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https://github.com/msberends/AMR.git
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add oxygen tolerance
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@ -247,19 +247,14 @@ add_custom_microorganisms <- function(x) {
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"CUSTOM",
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seq.int(from = current + 1, to = current + nrow(x), by = 1),
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"_",
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toupper(unname(abbreviate(
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gsub(
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" +", " _ ",
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gsub(
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"[^A-Za-z0-9-]", " ",
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trimws2(paste(x$genus, x$species, x$subspecies))
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)
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),
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minlength = 10
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)))
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)
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trimws(
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paste(abbreviate_mo(x$genus, 5),
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abbreviate_mo(x$species, 4, hyphen_as_space = TRUE),
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abbreviate_mo(x$subspecies, 4, hyphen_as_space = TRUE),
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sep = "_"),
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whitespace = "_"))
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stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
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# add to package ----
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AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
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class(AMR_env$MO_lookup$mo) <- "character"
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@ -306,3 +301,26 @@ clear_custom_microorganisms <- function() {
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AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE]
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message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.")
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}
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abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE, ...) {
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if (hyphen_as_space == TRUE) {
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x <- gsub("-", " ", x, fixed = TRUE)
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}
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# keep a starting Latin ae
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suppressWarnings(
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gsub("(\u00C6|\u00E6)+",
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"AE",
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toupper(
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paste0(prefix,
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abbreviate(
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gsub("^ae",
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"\u00E6\u00E6",
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x,
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ignore.case = TRUE),
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minlength = minlength,
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use.classes = TRUE,
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method = "both.sides",
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...
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))))
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)
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}
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