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(v1.4.0.9040) LA-MRSA / CA-MRSA

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dr. M.S. (Matthijs) Berends
2020-12-16 16:18:53 +01:00
parent 203bc20eb0
commit 1faa816090
19 changed files with 366 additions and 364 deletions
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16
R/eucast_rules.R
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@ -636,14 +636,18 @@ eucast_rules <- function(x,
ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE)
ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE)
# Set base to R where base + enzyme inhibitor is R
# Set base to R where base + enzyme inhibitor is R ----
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
cat(word_wrap(rule_current))
if (info == TRUE) {
cat(word_wrap(rule_current))
cat("\n")
}
run_changes <- edit_rsi(x = x,
col_mo = col_mo,
to = "R",
rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
rule = c(rule_current, "Other rules", "",
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"),
cols = cols_ab[ab_enzyme[i, ]$base_ab],
last_verbose_info = verbose_info,
@ -664,16 +668,18 @@ eucast_rules <- function(x,
n_changed <- 0
}
# Set base + enzyme inhibitor to S where base is S
# Set base + enzyme inhibitor to S where base is S ----
rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
if (info == TRUE) {
cat(word_wrap(rule_current))
cat("\n")
}
run_changes <- edit_rsi(x = x,
col_mo = col_mo,
to = "S",
rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
rule = c(rule_current, "Other rules", "",
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"),
cols = cols_ab[ab_enzyme[i, ]$ab],
last_verbose_info = verbose_info,