2018-02-21 11:52:31 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
|
|
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
|
|
|
# #
|
|
|
|
|
# AUTHORS #
|
|
|
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
|
|
|
|
# This program is free software; you can redistribute it and/or modify #
|
|
|
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
|
|
|
# as published by the Free Software Foundation. #
|
|
|
|
|
# #
|
|
|
|
|
# This program is distributed in the hope that it will be useful, #
|
|
|
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
|
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
|
|
|
# GNU General Public License for more details. #
|
|
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2018-09-01 21:19:46 +02:00
|
|
|
globalVariables(c(".",
|
|
|
|
|
"antibiotic",
|
|
|
|
|
"Antibiotic",
|
|
|
|
|
"antibiotics",
|
|
|
|
|
"cnt",
|
|
|
|
|
"count",
|
|
|
|
|
"cum_count",
|
|
|
|
|
"cum_percent",
|
|
|
|
|
"date_lab",
|
|
|
|
|
"days_diff",
|
|
|
|
|
"fctlvl",
|
|
|
|
|
"first_isolate_row_index",
|
|
|
|
|
"Freq",
|
|
|
|
|
"genus",
|
|
|
|
|
"gramstain",
|
|
|
|
|
"Interpretation",
|
|
|
|
|
"item",
|
|
|
|
|
"key_ab",
|
|
|
|
|
"key_ab_lag",
|
|
|
|
|
"key_ab_other",
|
2018-09-16 22:11:17 +02:00
|
|
|
"lbl",
|
2018-09-01 21:19:46 +02:00
|
|
|
"median",
|
|
|
|
|
"mic",
|
|
|
|
|
"microorganisms",
|
|
|
|
|
"mo",
|
|
|
|
|
"n",
|
|
|
|
|
"observations",
|
|
|
|
|
"other_pat_or_mo",
|
|
|
|
|
"Pasted",
|
|
|
|
|
"patient_id",
|
2018-09-16 16:43:29 +02:00
|
|
|
"prevalence",
|
2018-09-01 21:19:46 +02:00
|
|
|
"R",
|
|
|
|
|
"real_first_isolate",
|
|
|
|
|
"S",
|
|
|
|
|
"septic_patients",
|
|
|
|
|
"species",
|
|
|
|
|
"value",
|
2018-09-16 22:11:17 +02:00
|
|
|
"Value",
|
2018-09-01 21:19:46 +02:00
|
|
|
"y"))
|
