2018-02-21 11:52:31 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
|
|
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
|
|
|
# #
|
2019-01-02 23:24:07 +01:00
|
|
|
# SOURCE #
|
|
|
|
|
# https://gitlab.com/msberends/AMR #
|
2018-02-21 11:52:31 +01:00
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
2019-01-02 23:24:07 +01:00
|
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
2018-02-21 11:52:31 +01:00
|
|
|
# #
|
2019-01-02 23:24:07 +01:00
|
|
|
# This R package is free software; you can freely use and distribute #
|
|
|
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
|
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
|
|
|
# the Free Software Foundation. #
|
|
|
|
|
# #
|
|
|
|
|
# This R package was created for academic research and was publicly #
|
|
|
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
|
|
|
# ANY WARRANTY OR LIABILITY. #
|
2019-04-05 18:47:39 +02:00
|
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
2018-02-21 11:52:31 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2018-09-01 21:19:46 +02:00
|
|
|
globalVariables(c(".",
|
2018-09-24 23:33:29 +02:00
|
|
|
"..property",
|
2019-05-10 16:44:59 +02:00
|
|
|
"ab",
|
2019-09-25 15:43:22 +02:00
|
|
|
"ab_txt",
|
2019-05-10 16:44:59 +02:00
|
|
|
"abbreviations",
|
2018-09-01 21:19:46 +02:00
|
|
|
"antibiotic",
|
2019-04-05 18:47:39 +02:00
|
|
|
"CNS_CPS",
|
2019-02-20 00:04:48 +01:00
|
|
|
"col_id",
|
2018-09-01 21:19:46 +02:00
|
|
|
"count",
|
2018-10-01 11:39:43 +02:00
|
|
|
"count.x",
|
2018-09-01 21:19:46 +02:00
|
|
|
"date_lab",
|
2018-10-01 14:44:40 +02:00
|
|
|
"diff.percent",
|
2019-07-02 16:48:52 +02:00
|
|
|
"First name",
|
2018-09-01 21:19:46 +02:00
|
|
|
"first_isolate_row_index",
|
2018-09-24 23:33:29 +02:00
|
|
|
"fullname",
|
2019-02-27 17:39:39 +01:00
|
|
|
"fullname_lower",
|
2018-09-01 21:19:46 +02:00
|
|
|
"genus",
|
|
|
|
|
"gramstain",
|
2019-08-12 15:34:49 +02:00
|
|
|
"group",
|
2018-11-16 22:28:55 +01:00
|
|
|
"index",
|
2019-02-27 19:02:47 +01:00
|
|
|
"input",
|
2019-06-13 16:40:35 +02:00
|
|
|
"interpretation",
|
2019-06-27 11:57:45 +02:00
|
|
|
"isolates",
|
2018-09-01 21:19:46 +02:00
|
|
|
"item",
|
|
|
|
|
"key_ab",
|
|
|
|
|
"key_ab_lag",
|
|
|
|
|
"key_ab_other",
|
2019-02-20 00:04:48 +01:00
|
|
|
"kingdom",
|
2019-09-22 12:41:45 +02:00
|
|
|
"kingdom_index",
|
2019-05-10 16:44:59 +02:00
|
|
|
"lang",
|
2019-07-02 16:48:52 +02:00
|
|
|
"Last name",
|
2019-05-10 16:44:59 +02:00
|
|
|
"lookup",
|
2019-06-27 11:57:45 +02:00
|
|
|
"mdr",
|
2019-10-26 22:21:26 +02:00
|
|
|
"MDRO",
|
2018-09-01 21:19:46 +02:00
|
|
|
"median",
|
|
|
|
|
"microorganisms",
|
2019-09-23 20:55:54 +02:00
|
|
|
"microorganisms.codes",
|
2019-06-27 11:57:45 +02:00
|
|
|
"missing_names",
|
2018-09-01 21:19:46 +02:00
|
|
|
"mo",
|
2019-06-27 11:57:45 +02:00
|
|
|
"mono_count",
|
2019-01-02 23:24:07 +01:00
|
|
|
"more_than_episode_ago",
|
2019-06-27 11:57:45 +02:00
|
|
|
"name",
|
2019-03-28 22:05:03 +01:00
|
|
|
"new",
|
2019-08-09 14:28:46 +02:00
|
|
|
"newvar_date",
|
|
|
|
|
"newvar_genus_species",
|
|
|
|
|
"newvar_mo",
|
|
|
|
|
"newvar_patient_id",
|
|
|
|
|
"newvar_row_index",
|
|
|
|
|
"newvar_row_index_sorted",
|
2018-09-01 21:19:46 +02:00
|
|
|
"observations",
|
2019-01-17 12:08:04 +01:00
|
|
|
"observed",
|
2019-03-28 22:05:03 +01:00
|
|
|
"old",
|
2019-09-18 15:46:09 +02:00
|
|
|
"old_name",
|
2018-09-01 21:19:46 +02:00
|
|
|
"other_pat_or_mo",
|
2019-09-16 12:00:56 +02:00
|
|
|
"package_version",
|
2018-09-01 21:19:46 +02:00
|
|
|
"patient_id",
|
2019-06-12 16:08:20 +02:00
|
|
|
"pattern",
|
2019-04-05 18:47:39 +02:00
|
|
|
"plural",
|
2018-09-16 16:43:29 +02:00
|
|
|
"prevalence",
|
2018-09-01 21:19:46 +02:00
|
|
|
"R",
|
|
|
|
|
"real_first_isolate",
|
2019-01-17 12:08:04 +01:00
|
|
|
"ref",
|
2019-04-05 18:47:39 +02:00
|
|
|
"rule_group",
|
|
|
|
|
"rule_name",
|
2018-09-01 21:19:46 +02:00
|
|
|
"S",
|
2019-01-17 12:08:04 +01:00
|
|
|
"se_max",
|
|
|
|
|
"se_min",
|
2019-06-27 11:57:45 +02:00
|
|
|
"second",
|
2019-01-29 20:38:45 +01:00
|
|
|
"Sex",
|
2018-09-01 21:19:46 +02:00
|
|
|
"species",
|
2019-03-26 14:24:03 +01:00
|
|
|
"species_id",
|
2019-03-26 14:42:56 +01:00
|
|
|
"subspecies",
|
2019-05-10 16:44:59 +02:00
|
|
|
"synonyms",
|
2019-08-25 23:25:12 +02:00
|
|
|
"total",
|
2019-04-05 18:47:39 +02:00
|
|
|
"txt",
|
2019-09-16 12:00:56 +02:00
|
|
|
"uncertainty_level",
|
2018-09-01 21:19:46 +02:00
|
|
|
"value",
|
2019-09-16 12:00:56 +02:00
|
|
|
"x",
|
2019-06-27 11:57:45 +02:00
|
|
|
"xdr",
|
2018-09-24 23:33:29 +02:00
|
|
|
"y",
|
|
|
|
|
"year"))
|
