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https://github.com/msberends/AMR.git
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(v2.1.1.9142) unit test fix
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@ -460,16 +460,14 @@ eucast_rules <- function(x,
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# >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
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if (any(c("all", "other") %in% rules)) {
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if (isTRUE(info)) {
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cat("\n")
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cat(paste0("\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
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cat(word_wrap(
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font_bold(paste0(
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"Rules by this AMR package (",
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font_red(paste0(
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"v", utils::packageDescription("AMR")$Version, ", ",
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format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y")
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)), "), see `?eucast_rules`\n"
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))
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paste0("Rules by the ",
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font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
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" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
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"), see `?eucast_rules`\n")
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))
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cat("\n\n")
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}
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ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
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colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
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@ -495,8 +493,8 @@ eucast_rules <- function(x,
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## Set base to R where base + enzyme inhibitor is R ----
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rule_current <- paste0(
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ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
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tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R"
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ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
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tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R"
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)
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if (isTRUE(info)) {
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cat(word_wrap(rule_current,
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@ -536,8 +534,8 @@ eucast_rules <- function(x,
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## Set base + enzyme inhibitor to S where base is S ----
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rule_current <- paste0(
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ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
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tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S"
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ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
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tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
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)
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if (isTRUE(info)) {
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@ -559,7 +557,8 @@ eucast_rules <- function(x,
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original_data = x.bak,
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warned = warned,
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info = info,
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verbose = verbose
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verbose = verbose,
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overwrite = overwrite
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)
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n_added <- n_added + run_changes$added
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n_changed <- n_changed + run_changes$changed
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@ -1037,9 +1036,9 @@ eucast_rules <- function(x,
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cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
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if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
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cat("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
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cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
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} else if (isTRUE(verbose)) {
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cat("\n", word_wrap("Used 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data."), "\n\n", sep = "")
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cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
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}
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}
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