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Commit Graph

422 Commits

Author SHA1 Message Date
95050ee3e0 (v1.7.1.9007) Updated antibiotics dataset, fixes #41 2021-06-23 10:03:17 +02:00
1dc9d237f6 (v1.7.1.9006) unit tests 2021-06-22 13:09:41 +02:00
d04e83f494 (v1.7.1.9005) ab class selectors for R-3.0 and R-3.1 2021-06-22 12:16:42 +02:00
c44d9392ca (v1.7.1.9004) more extensive unit tests 2021-06-15 10:51:04 +02:00
556bf0014d (v1.7.1.9003) unit test 2021-06-14 22:37:05 +02:00
99be4c7e7e (v1.7.1.9002) ab class selectors update 2021-06-14 22:04:04 +02:00
683a0e748a (v1.7.1.9001) unit tests 2021-06-05 15:12:01 +02:00
1908e7cc7a (v1.7.1.9000) ab_class update, unit tests 2021-06-04 21:07:55 +02:00
7e70403efb (v1.7.1) New CRAN release 2021-06-03 15:19:21 +02:00
279376fccb (v1.7.0.9002) old MO codes 2021-06-01 16:36:33 +02:00
bef0f42f66 (v1.7.0.9001) CLSI 2020 guideline 2021-06-01 15:33:06 +02:00
f406319503 (v1.7.0.9000) package size 2021-05-30 22:14:38 +02:00
f1d9b489c5 (v1.7.0) unit tests 2021-05-26 14:04:12 +02:00
41d279daa1 (v1.7.0) v1.7.0 2021-05-26 11:10:34 +02:00
ac73a8d849 v1.7.0 2021-05-24 15:29:17 +02:00
e5599bc694 (v1.6.0.9065) unit tests 2021-05-24 11:01:32 +02:00
4fbf9e1720 (v1.6.0.9064) prepare new release 2021-05-24 09:34:08 +02:00
a13fd98e8b (v1.6.0.9063) prepare new release 2021-05-24 09:00:11 +02:00
06302d296a (v1.6.0.9062) code consistency 2021-05-24 00:06:28 +02:00
07939b1a14 (v1.6.0.9061) age() update 2021-05-23 23:11:16 +02:00
fa2f5214b9 (v1.6.0.9060) unit tests 2021-05-22 10:05:59 +02:00
0b1f59edec (v1.6.0.9058) unit tests 2021-05-22 08:58:51 +02:00
65a8b58aa6 (v1.6.0.9056) support codecov again 2021-05-21 20:30:48 +02:00
b210f1327c (v1.6.0.9055) support codecov again 2021-05-21 20:20:51 +02:00
fecc5d183c (v1.6.0.9054) unit tests 2021-05-20 15:06:08 +02:00
69a656abc0 (v1.6.0.9053) unit tests 2021-05-20 13:42:17 +02:00
4a2a48b7c1 (v1.6.0.9052) unit tests 2021-05-20 11:42:39 +02:00
04ef5b28e7 (v1.6.0.9050) printing NA in custom_eucast_rules() 2021-05-20 10:10:40 +02:00
9a2879cba9 (v1.6.0.9049) unit tests 2021-05-20 00:07:27 +02:00
2413efd5c1 (v1.6.0.9048) ab selectors overhaul 2021-05-19 22:55:42 +02:00
6920c0be41 (v1.6.0.9047) filter_ab_class() fixes 2021-05-18 11:29:31 +02:00
d67371acd1 that 1 AM error 2021-05-18 00:58:39 +02:00
cfb7df823e (v1.6.0.9044) betalactams() selector 2021-05-18 00:53:04 +02:00
be49131ed7 (v1.6.0.9043) translation update 2021-05-17 19:43:01 +02:00
83fec69a03 (v1.6.0.9042) translation update 2021-05-17 11:26:12 +02:00
916df6e90c (v1.6.0.9041) filter_ab_class() fix 2021-05-16 10:50:00 +02:00
00496e45b7 (v1.6.0.9040) unit tests 2021-05-16 09:25:36 +02:00
6c3ab19e3a (v1.6.0.9038) unit tests 2021-05-15 23:47:36 +02:00
3619c1327c (v1.6.0.9037) unit tests 2021-05-15 23:36:02 +02:00
73fb0374c3 (v1.6.0.9036) unit tests 2021-05-15 23:25:10 +02:00
229e1bb407 (v1.6.0.9035) unit tests 2021-05-15 22:55:12 +02:00
6e60ddf8d7 (v1.6.0.9034) unit tests 2021-05-15 22:35:57 +02:00
