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(v1.4.0.9040) LA-MRSA / CA-MRSA
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@ -636,14 +636,18 @@ eucast_rules <- function(x,
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ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE)
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ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE)
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# Set base to R where base + enzyme inhibitor is R
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# Set base to R where base + enzyme inhibitor is R ----
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rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
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ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
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cat(word_wrap(rule_current))
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if (info == TRUE) {
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cat(word_wrap(rule_current))
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cat("\n")
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}
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run_changes <- edit_rsi(x = x,
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col_mo = col_mo,
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to = "R",
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rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
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rule = c(rule_current, "Other rules", "",
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paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
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rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"),
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cols = cols_ab[ab_enzyme[i, ]$base_ab],
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last_verbose_info = verbose_info,
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@ -664,16 +668,18 @@ eucast_rules <- function(x,
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n_changed <- 0
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}
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# Set base + enzyme inhibitor to S where base is S
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# Set base + enzyme inhibitor to S where base is S ----
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rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
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ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
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if (info == TRUE) {
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cat(word_wrap(rule_current))
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cat("\n")
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}
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run_changes <- edit_rsi(x = x,
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col_mo = col_mo,
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to = "S",
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rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
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rule = c(rule_current, "Other rules", "",
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paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
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rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"),
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cols = cols_ab[ab_enzyme[i, ]$ab],
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last_verbose_info = verbose_info,
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