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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 07:26:12 +01:00
Commit Graph

428 Commits

Author SHA1 Message Date
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
f67c739892 (v0.7.1.9029) unit test 2019-08-07 18:56:14 +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
14c47da656 (v0.7.1.9026) NAMESPACE fix 2019-08-06 15:57:51 +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
643c5ed807 (v0.7.1.9022) CI fix for codecov 2019-08-04 11:33:56 +02:00
d6ab3896a1 (v0.7.1.9021) CI fix for resistance_predict 2019-08-04 10:48:41 +02:00
4f3ef53c78 (v0.7.1.9020) CI fix 2 2019-08-03 21:51:08 +02:00
a6606d334c (v0.7.1.9019) CI fix 2019-07-30 19:20:13 +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
d9e257f8db (v0.7.1.9008) ab update 2019-07-04 19:08:18 +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
6013fbefae (v0.7.1.9003) website update 2019-06-23 21:35:17 +02:00
f2d7a19118 (v0.7.1.9002) website update 2019-06-23 17:44:36 +02:00
78ec32b990 v0.7.1 2019-06-23 17:41:31 +02:00
278244140c (v0.7.0.9015) vignette fix 2019-06-22 21:33:13 +02:00
b94638d53e (v0.7.0.9014) unit tests 2019-06-22 20:14:06 +02:00
c9156c004a (v0.7.0.9013) mo_synonym fix 2019-06-22 14:49:12 +02:00
409397a337 (v0.7.0.9012) unit test 2019-06-18 19:28:26 +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
f6c47c8c88 (v0.7.0.9004) pkgdown update 2019-06-09 08:57:54 +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
04c75e8e36 (v0.7.0.9000) new dev version 2019-06-03 20:52:24 +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
8de0495008 (v0.6.1.9052) website update 2019-06-01 21:28:18 +02:00
5608b27c7c (v0.6.1.9051) support staged install 2019-06-01 20:54:56 +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
4bac768557 (v0.6.1.9048) data creation fox 2019-05-31 21:01:14 +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
27380fa021 fixes for microorganisms.codes 2019-05-28 16:50:40 +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
c3ae6b7699 freq fix 2019-05-17 09:09:18 +02:00
4c3cf85a65 ab_info, other bug fixes 2019-05-16 21:20:00 +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
cffb7787d8 cfta streptococci 2019-04-09 10:34:40 +02:00
9e20ade0a7 ci update 2019-04-06 20:03:46 +02:00
c6bf982ba6 ci update 2019-04-06 16:50:59 +02:00
0ff299394a an another go 2019-04-06 16:23:43 +02:00
501f5db020 prevent staged install 2019-04-06 11:09:06 +02:00
fbc9191b13 new EUCAST rules algorithm 2019-04-05 18:47:39 +02:00
248e508e9b CI - test also on r-devel 2019-03-29 14:34:39 +01:00
b25f2d6213 v0.6.1 2019-03-28 21:33:28 +01:00
429814c29b v0.6.0 2019-03-27 11:22:36 +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
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
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
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
13120f465f website update 2019-02-20 13:57:23 +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
9209787a53 SPSS tutorial 2019-02-14 15:18:17 +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
70105086c8 as.rsi warning, site update 2019-02-10 08:42:28 +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
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
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
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
c6c3088e9f select() fix for freq 2019-01-17 12:08:04 +01:00
046d195064 resistance predict 2019-01-15 12:45:24 +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
f01d62ee5d language 2019-01-05 21:51:48 +01:00
6b2d464f8c big website update, licence txt update 2019-01-02 23:24:07 +01:00
2e4d703338 eucast rules fix, 1st isolate fix, website update 2018-12-31 01:48:53 +01:00
469b145d8c bye bye packrat 2018-12-30 12:00:53 +01:00
92a32b62a7 new website, freq updates 2018-12-29 22:24:19 +01:00
92d2553dfe gitlab pages 2018-12-23 21:26:21 +01:00
0b8084871d dplyr 0.8.0 support, fixes #7 2018-12-22 22:39:34 +01:00
2018d5b477 age and age_groups 2018-12-15 22:40:07 +01:00
81af7be36e note about portions 2018-12-14 07:23:25 +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
5cfa5bbfe3 v0.5.0 2018-11-30 16:16:04 +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
a8132922af unit test read.4d, unselecting freq cols 2018-11-19 13:00:22 +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
d07e9b904e new function get_locale 2018-11-05 13:20:32 +01:00
5476fecc73 eucast update 2018-11-01 20:23:33 +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
87757748bd switch to gitlab 2018-10-23 16:49:40 +02:00
299c5bea43 na freq, removed factors 2018-10-23 09:42:26 +02:00
c2a93b46db breaks param, tidyr dep change, freq markdown 2018-10-22 12:32:59 +02:00
86b03577a7 fix for as.mo, added also_single_tested 2018-10-19 13:53:31 +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
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
c7c57f4042 0.4.0, just published on CRAN 2018-10-01 19:36:42 +02:00
3119a221e5 authors from ITIS, diff for freq 2018-10-01 11:39:43 +02:00