08-22 00:02:26 +02:00
59ce1eb1b1
ggplot_rsi improvements
2018-08-13 16:42:37 +02:00
dba06c3295
abname improvement, small fixes
2018-08-13 11:00:53 +02:00
ce2cdb9309
support groups for portion_df, update README
2018-08-12 22:34:03 +02:00
e5d32cafe0
new unit tests for ggplot, small fixes
2018-08-12 17:44:06 +02:00
1ba7d883fe
new ggplot enhancement
2018-08-11 21:30:00 +02:00
53fa198e35
new portion functions
2018-08-10 15:01:05 +02:00
ae2433a020
rsi family for resistance analysis
2018-08-03 14:49:29 +02:00
227121af3d
add Dialister to microorganisms
2018-08-03 11:46:06 +02:00
db5a0d32a5
typos of Becker algorithm
2018-08-03 10:58:48 +02:00
bd9bcfef78
thesis advisors
2018-08-03 09:59:39 +02:00
6262315527
Becker classification
...
Lancefield classification
Added Lancefield groups to `microorganisms` data set
2018-08-02 13:15:45 +02:00
edd2dd09dc
rsi for freq
2018-08-01 22:37:28 +02:00
d8f70a74de
clipboard error
2018-08-01 10:32:24 +02:00
a59d0661f7
check CMD error
2018-08-01 09:45:11 +02:00
7c667eb732
emph guess_bactid
2018-08-01 08:03:31 +02:00
211e3bae14
remove reshape2 dependency
2018-07-30 01:18:40 +02:00
510e8f22aa
more unit tests
2018-07-30 00:57:49 +02:00
d0a115d995
bactid speed improvement
2018-07-30 00:14:06 +02:00
826694323b
new functions R, RI, SI, S
2018-07-29 22:14:51 +02:00
8421e3f005
more mic classes
2018-07-28 10:48:27 +02:00
feab1cad6b
small fixes
2018-07-28 09:34:03 +02:00
498e88b5cf
improvement for forecasting resistance
2018-07-26 16:30:42 +02:00
d9e204031d
update to septic_patients, speed improvements
2018-07-25 14:17:04 +02:00
03a3cb397b
clipboard update
2018-07-23 15:09:19 +02:00
8421638b60
new class bactid
2018-07-23 14:14:03 +02:00
9920ac8a5c
fix for keyab, more examples
2018-07-23 10:35:39 +02:00
ad662d7bab
new col names for key_antibiotics
2018-07-19 15:11:23 +02:00
0d64c166f0
keyab fixes
2018-07-17 19:51:09 +02:00
2a4d759fbc
check fails
2018-07-17 14:48:11 +02:00
5cb9c541f8
new algorithm key abs
2018-07-17 13:02:05 +02:00
a5a4354651
speed improvements
2018-07-17 10:32:26 +02:00
715a7630ca
support format.freq
2018-07-16 16:41:48 +02:00
6eaf33baf3
speed improvements
2018-07-15 22:56:41 +02:00
b6655f6454
Welcome C++!
2018-07-13 17:23:46 +02:00
a28289562a
remove print function, out of scope
2018-07-11 20:12:19 +02:00
e3e10c2e88
fix for macOS and older tidyr versions
2018-07-11 12:34:02 +02:00
f63414d519
new g.test, extra unit tests
2018-07-10 12:27:07 +02:00
fc30d3fb13
freq: support for table
2018-07-09 14:02:58 +02:00
14b990d769
kurtosis, skewness, start with ML
2018-07-08 22:14:55 +02:00
34ee0247ac
addins and small improvements to microorganisms dataset
2018-07-04 17:20:03 +02:00
10fce8382c
include IQR and MAD in freq
2018-07-03 11:30:40 +02:00
3d0d21f322
rename vector2ratio to ratio
2018-07-02 11:14:20 +02:00
2ca01e2d8d
remove rlang dependency
2018-07-01 22:23:34 +02:00
3527894b49
new g.test() and edited freq()
2018-07-01 21:40:37 +02:00
f7af8a81da
update man page
2018-06-29 09:06:47 +02:00
6ee713cec1
move tbl_parse_guess
2018-06-29 08:56:03 +02:00
649a8025aa
add clipboard functions again
2018-06-27 15:54:56 +02:00
a9bd5472d0
top_freq
2018-06-20 14:47:37 +02:00
4a027f3c34
extra unit tests, add row.names to freq
2018-06-19 15:20:14 +02:00
bdc860e29c
atc_groups
2018-06-19 10:05:38 +02:00
0a5898b17d
fix for printing tibbles, improve guess_bactid
2018-06-08 12:06:54 +02:00
efdf5a3dc5
prevent dplyr:row_number warning
2018-05-31 14:19:25 +02:00
MS Berends
7a6d5fb6b7
rsi/mic fix
2018-05-31 09:02:49 +02:00
5593aee19e
edit as.rsi algor.
