mirror of https://github.com/msberends/AMR.git
62 lines
2.7 KiB
R
62 lines
2.7 KiB
R
# Run this file to update the package -------------------------------------
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# source("data-raw/internals.R")
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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eucast_rules_file <- 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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# take the order of the reference.rule_group column in the orginal data file
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eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
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levels = unique(eucast_rules_file$reference.rule_group),
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ordered = TRUE)
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eucast_rules_file <- dplyr::arrange(eucast_rules_file,
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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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