86736ab9a7 (v1.6.0.9032) unit tests 2021-05-15 21:54:56 +02:00
d8c91d5876 (v1.6.0.9031) tinytest unit tests 2021-05-15 21:36:22 +02:00
9a381c8d18 (v1.6.0.9030) new unit test flow 2021-05-13 23:07:31 +02:00
9ed2f6490f (v1.6.0.9028) new unit test flow 2021-05-13 22:44:11 +02:00
5b9fb8daf4 (v1.6.0.9027) new unit test flow 2021-05-13 21:54:15 +02:00
b1d942be91 (v1.6.0.9026) new unit test flow 2021-05-13 21:16:22 +02:00
aeea00881e (v1.6.0.9023) new unit test flow 2021-05-13 19:31:47 +02:00
655b813e99 (v1.6.0.9022) unit test fix 2021-05-13 15:56:12 +02:00
29dbfa2f49 (v1.6.0.9021) join functions update 2021-05-12 18:15:03 +02:00
3319fbae58 (v1.6.0.9020) fix for skimr in dplyr 1.0.6 2021-05-06 15:17:11 +02:00
5899678b74 (v1.6.0.9019) website fix 2021-05-05 15:47:39 +02:00
0aca719929 (v1.6.0.9018) unit tests 2021-05-04 15:20:43 +02:00
5679ccdaf9 (v1.6.0.9017) extra system codes 2021-05-04 12:47:33 +02:00
f33e61bac7 (v1.6.0.9016) website update and c() fixes 2021-05-03 13:06:43 +02:00
12a8d59869 (v1.6.0.9015) italicise_taxonomy 2021-05-03 10:47:32 +02:00
e405de079c (v1.6.0.9014) as.rsi() for numeric values 2021-04-30 13:18:48 +02:00
a9fd4aa49f (v1.6.0.9013) website update 2021-04-29 17:16:30 +02:00
5e06b20d43 (v1.6.0.9012) unit tests 2021-04-27 11:28:17 +02:00
c5fff1c95c (v1.6.0.9011) unit tests 2021-04-27 10:27:13 +02:00
93683a4ae2 (v1.6.0.9010) big first_isolate() update 2021-04-26 23:57:37 +02:00
5f9e7bd3ee (v1.6.0.9009) key_antibiotics update 2021-04-23 16:13:26 +02:00
70b803dbb6 (v1.6.0.9008) unlike, bugfix for col_mo naming 2021-04-23 09:59:36 +02:00
c6289c3fc3 (v1.6.0.9007) documentation custom eucast rules, progress bar as.mo 2021-04-20 10:46:17 +02:00
de66eccf43 (v1.6.0.9006) eucast rules fix for Ochrobactrum anthropi 2021-04-16 14:59:57 +02:00
24ac18a99d (v1.6.0.9005) unit test fix 2021-04-16 13:24:59 +02:00
9842ef9660 (v1.6.0.9004) unit test fix 2021-04-16 12:02:57 +02:00
00d3e437a8 (v1.6.0.9003) like() fix 2021-04-16 11:41:05 +02:00
d277d58475 (v1.6.0.9002) R-3.0 installation fix 2021-04-12 14:24:40 +02:00
6ff5448192 (v1.6.0.9001) support Inf for episodes 2021-04-12 12:35:13 +02:00
7a3139f7cc (v1.6.0.9000) custom EUCAST rules 2021-04-07 08:37:42 +02:00
551f99dc8f v1.6.0 2021-03-15 07:23:21 +01:00
4e0a9533ad (v1.5.0.9041) SNOMED update 2021-03-11 21:42:30 +01:00
8d6ceb6a15 (v1.5.0.9040) removal of isolate_identifier 2021-03-08 09:44:17 +01:00
a7c9b4c295 (v1.5.0.9039) handle first isolates for missing antibiograms 2021-03-08 02:38:32 +01:00
450bbe5fb7 (v1.5.0.9034) unit test fix 2021-03-07 21:16:45 +01:00
1bbf409fe5 (v1.5.0.9033) as.rsi fix 2021-03-07 16:15:43 +01:00
850c123de7 (v1.5.0.9032) All group generics for MICs 2021-03-07 13:52:39 +01:00
91dd755cac (v1.5.0.9031) math processing of MICs 2021-03-05 15:36:39 +01:00
0d29bde693 (v1.5.0.9030) as.ab() speed improvement 2021-03-05 10:32:09 +01:00
0e0e3c4ffa (v1.5.0.9029) added missing families and orders 2021-03-05 01:31:46 +01:00
