622 Commits

Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	47fe8b7820	(v1.0.0.9004) add example_isolaten_unclean	2020-02-21 16:05:19 +01:00
dr. M.S. (Matthijs) Berends	bb3728f023	(v1.0.0.9003) prepare for short update	2020-02-21 13:13:34 +01:00
dr. M.S. (Matthijs) Berends	bdb26f624f	(v1.0.0.9001) add uti to as.rsi()	2020-02-20 17:21:01 +01:00
dr. M.S. (Matthijs) Berends	c6184a0fb8	(v0.9.0.9029) add uti to as.rsi()	2020-02-20 13:19:23 +01:00
dr. M.S. (Matthijs) Berends	c8981a563e	(v0.9.0.9027) documentation fix	2020-02-17 15:07:25 +01:00
dr. M.S. (Matthijs) Berends	5e2b294351	(v0.9.0.9026) update documentation	2020-02-17 14:38:01 +01:00
dr. M.S. (Matthijs) Berends	11f00f8a0a	(v0.9.0.9025) update as.rsi documentation	2020-02-16 22:43:56 +01:00
dr. M.S. (Matthijs) Berends	c7a93af3d0	(v0.9.0.9024) global vars fix	2020-02-14 20:03:43 +01:00
dr. M.S. (Matthijs) Berends	9b8b02960e	(v0.9.0.9023) EUCAST 2020 guidelines	2020-02-14 19:54:13 +01:00
dr. M.S. (Matthijs) Berends	c7a76ba713	(v0.9.0.9020) as.mo() improvement	2020-02-09 22:04:29 +01:00
dr. M.S. (Matthijs) Berends	4e1c16c5a5	(v0.9.0.9019) website update	2020-02-01 15:09:36 +01:00
dr. M.S. (Matthijs) Berends	f152ab9a48	(v0.9.0.9018) Remove mo_history	2020-01-31 23:27:38 +01:00
dr. M.S. (Matthijs) Berends	1b80773c22	(v0.9.0.9017) documentation fix	2020-01-27 19:30:26 +01:00
dr. M.S. (Matthijs) Berends	a13c62e6e8	(v0.9.0.9016) Support SNOMED codes	2020-01-27 19:14:23 +01:00
dr. M.S. (Matthijs) Berends	9a3891efe4	(v0.9.0.9014) Machine reading guidelines	2020-01-27 11:05:39 +01:00
dr. M.S. (Matthijs) Berends	423d1d3c41	(v0.9.0.9013) Support for LOINC codes	2020-01-26 20:38:54 +01:00
dr. M.S. (Matthijs) Berends	449d9bde35	(v0.9.0.9012) Support for LOINC codes	2020-01-26 20:20:00 +01:00
dr. M.S. (Matthijs) Berends	64f5ceef03	(v0.9.0.9009) antibiotics data set update	2020-01-08 11:30:33 +01:00
dr. M.S. (Matthijs) Berends	ced1a7b7fa	(v0.9.0.9008) Happy new year! Add lifecycles	2020-01-05 17:22:09 +01:00
dr. M.S. (Matthijs) Berends	ba3ce77f02	(v0.9.0.9005) as.mo for G. species	2019-12-21 10:56:06 +01:00
dr. M.S. (Matthijs) Berends	56ce9bf665	(v0.9.0) website fixes	2019-11-30 12:01:50 +01:00
dr. M.S. (Matthijs) Berends	bb2ed55842	(v0.9.0) v0.9.0	2019-11-29 19:43:23 +01:00
dr. M.S. (Matthijs) Berends	9feef53bde	(v0.8.0.9037) complete documentation rewrite	2019-11-28 23:00:37 +01:00
dr. M.S. (Matthijs) Berends	c5f00f4a9f	(v0.8.0.9036) complete documentation rewrite	2019-11-28 22:32:17 +01:00
dr. M.S. (Matthijs) Berends	7c28b392b1	(v0.8.0.9035) add more mo codes	2019-11-24 22:48:56 +01:00
dr. M.S. (Matthijs) Berends	e53cc4990c	(v0.8.0.9034) add cid to antivirals	2019-11-23 12:39:57 +01:00
dr. M.S. (Matthijs) Berends	267320f15f	(v0.8.0.9033) antivirals data set, cleanup	2019-11-18 12:10:47 +01:00
dr. M.S. (Matthijs) Berends	09e2730b53	(v0.8.0.9031) as.mo() improvements	2019-11-15 15:25:03 +01:00
dr. M.S. (Matthijs) Berends	248b45da71	(v0.8.0.9030) depend on tidyr >= 1.0.0	2019-11-11 10:46:39 +01:00
dr. M.S. (Matthijs) Berends	d22834c5b8	(v0.8.0.9029) cleanup	2019-11-10 15:50:18 +01:00
dr. M.S. (Matthijs) Berends	54b6322056	(v0.8.0.9028) examples fix	2019-11-10 13:17:20 +01:00
dr. M.S. (Matthijs) Berends	59ededa8dc	(v0.8.0.9027) adding susceptibility() and resistance()	2019-11-10 12:16:56 +01:00
dr. M.S. (Matthijs) Berends	e2d05cb1b0	(v0.8.0.9017) keywords update	2019-11-06 14:43:23 +01:00
dr. M.S. (Matthijs) Berends	2560aa1a53	(v0.8.0.9013) unit test update	2019-11-05 21:52:58 +01:00
dr. M.S. (Matthijs) Berends	0bb531f3e0	(v0.8.0.9009) unit test	2019-11-03 22:41:29 +01:00
dr. M.S. (Matthijs) Berends	29e448883d	(v0.8.0.9008) new verbose mode for MDROs	2019-11-03 22:24:42 +01:00
dr. M.S. (Matthijs) Berends	09c4b04cd0	(v0.8.0.9007) Enterobacterales order	2019-10-30 23:02:50 +01:00