2018-05-30 23:02:16 +02:00
uscloud
dcc26dd942
Update freq function
2018-05-22 16:34:22 +02:00
MS Berends
0d80647d41
fix SI and IR
2018-05-16 11:19:45 +02:00
f05e7178cb
added vignette of freq
2018-05-09 11:44:46 +02:00
25b3346d9a
edit methodology of rsi
2018-05-03 10:19:02 +02:00
c0fc82c794
Added function n_rsi
2018-05-02 14:56:25 +02:00
6eaf594cb7
update data info
2018-05-01 09:57:50 +02:00
19ccc51f40
remove clipboard functions
2018-05-01 09:36:45 +02:00
6fa93fc286
fix clipboard check
2018-04-30 16:54:37 +02:00
8fe70d5652
Fix Latex PDF error
2018-04-30 16:24:11 +02:00
970e3ed7f1
EUCAST rules for MDRO
2018-04-25 15:33:58 +02:00
0b22ddef8e
more unit tests
2018-04-20 13:45:34 +02:00
82fec5cc51
Try to support older R versions
2018-04-19 14:10:57 +02:00
e7396b8f39
Try to support older R versions
2018-04-19 12:50:23 +02:00
d79132b29f
Try to support older R versions
2018-04-18 15:41:27 +02:00
4b5530ed64
Try to support older R versions
2018-04-18 15:19:00 +02:00
a814d82b4b
try to support older R versions
2018-04-18 14:50:16 +02:00
2509e2413d
MDRO, freq tables, new print format for tibbles
2018-04-18 12:24:54 +02:00
3165c50d06
more MOs
2018-04-03 16:07:32 +02:00
07bdd61241
update dependencies
2018-04-02 16:05:09 +02:00
c182a9673d
fix clipboard on linux
2018-04-02 11:11:21 +02:00
MS Berends
b7f29aa748
Update first_isolates.R
2018-03-29 15:15:31 +02:00
MS Berends
f1dbed6fcc
Update clipboard.R
2018-03-29 14:56:40 +02:00
MS Berends
136272cb71
Update clipboard.R
2018-03-29 14:16:42 +02:00
MS Berends
fd04df5f9d
Update clipboard.R
2018-03-29 13:23:02 +02:00
MS Berends
2f4823f7a7
Update clipboard.R
2018-03-29 13:10:55 +02:00
6f7730dcaa
add tests using testthat
2018-03-27 17:43:42 +02:00
MS Berends
9637b43357
Remove Windows only function
2018-03-23 14:59:02 +01:00
MS Berends
1b3daebc84
Remove Windows only function
2018-03-23 14:52:56 +01:00
53464ff1c8
- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive
...
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
2018-03-23 14:46:02 +01:00
fe803f7279
use guess_bactid for GLIMS codes
2018-03-19 21:23:21 +01:00
c765f424ab
typo
2018-03-19 21:03:23 +01:00
dd2517ecb7
- Added new algorithm to determine weighted isolates, can now be points or keyantibiotics, see ?first_isolate`
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- Function `first_isolate` supports tidyverse-like evaluation of parameters (no need to quote them anymore)
- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
2018-03-19 20:39:23 +01:00
502a44eb25
- Added new function guess_bactid to determine the ID of a microorganism based on genus/species
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- Renamed `ablist` to `antibiotics`
- Added support for character vector in join functions
- Altered `%like%` to make it case insensitive
2018-03-19 12:43:22 +01:00
6c67c8f6c1
examples edit
2018-03-14 09:58:58 +01:00
46db3f7b13
import from graphics
2018-03-13 15:40:10 +01:00
53959d40c7
typo in examples
2018-03-13 14:40:52 +01:00
04fc3573ec
add barplots
2018-03-13 14:34:10 +01:00
e4b371d30a
add MIC values
...
add badges to readme
2018-03-13 11:57:30 +01:00
4ea0333349
Minor text changes for DDD definition
2018-03-13 11:48:30 +01:00
34e70a65ed
added septic_patients
2018-02-27 20:01:02 +01:00
8a603876d2
misc
2018-02-26 15:53:09 +01:00
915d4db23b
add rows to summary
2018-02-26 14:37:40 +01:00
6fa05fe33b
first isolates
2018-02-26 14:06:31 +01:00
d36a391747
export first_isolate
2018-02-26 12:15:52 +01:00
be51a95448
rename columns
2018-02-26 10:53:54 +01:00
11683b082e
EUCAST man pages
2018-02-22 21:42:01 +01:00
10380bcfae
add NEWS
2018-02-22 21:37:10 +01:00
d8da8daf9a
First CRAN submission edits
2018-02-22 20:48:48 +01:00
ab0503f8b8
abname, logo
2018-02-21 12:10:00 +01:00
62304dc23f
first commit
2018-02-21 11:52:31 +01:00