ddf88345f1 (v1.5.0.9028) Updated taxonomy until March 2021 2021-03-04 23:28:32 +01:00
41f94cde97 (v1.5.0.9027) website update 2021-02-26 12:11:29 +01:00
1737d56ae4 (v1.5.0.9026) vignette update, support for GISA 2021-02-25 12:31:12 +01:00
a673407904 (v1.5.0.9025) big plot and ggplot generics update 2021-02-25 10:33:08 +01:00
31ceba5441 (v1.5.0.9024) more speed improvements 2021-02-22 20:21:33 +01:00
0fdabff1ba (v1.5.0.9023) mo properties speed improvement 2021-02-21 23:19:40 +01:00
062c49fca1 (v1.5.0.9022) mo properties speed improvement 2021-02-21 22:56:35 +01:00
5ef8cb41a7 (v1.5.0.9021) improve speed of %like% 2021-02-21 20:15:09 +01:00
daa12ced2c (v1.5.0.9020) translation fix 2021-02-18 23:23:14 +01:00
601ea7377c (v1.5.0.9019) use functions without loading AMR pkg 2021-02-17 10:58:13 +01:00
2dd0656355 (v1.5.0.9018) fix unit tests 2021-02-09 12:28:15 +01:00
cb404492b2 (v1.5.0.9017) unit testing 2021-02-08 21:09:36 +01:00
4a84894f79 (v1.5.0.9016) only_rsi_columns update, documentation 2021-02-08 14:18:42 +01:00
8fda473e49 (v1.5.0.9015) unit test fix, grouped first isolates 2021-02-04 16:48:16 +01:00
2eca8c3f01 (v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement 2021-02-02 23:57:35 +01:00
20d638c193 (v1.5.0.9013) updated tibble printing colours 2021-01-28 16:09:30 +01:00
331c1f6508 (v1.5.0.9012) ampc_cephalosporin_resistance for I 2021-01-25 21:58:00 +01:00
24eb4453db (v1.5.0.9011) small dosage update 2021-01-24 23:27:11 +01:00
286eaa9699 (v1.5.0.9010) MDRO vignette update, get_episode for < day 2021-01-24 14:48:56 +01:00
1a88caa119 (v1.5.0.9009) unit test fixes 2021-01-22 10:55:07 +01:00
1ba44776a1 (v1.5.0.9008) Internal data sets to pkg, speed for auto col determination 2021-01-22 10:20:41 +01:00
27f084d819 (v1.5.0.9007) updated unit tests 2021-01-18 18:45:43 +01:00
4eab095306 (v1.5.0.9006) major documentation update 2021-01-18 16:57:56 +01:00
e95218c0d1 (v1.5.0.9005) custom MDRO guideline 2021-01-17 10:35:21 +01:00
e699de955c (v1.5.0.9004) custom MDRO guideline 2021-01-17 00:26:48 +01:00
7ebc534ccd (v1.5.0.9003) verbose output of mdro() 2021-01-15 22:44:52 +01:00
6745f3fb17 (v1.5.0.9002) doc update 2021-01-14 15:51:41 +01:00
bc00470dca (v1.5.0.9001) more informative argument errors 2021-01-14 14:41:44 +01:00
d014955ce0 (v.1.5.0.9000) implementation of EUCAST rules v11 (2021) 2021-01-12 22:08:04 +01:00
3b84b8be75 v1.5.0 2021-01-06 11:16:17 +01:00
1563dcd1aa (v1.4.0.9062) unit test fix 2021-01-04 14:46:17 +01:00
a7ea4c9d2f (v1.4.0.9061) ab class selector fix 2021-01-04 14:16:09 +01:00
8d117820b8 (v1.4.0.9060) ab class selector fix 2021-01-04 13:39:06 +01:00
c9de74c81a (v1.4.0.9059) ab class selector fix 2021-01-04 12:29:25 +01:00
82cfa24ea4 (v1.4.0.9058) GH actions update 2021-01-04 11:27:37 +01:00
daac96fefe (v1.4.0.9057) GH actions update 2021-01-04 09:49:42 +01:00
63a4dda467 (v1.4.0.9056) subsetting ab class selectors for base R 2021-01-03 23:40:05 +01:00
