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Commit Graph

1031 Commits

Author SHA1 Message Date
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
2667fff8a7 (v0.6.1.9050) support staged install 2019-06-01 20:40:49 +02:00
4ed27c7e7a (v0.6.1.9046) ggplot fix 2019-05-31 20:25:57 +02:00
493ae2ba0c (v0.6.1.9044) first_isolate fix for species 2019-05-31 14:25:11 +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
60983a1640 added mdr_tb() 2019-05-23 16:58:59 +02:00
f6bf54b37d documentation fix 2019-05-13 20:16:51 +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
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
13f85ac80f small news update 2019-04-07 09:31:11 +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
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
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
e835525cf6 unknown codes, rsi fix 2019-03-02 22:47:04 +01:00
2565b60024 rlang dependency, new fungi 2019-02-28 13:56:28 +01:00
f9ded23023 as.mo improvement 2019-02-26 12:33:26 +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
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
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
0b3dc0231f freq fix 2019-01-30 16:00:55 +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
18b75356a9 re-add atc_ddd and atc_groups 2019-01-27 13:33:43 +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
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
046d195064 resistance predict 2019-01-15 12:45:24 +01:00
3661df7365 direct warning if failing as.mo 2019-01-12 16:45:20 +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
0205b6178d guess_mo deprecation 2019-01-06 16:40:55 +01:00
2c798547bf language 2019-01-05 21:40:04 +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
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
2018d5b477 age and age_groups 2018-12-15 22:40:07 +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
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
5cfa5bbfe3 v0.5.0 2018-11-30 16:16:04 +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
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
d0bc05e5b1 speed improvement is.rsi.eligible 2018-11-02 14:55:29 +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
87757748bd switch to gitlab 2018-10-23 16:49:40 +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
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
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
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
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
768fe17324 removed clipboard functions as it violated CRAN policies 2018-09-28 16:05:18 +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
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
26f5be0033 support for portuguese, language determination based on system 2018-09-08 16:06:47 +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
5405002119 news update 2018-09-03 11:22:28 +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
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
8ab93b6688 unit tests 2018-08-23 01:01:50 +02:00
da5379c881 quasiquotation, alpha for geom_rsi 2018-08-23 00:40:36 +02:00
Christian Luz
87d08905cc
small change in mutate example 2018-08-22 12:55:05 +02:00
3e87c8f409 count_* functions 2018-08-22 00:02:26 +02:00
bc7e36b533 v0.3.0 2018-08-14 14:06:18 +02:00
7584c929a5 new AppVeyor environment 2018-08-14 08:57:17 +02:00
e5193c7749 AppVeyor 2018-08-13 23:05:53 +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
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
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
7c667eb732 emph guess_bactid 2018-08-01 08:03:31 +02:00
837dae925d travis update 2018-07-30 01:21:37 +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
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
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
8421638b60 new class bactid 2018-07-23 14:14:03 +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
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
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
3527894b49 new g.test() and edited freq() 2018-07-01 21:40:37 +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
uscloud
dcc26dd942 Update freq function 2018-05-22 16:34:22 +02:00
95f7c78fd6 edit vignette title 2018-05-14 11:54:08 +02:00
f05e7178cb added vignette of freq 2018-05-09 11:44:46 +02:00
c0fc82c794 Added function n_rsi 2018-05-02 14:56:25 +02:00
19ccc51f40 remove clipboard functions 2018-05-01 09:36:45 +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
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