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63 lines
3.2 KiB
R
63 lines
3.2 KiB
R
# ---------------------------------------------------------------------------------------------------
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# For editing this EUCAST reference file, these values can all be used for target antibiotics:
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# all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones,
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# glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
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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 if_mo_property column 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'. All species in this group can be found in:
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# LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
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# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
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# ---------------------------------------------------------------------------------------------------
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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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skip = 10,
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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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# Old microorganism codes -------------------------------------------------
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microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
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# Export to package as internal data ----
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usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
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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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rm(microorganisms.translation)
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# Clean mo history ----
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usethis::ui_done(paste0("Resetting {usethis::ui_value('mo_history.csv')}"))
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tryCatch(
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write.csv(x = data.frame(x = character(0),
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mo = character(0),
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uncertainty_level = integer(0),
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package_version = character(0),
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stringsAsFactors = FALSE),
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row.names = FALSE,
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file = "inst/mo_history/mo_history.csv"),
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warning = function(w) cat("Warning:", w$message, "\n"),
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error = function(e) cat("Error:", e$message, "\n"))
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