ecac443f86 (v1.4.0.9055) more unit tests 2020-12-31 13:44:58 +01:00
10dec96058 (v1.4.0.9054) unit test update 2020-12-29 22:06:01 +01:00
d3f007bf65 (v1.4.0.9053) unit test old R versions 2020-12-29 21:23:01 +01:00
526f8afb08 (v1.4.0.9052) replaced all sapply's with type-safe vapply's 2020-12-28 22:24:33 +01:00
ed198916bf (v1.4.0.9048) AmpC de-repressed cephalo-resistant mutants 2020-12-27 14:23:11 +01:00
8b52f9b1be (v1.4.0.9047) unit tests 2020-12-27 00:30:28 +01:00
df37584189 (v1.4.0.9044) mo tibble printing, mo_shortname() fix 2020-12-24 23:29:10 +01:00
81af41da3a (v1.4.0.9041) updates based on review 2020-12-17 16:22:25 +01:00
28e77680c5 (v1.4.0) matching score update 2020-10-08 11:16:03 +02:00
4e0374af29 (v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup 2020-09-29 23:35:46 +02:00
9667c2994f (v1.3.0.9029) eucast rules fix, unique() 2020-09-25 14:44:50 +02:00
c19095a3d5 (v1.3.0.9026) eucast expert rules 3.2 2020-09-24 00:30:11 +02:00
2f0186ace2 (v1.3.0.9024) optimalisation 2020-09-19 12:57:51 +02:00
d049cce69b (v1.3.0.9023) optimalisation 2020-09-19 11:54:01 +02:00
4e40e42011 (v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix 2020-09-18 16:05:53 +02:00
354c606d6a (v1.3.0.9019) small fix 2020-09-14 14:08:07 +02:00
7b6dd676f7 (v1.3.0.9018) language corrections 2020-09-14 12:21:23 +02:00
0f6760d427 (v1.3.0.9017) small fix 2020-09-12 13:54:21 +02:00
3ff871afeb (v1.3.0.9016) mo_uncertainties() overhaul 2020-09-12 08:49:01 +02:00
68e9cb78e9 (v1.3.0.9015) as.mo() speedup for valid taxonomic names 2020-09-03 20:59:21 +02:00
c4b87fe241 (v1.3.0.9014) as.mo() speed improvement 2020-09-03 12:31:48 +02:00
18e52f2725 (v1.3.0.9013) data sets vignette update 2020-08-29 21:52:51 +02:00
4f72b3bfc4 (v1.3.0.9012) data sets vignette update 2020-08-29 21:41:46 +02:00
50b953b141 (v1.3.0.9011) suggests pkg update 2020-08-29 12:04:23 +02:00
74a172ef55 (v1.3.0.9010) S3 extensions without dependencies 2020-08-28 21:55:47 +02:00
81af0b001c (v1.3.0.9009) documentation update 2020-08-26 16:13:40 +02:00
9b8db57c65 (v1.3.0.9008) also tibble printing for ab 2020-08-26 15:34:12 +02:00
5e45fdcf2a (v1.3.0.9007) tibble printing 2020-08-26 11:33:54 +02:00
c8c8bb4e3a (v1.3.0.9006) website update 2020-08-21 11:40:13 +02:00
818d0441e0 (v1.3.0.9005) website update 2020-08-17 21:49:58 +02:00
dab017a50f (v1.3.0.9004) data sets, as.disk() improvement 2020-08-16 21:38:42 +02:00
08d62bb5d5 (v1.3.0.9002) intrinsic_resistant data set 2020-08-14 13:36:10 +02:00
c8edcb7439 (v1.3.0) small fixes 2020-07-30 15:15:52 +02:00
453f7f210b (v1.2.0.9038) CLSI 2019 fix 2020-07-29 10:33:47 +02:00
1b65d76cfb (v1.2.0.9037) survey on website 2020-07-28 18:39:57 +02:00
09fba38ea6 (v1.2.0.9035) as.mo() speed improvement 2020-07-22 10:24:23 +02:00
1d66b5c43c (v1.2.0.9032) Permanently move to GitHub 2020-07-09 20:07:39 +02:00
76fc8e1b14 (v1.2.0.9026) move to github 2020-07-08 14:48:06 +02:00
344bbd57f4 (v1.2.0.9014) ab_from_text() 2020-06-25 17:34:50 +02:00