dr. M.S. (Matthijs) Berends	7ff2ad8188	(v0.8.0.9006) small typos	2019-10-27 00:31:59 +02:00
dr. M.S. (Matthijs) Berends	d2e8249edd	(v0.8.0.9004) added MDR guideline by Magiorakos et al.	2019-10-26 21:56:41 +02:00
dr. M.S. (Matthijs) Berends	00cdb498a0	(v0.7.1.9102) lintr	2019-10-11 17:21:02 +02:00
dr. M.S. (Matthijs) Berends	c8f6b97847	(v0.7.1.9100) bug_drug speed, MIC levels	2019-10-08 22:21:33 +02:00
dr. M.S. (Matthijs) Berends	f479dfce60	(v0.7.1.9097) mdro() examples fix	2019-10-07 14:57:27 +02:00
dr. M.S. (Matthijs) Berends	4e9c4c1b4e	(v0.7.1.9096) German guideline for mdro()	2019-10-07 14:32:06 +02:00
dr. M.S. (Matthijs) Berends	8bc4081b03	(v0.7.1.9092) as.ab() improvements	2019-10-04 15:36:12 +02:00
dr. M.S. (Matthijs) Berends	edb599ae0b	(v0.7.1.9091) percentage from clean pkg	2019-09-30 16:45:36 +02:00
dr. M.S. (Matthijs) Berends	99d0fe76dd	(v0.7.1.9088) bug_drug improvement	2019-09-25 15:43:22 +02:00
dr. M.S. (Matthijs) Berends	a8c6b8f9c4	(v0.7.1.9082) CI fix	2019-09-23 14:37:24 +02:00
dr. M.S. (Matthijs) Berends	64d9829030	(v0.7.1.9081) bug_drug fixes	2019-09-23 13:53:50 +02:00
dr. M.S. (Matthijs) Berends	66d405ff57	(v0.7.1.9080) new LIS codes	2019-09-22 17:19:59 +02:00
dr. M.S. (Matthijs) Berends	40e6b3e8f6	(v0.7.1.9077) mo codes fix	2019-09-20 14:18:29 +02:00
dr. M.S. (Matthijs) Berends	3596adb295	(v0.7.1.9076) mo codes	2019-09-20 12:33:05 +02:00
dr. M.S. (Matthijs) Berends	e2aa4f996b	(v0.7.1.9075) new microorganism codes	2019-09-18 15:46:09 +02:00
dr. M.S. (Matthijs) Berends	398c5bdc4f	(v0.7.1.9073) as.mo() self-learning algorithm	2019-09-15 22:57:30 +02:00
dr. M.S. (Matthijs) Berends	cd178ee569	(v0.7.1.9072) key_antibiotics() for foreign systems	2019-09-12 15:08:53 +02:00
dr. M.S. (Matthijs) Berends	b5d2a08401	(v0.7.1.9071) p_symbol()	2019-09-03 09:47:39 +02:00
dr. M.S. (Matthijs) Berends	06b6266366	(v0.7.1.9070) na.rm for age(), age_groups()	2019-09-02 15:17:41 +02:00
dr. M.S. (Matthijs) Berends	e2b78fa428	(v0.7.1.9066) bug-drug fix	2019-08-27 23:00:00 +02:00
dr. M.S. (Matthijs) Berends	248638ad91	(v0.7.1.9065) bug-drug fix	2019-08-27 22:41:09 +02:00
dr. M.S. (Matthijs) Berends	f3276592b7	(v0.7.1.9064) bug-drug fix	2019-08-27 19:15:04 +02:00
dr. M.S. (Matthijs) Berends	93be16484b	(v0.7.1.9063) septic_patients -> example_isolates	2019-08-27 16:45:42 +02:00
dr. M.S. (Matthijs) Berends	7a6fce4eb8	(v0.7.1.9062) mo/ab assignment improvements	2019-08-26 16:02:03 +02:00
dr. M.S. (Matthijs) Berends	e46cb0399f	(v0.7.1.9059) bug_drug_combinations	2019-08-25 22:53:22 +02:00
dr. M.S. (Matthijs) Berends	920212e815	(v0.7.1.9056) mo and ab subsetting	2019-08-14 14:57:06 +02:00
dr. M.S. (Matthijs) Berends	7108454ba5	(v0.7.1.9055) algorithm improvements	2019-08-13 16:15:08 +02:00
dr. M.S. (Matthijs) Berends	bd252a2984	(v0.7.1.9036) preserve ab/mo classes in subsetting	2019-08-12 14:48:09 +02:00
dr. M.S. (Matthijs) Berends	1d423cca89	(v0.7.1.9035) cephalosporins and unit tests	2019-08-11 19:07:26 +02:00
dr. M.S. (Matthijs) Berends	3f5828e74a	(v0.7.1.9034) mo.codes fix for Dracunculus spp.	2019-08-09 23:45:26 +02:00
dr. M.S. (Matthijs) Berends	6598c5615d	(v0.7.1.9033) 5000 new fungi	2019-08-09 23:22:10 +02:00
dr. M.S. (Matthijs) Berends	6a349bf757	(v0.7.1.9032) eucast_rules() improvements	2019-08-09 14:28:46 +02:00
dr. M.S. (Matthijs) Berends	1ce4b72dd2	(v0.7.1.9031) include_unknown for first_isolate()	2019-08-08 22:39:42 +02:00
dr. M.S. (Matthijs) Berends	bfa92eb166	(v0.7.1.9028) predict update	2019-08-07 15:58:32 +02:00
dr. M.S. (Matthijs) Berends	90c874025a	(v0.7.1.9027) tibble printing	2019-08-07 15:37:39 +02:00
dr. M.S. (Matthijs) Berends	3a1f960f89	(v0.7.1.9024) eucast_rules() fix, new MOs	2019-08-06 14:39:22 +02:00
dr. M.S. (Matthijs) Berends	d6ab3896a1	(v0.7.1.9021) CI fix for resistance_predict	2019-08-04 10:48:41 +02:00
