mirror of https://github.com/msberends/AMR.git
41 lines
2.0 KiB
R
41 lines
2.0 KiB
R
# EUCAST rules ----
|
|
# For editing the reference file, these values can all be used for target antibiotics:
|
|
# "aminoglycosides", "tetracyclines", "polymyxins", "macrolides", "glycopeptides",
|
|
# "streptogramins", "cephalosporins", "cephalosporins_without_CAZ", "carbapenems",
|
|
# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
|
|
# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
|
|
# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
|
# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
|
|
# LiPuma JJ, 2015 (PMID 16217180).
|
|
eucast_rules_file <- dplyr::arrange(
|
|
.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
|
sep = "\t",
|
|
stringsAsFactors = FALSE,
|
|
header = TRUE,
|
|
strip.white = TRUE,
|
|
na = c(NA, "", NULL)),
|
|
reference.rule_group,
|
|
reference.rule)
|
|
|
|
# Translations -----
|
|
translations_file <- utils::read.table(file = "data-raw/translations.tsv",
|
|
sep = "\t",
|
|
stringsAsFactors = FALSE,
|
|
header = TRUE,
|
|
blank.lines.skip = TRUE,
|
|
fill = TRUE,
|
|
strip.white = TRUE,
|
|
encoding = "UTF-8",
|
|
fileEncoding = "UTF-8",
|
|
na.strings = c(NA, "", NULL))
|
|
|
|
# Export to package as internal data ----
|
|
usethis::use_data(eucast_rules_file, translations_file,
|
|
internal = TRUE,
|
|
overwrite = TRUE,
|
|
version = 2)
|
|
|
|
# Remove from global environment ----
|
|
rm(eucast_rules_file)
|
|
rm(translations_file)
|