352508889c (v1.2.0.9005) data set fix 2020-06-09 16:31:44 +02:00
8b692ecfcf (v1.2.0.9004) rsi_df() fix for groups 2020-06-09 16:18:03 +02:00
40221e5244 (v1.2.0.9003) better terminal colour support 2020-06-05 13:56:05 +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
1b1e243d14 (v1.1.0.9016) small fix 2020-05-21 12:28:57 +02:00
19703eb5d3 (v1.1.0.9012) lose dependencies 2020-05-19 12:08:49 +02:00
7f3da74b17 (v1.1.0.9004) lose dependencies 2020-05-16 13:05:47 +02:00
4be54d608c (v1.0.1.9008) RIVM abbreviations for drugs 2020-04-14 20:38:09 +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
fa0d9c58d9 (v1.0.1.9000) first PCA implementation 2020-03-07 21:48:21 +01:00
47fe8b7820 (v1.0.0.9004) add example_isolaten_unclean 2020-02-21 16:05:19 +01:00
c6184a0fb8 (v0.9.0.9029) add uti to as.rsi() 2020-02-20 13:19:23 +01:00
5e2b294351 (v0.9.0.9026) update documentation 2020-02-17 14:38:01 +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
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
a13c62e6e8 (v0.9.0.9016) Support SNOMED codes 2020-01-27 19:14:23 +01:00
42b079cdb7 (v0.9.0.9015) Fix for as.rsi.disk() 2020-01-27 11:37:00 +01:00
9a3891efe4 (v0.9.0.9014) Machine reading guidelines 2020-01-27 11:05:39 +01:00
449d9bde35 (v0.9.0.9012) Support for LOINC codes 2020-01-26 20:20:00 +01:00
895e97c310 (v0.9.0.9010) Support R 4.0 2020-01-15 15:24:08 +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
cc8cd043e1 (v0.9.0.9004) website fix 2019-12-20 21:06:39 +01:00
2db2a2458a (v0.9.0.9003) as.mo() speedup for fullnames 2019-12-20 15:05:58 +01:00
f7eb6e4107 (v0.9.0.9002) website updates 2019-12-16 11:08:25 +01:00
c5f00f4a9f (v0.8.0.9036) complete documentation rewrite 2019-11-28 22:32:17 +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
09e2730b53 (v0.8.0.9031) as.mo() improvements 2019-11-15 15:25:03 +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
d2e8249edd (v0.8.0.9004) added MDR guideline by Magiorakos et al. 2019-10-26 21:56:41 +02:00
3e5ab53209 (v0.8.0.9002) eucast_rules() fix for S. maltophilia 2019-10-23 14:48:25 +02:00
59af355a89 (v0.7.1.9101) NEWS update, fix authors 2019-10-09 10:52:19 +02:00
c8f6b97847 (v0.7.1.9100) bug_drug speed, MIC levels 2019-10-08 22:21:33 +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
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
7108454ba5 (v0.7.1.9055) algorithm improvements 2019-08-13 16:15:08 +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
22a206ffd8 (v0.7.1.9030) eucast_rules() fix 2019-08-08 15:52:07 +02:00
3a1f960f89 (v0.7.1.9024) eucast_rules() fix, new MOs 2019-08-06 14:39:22 +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
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
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
f02679fb63 (v0.7.0.9001) new pathovars, small fixes 2019-06-07 22:47:37 +02:00
2667fff8a7 (v0.6.1.9050) support staged install 2019-06-01 20:40:49 +02:00