dr. M.S. (Matthijs) Berends	2a62c3d62a	(v0.7.1.9018) deps	2019-07-30 13:12:40 +02:00
dr. M.S. (Matthijs) Berends	ec0ca20dee	(v0.7.1.9017) deps	2019-07-29 21:20:26 +02:00
dr. M.S. (Matthijs) Berends	b7e2d7b9b8	(v0.7.1.9016) deps	2019-07-29 17:34:57 +02:00
dr. M.S. (Matthijs) Berends	240f03a672	(v0.7.1.9015) Remove freq()	2019-07-29 13:33:48 +02:00
dr. M.S. (Matthijs) Berends	b452de2fe4	(v0.7.1.9010) eucast informative text in verbose mode	2019-07-09 13:36:03 +02:00
dr. M.S. (Matthijs) Berends	b15d59cf03	(v0.7.1.9009) note for WHOCC	2019-07-09 11:22:46 +02:00
dr. M.S. (Matthijs) Berends	c57ad26c5b	(v0.7.1.9007) mdro update	2019-07-04 15:26:07 +02:00
dr. M.S. (Matthijs) Berends	4ff20af123	(v0.7.1.9006) new rsi calculations, atc class removal	2019-07-02 16:48:52 +02:00
dr. M.S. (Matthijs) Berends	156d550895	(v0.7.1.9005) new rsi calculations, atc class removal	2019-07-01 14:03:15 +02:00
dr. M.S. (Matthijs) Berends	65c6702b21	(v0.7.1.9004) atc class removal	2019-06-27 11:57:45 +02:00
dr. M.S. (Matthijs) Berends	c9156c004a	(v0.7.0.9013) mo_synonym fix	2019-06-22 14:49:12 +02:00
dr. M.S. (Matthijs) Berends	9c39c35f86	(v0.7.0.9010) mo_synonyms, plot/barplot fixes	2019-06-16 21:42:40 +02:00
dr. M.S. (Matthijs) Berends	254745061c	(v0.7.0.9008) T. vaginalis, rsi_df	2019-06-13 14:28:46 +02:00
dr. M.S. (Matthijs) Berends	8f674e19bb	(v0.7.0.9005) ab algorithm update	2019-06-11 14:18:25 +02:00
dr. M.S. (Matthijs) Berends	ec48f1d83b	(v0.7.0.9003) scale fix	2019-06-08 23:50:06 +02:00
dr. M.S. (Matthijs) Berends	270aa0dd33	v0.7.0	2019-06-03 17:45:22 +02:00
dr. M.S. (Matthijs) Berends	702da574c0	website update	2019-06-02 19:50:22 +02:00
dr. M.S. (Matthijs) Berends	bd73988f15	(v0.6.1.9053) prerelease fixes	2019-06-02 19:23:19 +02:00
dr. M.S. (Matthijs) Berends	2667fff8a7	(v0.6.1.9050) support staged install	2019-06-01 20:40:49 +02:00
dr. M.S. (Matthijs) Berends	a665612cb8	(v0.6.1.9049) data creation fix	2019-05-31 21:20:16 +02:00
dr. M.S. (Matthijs) Berends	4ed27c7e7a	(v0.6.1.9046) ggplot fix	2019-05-31 20:25:57 +02:00
dr. M.S. (Matthijs) Berends	f03f71eced	(v0.6.1.9045) age test fix	2019-05-31 14:40:15 +02:00
dr. M.S. (Matthijs) Berends	493ae2ba0c	(v0.6.1.9044) first_isolate fix for species	2019-05-31 14:25:11 +02:00
dr. M.S. (Matthijs) Berends	1f8ee3ec3e	(v0.6.1.9043) age doc fix	2019-05-30 08:51:38 +02:00
dr. M.S. (Matthijs) Berends	8b5e2b030b	added boxplot for (grouped) freq()	2019-05-29 19:56:17 +02:00
dr. M.S. (Matthijs) Berends	62e6f41961	website update	2019-05-29 00:36:48 +02:00
dr. M.S. (Matthijs) Berends	7e0e171512	website update	2019-05-23 19:39:07 +02:00
dr. M.S. (Matthijs) Berends	bbf8b611e3	doc fix	2019-05-23 17:35:58 +02:00
dr. M.S. (Matthijs) Berends	60983a1640	added mdr_tb()	2019-05-23 16:58:59 +02:00
dr. M.S. (Matthijs) Berends	4ca00e1868	speed improvement eucast_rules(), support more old MO codes	2019-05-20 12:00:18 +02:00
dr. M.S. (Matthijs) Berends	b0033dae1b	website update	2019-05-17 20:22:04 +02:00
dr. M.S. (Matthijs) Berends	5eda991c47	ab_info fix	2019-05-16 22:07:31 +02:00
dr. M.S. (Matthijs) Berends	4c3cf85a65	ab_info, other bug fixes	2019-05-16 21:20:00 +02:00
dr. M.S. (Matthijs) Berends	f6bf54b37d	documentation fix	2019-05-13 20:16:51 +02:00
dr. M.S. (Matthijs) Berends	2ea0c93e44	documentation fix	2019-05-13 16:35:48 +02:00
dr. M.S. (Matthijs) Berends	cc403169c6	first isolate missing dates fix	2019-05-13 14:56:23 +02:00
dr. M.S. (Matthijs) Berends	0dc0715dc6	CI tests	2019-05-13 12:21:57 +02:00
dr. M.S. (Matthijs) Berends	38a4421450	CI tests	2019-05-13 10:10:16 +02:00
dr. M.S. (Matthijs) Berends	fcc77164e9	mdro fix	2019-05-11 23:30:10 +02:00
dr. M.S. (Matthijs) Berends	68cc7ef0d0	new antibiotics	2019-05-10 16:44:59 +02:00
dr. M.S. (Matthijs) Berends	461eec9bac	cfta streptococci, codecov.yml	2019-04-09 14:59:17 +02:00
