mirror of https://github.com/msberends/AMR.git
117 lines
4.2 KiB
R
Executable File
117 lines
4.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
globalVariables(c(".",
|
|
"..property",
|
|
"antibiotic",
|
|
"Antibiotic",
|
|
"antibiotics",
|
|
"atc",
|
|
"authors",
|
|
"Becker",
|
|
"certe",
|
|
"CNS_CPS",
|
|
"cnt",
|
|
"col_id",
|
|
"count",
|
|
"count.x",
|
|
"count.y",
|
|
"cum_count",
|
|
"cum_percent",
|
|
"date_lab",
|
|
"diff.percent",
|
|
"fctlvl",
|
|
"First name",
|
|
"first_isolate_row_index",
|
|
"Freq",
|
|
"fullname",
|
|
"fullname_lower",
|
|
"genus",
|
|
"gramstain",
|
|
"index",
|
|
"input",
|
|
"Interpretation",
|
|
"item",
|
|
"key_ab",
|
|
"key_ab_lag",
|
|
"key_ab_other",
|
|
"kingdom",
|
|
"labs",
|
|
"Lancefield",
|
|
"Last name",
|
|
"lbl",
|
|
"median",
|
|
"mic",
|
|
"microorganisms",
|
|
"microorganisms.codes",
|
|
"microorganisms.old",
|
|
"microorganisms.oldDT",
|
|
"microorganisms.prevDT",
|
|
"microorganisms.unprevDT",
|
|
"microorganismsDT",
|
|
"mo",
|
|
"mo.old",
|
|
"more_than_episode_ago",
|
|
"n",
|
|
"name",
|
|
"new",
|
|
"observations",
|
|
"observed",
|
|
"official",
|
|
"old",
|
|
"other_pat_or_mo",
|
|
"package_v",
|
|
"Pasted",
|
|
"patient_id",
|
|
"phylum",
|
|
"plural",
|
|
"prevalence",
|
|
"prevalent",
|
|
"property",
|
|
"psae",
|
|
"R",
|
|
"real_first_isolate",
|
|
"ref",
|
|
"reference.rule",
|
|
"reference.rule_group",
|
|
"rule_group",
|
|
"rule_name",
|
|
"S",
|
|
"se_max",
|
|
"se_min",
|
|
"septic_patients",
|
|
"Sex",
|
|
"shortname",
|
|
"species",
|
|
"species_id",
|
|
"subspecies",
|
|
"trade_name",
|
|
"transmute",
|
|
"tsn",
|
|
"tsn_new",
|
|
"txt",
|
|
"umcg",
|
|
"value",
|
|
"Value",
|
|
"x",
|
|
"y",
|
|
"year"))
|