mirror of https://github.com/msberends/AMR.git
43 lines
2.2 KiB
R
43 lines
2.2 KiB
R
# EUCAST rules ----
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# For editing the reference file, these values can all be used for target antibiotics:
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# "aminoglycosides", "tetracyclines", "polymyxins", "macrolides", "glycopeptides",
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# "streptogramins", "cephalosporins", "cephalosporins_without_CAZ", "carbapenems",
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# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
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# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
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# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
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# LiPuma JJ, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
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eucast_rules_file <- dplyr::arrange(
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.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)),
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reference.rule_group,
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reference.rule)
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# Translations -----
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translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL),
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allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
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quote = "")
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# Export to package as internal data ----
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usethis::use_data(eucast_rules_file, translations_file,
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internal = TRUE,
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overwrite = TRUE,
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version = 2)
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# Remove from global environment ----
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rm(eucast_rules_file)
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rm(translations_file)
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