dr. M.S. (Matthijs) Berends	cffb7787d8	cfta streptococci	2019-04-09 10:34:40 +02:00
dr. M.S. (Matthijs) Berends	30b559827c	documentation update	2019-04-07 22:40:02 +02:00
dr. M.S. (Matthijs) Berends	51fdc5d6cc	self-learning off	2019-04-06 09:38:23 +02:00
dr. M.S. (Matthijs) Berends	fbc9191b13	new EUCAST rules algorithm	2019-04-05 18:47:39 +02:00
dr. M.S. (Matthijs) Berends	b25f2d6213	v0.6.1	2019-03-28 21:33:28 +01:00
dr. M.S. (Matthijs) Berends	8a1d384d9c	ci fixes	2019-03-26 15:34:04 +01:00
dr. M.S. (Matthijs) Berends	29f444543d	added Becker 2019	2019-03-26 14:24:03 +01:00
dr. M.S. (Matthijs) Berends	c6a12266e7	DSMZ data	2019-03-18 14:29:41 +01:00
dr. M.S. (Matthijs) Berends	e18a1f1f17	as.mo improvement	2019-03-15 17:36:42 +01:00
dr. M.S. (Matthijs) Berends	fdffc2791b	memory for as.mo()	2019-03-15 13:57:25 +01:00
dr. M.S. (Matthijs) Berends	504a042fba	uncertainty levels, new WHONET codes	2019-03-12 12:19:27 +01:00
dr. M.S. (Matthijs) Berends	b319b89750	WHONET fix	2019-03-09 08:21:00 +01:00
dr. M.S. (Matthijs) Berends	0c0c6e289b	small as.mo fix	2019-03-06 14:39:02 +01:00
dr. M.S. (Matthijs) Berends	5c7a061a5d	filter_ab_class fix	2019-03-06 09:32:48 +01:00
dr. M.S. (Matthijs) Berends	74e0ae21fd	con WHONET, filter ab class	2019-03-05 22:47:42 +01:00
dr. M.S. (Matthijs) Berends	e835525cf6	unknown codes, rsi fix	2019-03-02 22:47:04 +01:00
dr. M.S. (Matthijs) Berends	c5efb272fd	mo_source improvement	2019-03-01 09:34:04 +01:00
dr. M.S. (Matthijs) Berends	2565b60024	rlang dependency, new fungi	2019-02-28 13:56:28 +01:00
dr. M.S. (Matthijs) Berends	54162522bd	age_groups fix	2019-02-27 11:36:12 +01:00
dr. M.S. (Matthijs) Berends	f9ded23023	as.mo improvement	2019-02-26 12:33:26 +01:00
dr. M.S. (Matthijs) Berends	c506d2893b	as.mo improvements	2019-02-25 15:52:32 +01:00
dr. M.S. (Matthijs) Berends	0ec76cfa98	as.mo improvement	2019-02-25 10:42:57 +01:00
dr. M.S. (Matthijs) Berends	1a6314769b	as.mo improvement	2019-02-23 16:02:31 +01:00
dr. M.S. (Matthijs) Berends	41ad7a22c8	mo_rank mo_url, added Tremellales	2019-02-22 22:12:10 +01:00
dr. M.S. (Matthijs) Berends	68a9a35ed6	algorithm update	2019-02-21 18:55:52 +01:00
dr. M.S. (Matthijs) Berends	c6e57ca456	website update	2019-02-20 14:18:11 +01:00
dr. M.S. (Matthijs) Berends	13120f465f	website update	2019-02-20 13:57:23 +01:00
dr. M.S. (Matthijs) Berends	8dc027309e	website update	2019-02-20 10:38:24 +01:00
dr. M.S. (Matthijs) Berends	fb1fc3686c	Catalogue of life	2019-02-20 00:04:48 +01:00
dr. M.S. (Matthijs) Berends	54f8258f8c	Catalogue of Life, replaces ITIS	2019-02-18 02:33:37 +01:00
dr. M.S. (Matthijs) Berends	efb2af9e3a	benchmarks plots	2019-02-14 10:23:51 +01:00
dr. M.S. (Matthijs) Berends	76ed26d27e	resistance predict update	2019-02-11 10:27:10 +01:00
dr. M.S. (Matthijs) Berends	c56b179857	as.rsi warning, site update	2019-02-09 22:16:24 +01:00
dr. M.S. (Matthijs) Berends	ed30312048	mo codes for WHONET	2019-02-08 16:06:54 +01:00
dr. M.S. (Matthijs) Berends	3d3366faf7	is.rsi.eligible update	2019-02-04 18:04:29 +01:00
dr. M.S. (Matthijs) Berends	587e00b7be	is.rsi.eligible update	2019-02-04 12:24:07 +01:00
dr. M.S. (Matthijs) Berends	0b3dc0231f	freq fix	2019-01-30 16:00:55 +01:00
dr. M.S. (Matthijs) Berends	3efb54d016	freq update	2019-01-29 20:20:09 +01:00
dr. M.S. (Matthijs) Berends	6aae206320	WHONET/EARS-Net support	2019-01-29 00:06:50 +01:00
dr. M.S. (Matthijs) Berends	f6336fdd89	quasiquotation for freq()	2019-01-28 11:20:32 +01:00
dr. M.S. (Matthijs) Berends	e76961a66b	less deps	2019-01-27 19:30:40 +01:00
dr. M.S. (Matthijs) Berends	a2d3ea280a	text updates	2019-01-27 13:55:23 +01:00
dr. M.S. (Matthijs) Berends	18b75356a9	re-add atc_ddd and atc_groups	2019-01-27 13:33:43 +01:00
dr. M.S. (Matthijs) Berends	6ec940bc75	atc_ functions	2019-01-27 10:53:59 +01:00
dr. M.S. (Matthijs) Berends	b39055c018	deprecated fix	2019-01-27 00:33:58 +01:00
dr. M.S. (Matthijs) Berends	f836722269	atc_ functions	2019-01-26 23:22:56 +01:00
dr. M.S. (Matthijs) Berends	f4ff98b470	WHO update, antibiotics update	2019-01-25 13:18:41 +01:00
dr. M.S. (Matthijs) Berends	46dcc7e2e8	set_mo_source	2019-01-21 15:53:01 +01:00
dr. M.S. (Matthijs) Berends	8db87a15e9	fixes	2019-01-15 16:38:54 +01:00
dr. M.S. (Matthijs) Berends	046d195064	resistance predict	2019-01-15 12:45:24 +01:00
dr. M.S. (Matthijs) Berends	cda7087722	website update	2019-01-12 19:31:30 +01:00
dr. M.S. (Matthijs) Berends	5aad26035c	edited g.test	2019-01-12 11:06:58 +01:00
dr. M.S. (Matthijs) Berends	641d866db2	guess_ab_col, benchmarks	2019-01-11 20:37:23 +01:00
dr. M.S. (Matthijs) Berends	193a2d2863	EUCAST update, as.mo bugfix for empty vlaues	2019-01-08 16:23:45 +01:00
dr. M.S. (Matthijs) Berends	bc15f660d6	guess_ab()	2019-01-06 20:23:49 +01:00
dr. M.S. (Matthijs) Berends	2c798547bf	language	2019-01-05 21:40:04 +01:00
dr. M.S. (Matthijs) Berends	6652f7d82b	fix warnings	2019-01-04 09:49:42 +01:00
dr. M.S. (Matthijs) Berends	80ea555663	guess_ab	2019-01-03 23:56:19 +01:00
dr. M.S. (Matthijs) Berends	6b2d464f8c	big website update, licence txt update	2019-01-02 23:24:07 +01:00
dr. M.S. (Matthijs) Berends	68baf058cd	website update	2018-12-31 10:35:26 +01:00
dr. M.S. (Matthijs) Berends	92a32b62a7	new website, freq updates	2018-12-29 22:24:19 +01:00
dr. M.S. (Matthijs) Berends	0b8084871d	dplyr 0.8.0 support, fixes #7	2018-12-22 22:39:34 +01:00
dr. M.S. (Matthijs) Berends	b937662a97	limits for scale_y_percent - Licence update	2018-12-16 22:45:12 +01:00
dr. M.S. (Matthijs) Berends	1ed0cc9bfd	age_groups fix	2018-12-16 11:40:54 +01:00
dr. M.S. (Matthijs) Berends	2018d5b477	age and age_groups	2018-12-15 22:40:07 +01:00
dr. M.S. (Matthijs) Berends	7e5fe75a17	small text fixes	2018-12-14 07:48:12 +01:00
dr. M.S. (Matthijs) Berends	81af7be36e	note about portions	2018-12-14 07:23:25 +01:00
dr. M.S. (Matthijs) Berends	01a6d56334	add kingdom to mo_taxonomy	2018-12-10 21:47:25 +01:00
dr. M.S. (Matthijs) Berends	5ab7eb07bc	keyab automatic	2018-12-10 15:14:29 +01:00
dr. M.S. (Matthijs) Berends	9478ab71be	freq - decimals	2018-12-10 10:13:40 +01:00
dr. M.S. (Matthijs) Berends	8e8a9cd190	AI improvements	2018-12-07 12:04:55 +01:00
dr. M.S. (Matthijs) Berends	60fe98bbbd	better as.mo handling	2018-12-06 14:36:39 +01:00
dr. M.S. (Matthijs) Berends	9ddf6dc530	support A. species for as.mo, cleanup	2018-11-24 20:25:09 +01:00
dr. M.S. (Matthijs) Berends	a8132922af	unit test read.4d, unselecting freq cols	2018-11-19 13:00:22 +01:00
dr. M.S. (Matthijs) Berends	83c7da85ab	unit tests	2018-11-16 22:28:55 +01:00
dr. M.S. (Matthijs) Berends	d22b7f00da	unit tests	2018-11-16 22:22:42 +01:00
dr. M.S. (Matthijs) Berends	4fcc2b409a	MDRO update	2018-11-16 20:50:50 +01:00
dr. M.S. (Matthijs) Berends	fab64e6728	read.4D improvements	2018-11-15 12:42:35 +01:00
dr. M.S. (Matthijs) Berends	6b0f4ffbd4	new kingdom	2018-11-09 13:11:54 +01:00
dr. M.S. (Matthijs) Berends	84e08f516a	grouping var for freq	2018-11-06 16:41:59 +01:00
dr. M.S. (Matthijs) Berends	d15bb2ab3f	read_4D	2018-11-05 15:30:49 +01:00
dr. M.S. (Matthijs) Berends	d07e9b904e	new function get_locale	2018-11-05 13:20:32 +01:00
dr. M.S. (Matthijs) Berends	e601fd259a	test syntax fix	2018-11-01 20:50:10 +01:00
dr. M.S. (Matthijs) Berends	5476fecc73	eucast update	2018-11-01 20:23:33 +01:00
dr. M.S. (Matthijs) Berends	f7687557c9	eucast updates	2018-11-01 17:06:08 +01:00
dr. M.S. (Matthijs) Berends	9cd4ab928a	speed improvement as.mo, freq title	2018-10-31 12:10:49 +01:00
dr. M.S. (Matthijs) Berends	1bf8dc2983	as.mo speedup: assigned to namespace	2018-10-29 17:26:17 +01:00
dr. M.S. (Matthijs) Berends	707aa20a37	fixes	2018-10-23 14:59:36 +02:00
dr. M.S. (Matthijs) Berends	7997de6a6d	mdro and 1st isolate improvements	2018-10-23 11:15:05 +02:00
dr. M.S. (Matthijs) Berends	c2a93b46db	breaks param, tidyr dep change, freq markdown	2018-10-22 12:32:59 +02:00
dr. M.S. (Matthijs) Berends	ec15b82fd6	param header for freq	2018-10-19 21:52:08 +02:00
dr. M.S. (Matthijs) Berends	86b03577a7	fix for as.mo, added also_single_tested	2018-10-19 13:53:31 +02:00
dr. M.S. (Matthijs) Berends	b464dd524a	new verbose	2018-10-19 00:17:03 +02:00
dr. M.S. (Matthijs) Berends	0ef91be3ac	param rules for EUCAST	2018-10-18 12:10:10 +02:00
dr. M.S. (Matthijs) Berends	693f64bdbf	new EUCAST rules: clinical breakpoints	2018-10-17 17:32:34 +02:00
dr. M.S. (Matthijs) Berends	d5a41de711	parameter combine_IR	2018-10-16 09:59:31 +02:00
dr. M.S. (Matthijs) Berends	5b5b95a47b	count_all and some fixes	2018-10-12 16:35:18 +02:00
dr. M.S. (Matthijs) Berends	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
dr. M.S. (Matthijs) Berends	ed17db0263	renamed year columns to ref	2018-10-01 14:44:40 +02:00
dr. M.S. (Matthijs) Berends	3119a221e5	authors from ITIS, diff for freq	2018-10-01 11:39:43 +02:00
dr. M.S. (Matthijs) Berends	92c9cc2608	diff for freq, fix for mo_shortname	2018-09-29 21:54:32 +02:00
dr. M.S. (Matthijs) Berends	a6aa9e95fb	completed old taxonomic names	2018-09-28 20:13:13 +02:00
dr. M.S. (Matthijs) Berends	768fe17324	removed clipboard functions as it violated CRAN policies	2018-09-28 16:05:18 +02:00
dr. M.S. (Matthijs) Berends	2b0080995e	speed improvement for as.mo, more old taxonomic names	2018-09-27 23:23:48 +02:00
dr. M.S. (Matthijs) Berends	450992baea	new: 1680 old taxonomic names	2018-09-25 16:44:40 +02:00
dr. M.S. (Matthijs) Berends	9c566585b0	first inclusion of ITIS data	2018-09-24 23:33:29 +02:00
dr. M.S. (Matthijs) Berends	5d80cef338	added taxonomic data from ITIS	2018-09-17 20:53:32 +02:00
dr. M.S. (Matthijs) Berends	db14781593	add labels_rsi_count	2018-09-16 22:11:17 +02:00
dr. M.S. (Matthijs) Berends	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
dr. M.S. (Matthijs) Berends	d049ec9e69	ggplot2_rsi fix	2018-09-13 14:48:34 +02:00
dr. M.S. (Matthijs) Berends	cb0d74a4f0	support for French and Italian, added quote to freq	2018-09-10 15:45:25 +02:00
dr. M.S. (Matthijs) Berends	b83e6a9380	algoritm improvement, removed all Catabacter except for C. hongkongensis	2018-09-10 11:40:54 +02:00
dr. M.S. (Matthijs) Berends	4816419f0c	AI improvements for microorganisms	2018-09-09 12:11:44 +02:00
dr. M.S. (Matthijs) Berends	26f5be0033	support for portuguese, language determination based on system	2018-09-08 16:06:47 +02:00
dr. M.S. (Matthijs) Berends	de36b0be23	fix for empty values in mo_property	2018-09-05 12:21:27 +02:00
dr. M.S. (Matthijs) Berends	e39a9a8b05	added mo_shortname	2018-09-05 10:51:46 +02:00
dr. M.S. (Matthijs) Berends	790bd1622d	added vanA to vanE positive Enterococci	2018-09-05 09:49:19 +02:00
dr. M.S. (Matthijs) Berends	b388e3fee7	Support for German and Spanish microorganism properties, cleanup	2018-09-04 11:33:30 +02:00
dr. M.S. (Matthijs) Berends	75fe4d401f	new MOs, cleanup	2018-09-01 21:19:46 +02:00
dr. M.S. (Matthijs) Berends	5965d3c794	replaced bactid by mo	2018-08-31 13:36:19 +02:00
dr. M.S. (Matthijs) Berends	98ff131680	support for older versions of ggplot2	2018-08-29 16:39:28 +02:00
dr. M.S. (Matthijs) Berends	d654444c8e	re added nrow	2018-08-29 16:35:32 +02:00
dr. M.S. (Matthijs) Berends	d9e68e0a50	ggplot_rsi example update, more unit tests	2018-08-29 16:25:57 +02:00
dr. M.S. (Matthijs) Berends	029157b3be	163 new trade names, added ab_tradenames	2018-08-29 12:27:37 +02:00
dr. M.S. (Matthijs) Berends	972fc4f6c7	ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid	2018-08-28 13:51:13 +02:00
dr. M.S. (Matthijs) Berends	2acdb1981c	atc and bactid functions, readme update	2018-08-25 22:01:14 +02:00
dr. M.S. (Matthijs) Berends	a100d07da6	removed ratio, better rsi_calc, update for freq	2018-08-24 11:08:20 +02:00
dr. M.S. (Matthijs) Berends	febd0ca885	geom_rsi - any parameter	2018-08-23 21:27:15 +02:00
dr. M.S. (Matthijs) Berends	da5379c881	quasiquotation, alpha for geom_rsi	2018-08-23 00:40:36 +02:00
dr. M.S. (Matthijs) Berends	3e87c8f409	count_* functions	2018-08-22 00:02:26 +02:00
dr. M.S. (Matthijs) Berends	1699d7b8b3	better example of grouping variable in ggplot_rsi	2018-08-14 12:07:03 +02:00
dr. M.S. (Matthijs) Berends	59ce1eb1b1	ggplot_rsi improvements	2018-08-13 16:42:37 +02:00
dr. M.S. (Matthijs) Berends	dba06c3295	abname improvement, small fixes	2018-08-13 11:00:53 +02:00
dr. M.S. (Matthijs) Berends	ce2cdb9309	support groups for portion_df, update README	2018-08-12 22:34:03 +02:00
dr. M.S. (Matthijs) Berends	e5d32cafe0	new unit tests for ggplot, small fixes	2018-08-12 17:44:06 +02:00
dr. M.S. (Matthijs) Berends	1ba7d883fe	new ggplot enhancement	2018-08-11 21:30:00 +02:00
dr. M.S. (Matthijs) Berends	53fa198e35	new portion functions	2018-08-10 15:01:05 +02:00
dr. M.S. (Matthijs) Berends	ae2433a020	rsi family for resistance analysis	2018-08-03 14:49:29 +02:00
dr. M.S. (Matthijs) Berends	6262315527	Becker classification ... Lancefield classification Added Lancefield groups to `microorganisms` data set	2018-08-02 13:15:45 +02:00
dr. M.S. (Matthijs) Berends	edd2dd09dc	rsi for freq	2018-08-01 22:37:28 +02:00
dr. M.S. (Matthijs) Berends	d8f70a74de	clipboard error	2018-08-01 10:32:24 +02:00
dr. M.S. (Matthijs) Berends	7c667eb732	emph guess_bactid	2018-08-01 08:03:31 +02:00
dr. M.S. (Matthijs) Berends	826694323b	new functions R, RI, SI, S	2018-07-29 22:14:51 +02:00
dr. M.S. (Matthijs) Berends	feab1cad6b	small fixes	2018-07-28 09:34:03 +02:00
dr. M.S. (Matthijs) Berends	498e88b5cf	improvement for forecasting resistance	2018-07-26 16:30:42 +02:00
dr. M.S. (Matthijs) Berends	d9e204031d	update to septic_patients, speed improvements	2018-07-25 14:17:04 +02:00
dr. M.S. (Matthijs) Berends	03a3cb397b	clipboard update	2018-07-23 15:09:19 +02:00
dr. M.S. (Matthijs) Berends	8421638b60	new class bactid	2018-07-23 14:14:03 +02:00
dr. M.S. (Matthijs) Berends	40de1b4ac2	man	2018-07-23 10:37:49 +02:00
dr. M.S. (Matthijs) Berends	9920ac8a5c	fix for keyab, more examples	2018-07-23 10:35:39 +02:00
dr. M.S. (Matthijs) Berends	ad662d7bab	new col names for `key_antibiotics`	2018-07-19 15:11:23 +02:00
dr. M.S. (Matthijs) Berends	2a4d759fbc	check fails	2018-07-17 14:48:11 +02:00
dr. M.S. (Matthijs) Berends	5cb9c541f8	new algorithm key abs	2018-07-17 13:02:05 +02:00
dr. M.S. (Matthijs) Berends	a5a4354651	speed improvements	2018-07-17 10:32:26 +02:00
dr. M.S. (Matthijs) Berends	715a7630ca	support format.freq	2018-07-16 16:41:48 +02:00
dr. M.S. (Matthijs) Berends	6eaf33baf3	speed improvements	2018-07-15 22:56:41 +02:00
dr. M.S. (Matthijs) Berends	b6655f6454	Welcome C++!	2018-07-13 17:23:46 +02:00
dr. M.S. (Matthijs) Berends	a28289562a	remove print function, out of scope	2018-07-11 20:12:19 +02:00
dr. M.S. (Matthijs) Berends	f63414d519	new g.test, extra unit tests	2018-07-10 12:27:07 +02:00
dr. M.S. (Matthijs) Berends	fc30d3fb13	freq: support for table	2018-07-09 14:02:58 +02:00
dr. M.S. (Matthijs) Berends	14b990d769	kurtosis, skewness, start with ML	2018-07-08 22:14:55 +02:00
dr. M.S. (Matthijs) Berends	34ee0247ac	addins and small improvements to microorganisms dataset	2018-07-04 17:20:03 +02:00
dr. M.S. (Matthijs) Berends	10fce8382c	include IQR and MAD in freq	2018-07-03 11:30:40 +02:00
dr. M.S. (Matthijs) Berends	3d0d21f322	rename vector2ratio to ratio	2018-07-02 11:14:20 +02:00
dr. M.S. (Matthijs) Berends	3527894b49	new g.test() and edited freq()	2018-07-01 21:40:37 +02:00
dr. M.S. (Matthijs) Berends	f7af8a81da	update man page	2018-06-29 09:06:47 +02:00
dr. M.S. (Matthijs) Berends	649a8025aa	add clipboard functions again	2018-06-27 15:54:56 +02:00
dr. M.S. (Matthijs) Berends	a9bd5472d0	top_freq	2018-06-20 14:47:37 +02:00
dr. M.S. (Matthijs) Berends	4a027f3c34	extra unit tests, add row.names to freq	2018-06-19 15:20:14 +02:00
dr. M.S. (Matthijs) Berends	bdc860e29c	atc_groups	2018-06-19 10:05:38 +02:00
dr. M.S. (Matthijs) Berends	0a5898b17d	fix for printing tibbles, improve guess_bactid	2018-06-08 12:06:54 +02:00
dr. M.S. (Matthijs) Berends	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
dr. M.S. (Matthijs) Berends	f05e7178cb	added vignette of freq	2018-05-09 11:44:46 +02:00
dr. M.S. (Matthijs) Berends	25b3346d9a	edit methodology of rsi	2018-05-03 10:19:02 +02:00
dr. M.S. (Matthijs) Berends	c0fc82c794	Added function `n_rsi`	2018-05-02 14:56:25 +02:00
dr. M.S. (Matthijs) Berends	e5ae7b98ac	update logo	2018-05-01 09:59:37 +02:00
dr. M.S. (Matthijs) Berends	6eaf594cb7	update data info	2018-05-01 09:57:50 +02:00
dr. M.S. (Matthijs) Berends	be5d714639	update README	2018-05-01 09:43:47 +02:00
dr. M.S. (Matthijs) Berends	19ccc51f40	remove clipboard functions	2018-05-01 09:36:45 +02:00
dr. M.S. (Matthijs) Berends	8fe70d5652	Fix Latex PDF error	2018-04-30 16:24:11 +02:00
dr. M.S. (Matthijs) Berends	970e3ed7f1	EUCAST rules for MDRO	2018-04-25 15:33:58 +02:00
dr. M.S. (Matthijs) Berends	0b22ddef8e	more unit tests	2018-04-20 13:45:34 +02:00
dr. M.S. (Matthijs) Berends	82fec5cc51	Try to support older R versions	2018-04-19 14:10:57 +02:00
dr. M.S. (Matthijs) Berends	2509e2413d	MDRO, freq tables, new print format for tibbles	2018-04-18 12:24:54 +02:00
dr. M.S. (Matthijs) Berends	3165c50d06	more MOs	2018-04-03 16:07:32 +02:00
dr. M.S. (Matthijs) Berends	07bdd61241	update dependencies	2018-04-02 16:05:09 +02:00
dr. M.S. (Matthijs) Berends	c182a9673d	fix clipboard on linux	2018-04-02 11:11:21 +02:00
dr. M.S. (Matthijs) Berends	6f7730dcaa	add tests using testthat	2018-03-27 17:43:42 +02:00
dr. M.S. (Matthijs) Berends	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
dr. M.S. (Matthijs) Berends	fe803f7279	use guess_bactid for GLIMS codes	2018-03-19 21:23:21 +01:00
dr. M.S. (Matthijs) Berends	dd2517ecb7	- Added new algorithm to determine weighted isolates, can now be `points` or `keyantibiotics, see `?first_isolate` ... - 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
dr. M.S. (Matthijs) Berends	502a44eb25	- Added new function `guess_bactid` to determine the ID of a microorganism based on genus/species ... - 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
dr. M.S. (Matthijs) Berends	6c67c8f6c1	examples edit	2018-03-14 09:58:58 +01:00
dr. M.S. (Matthijs) Berends	46db3f7b13	import from graphics	2018-03-13 15:40:10 +01:00
dr. M.S. (Matthijs) Berends	04fc3573ec	add barplots	2018-03-13 14:34:10 +01:00
dr. M.S. (Matthijs) Berends	e4b371d30a	add MIC values ... add badges to readme	2018-03-13 11:57:30 +01:00
dr. M.S. (Matthijs) Berends	34e70a65ed	added septic_patients	2018-02-27 20:01:02 +01:00
dr. M.S. (Matthijs) Berends	8a603876d2	misc	2018-02-26 15:53:09 +01:00
dr. M.S. (Matthijs) Berends	6fa05fe33b	first isolates	2018-02-26 14:06:31 +01:00
dr. M.S. (Matthijs) Berends	d36a391747	export first_isolate	2018-02-26 12:15:52 +01:00
dr. M.S. (Matthijs) Berends	11683b082e	EUCAST man pages	2018-02-22 21:42:01 +01:00
dr. M.S. (Matthijs) Berends	10380bcfae	add NEWS	2018-02-22 21:37:10 +01:00
dr. M.S. (Matthijs) Berends	d8da8daf9a	First CRAN submission edits	2018-02-22 20:48:48 +01:00
dr. M.S. (Matthijs) Berends	77194527b5	readme	2018-02-21 12:21:34 +01:00
dr. M.S. (Matthijs) Berends	ab0503f8b8	abname, logo	2018-02-21 12:10:00 +01:00
dr. M.S. (Matthijs) Berends	62304dc23f	first commit	2018-02-21 11:52:31 +01:00