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(v1.4.0.9013) is_gram_negative/positive update

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dr. M.S. (Matthijs) Berends
2020-11-09 13:07:02 +01:00
parent 423879c034
commit d3b1d33210
22 changed files with 149 additions and 82 deletions
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2
R/eucast_rules.R
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@ -773,7 +773,7 @@ eucast_rules <- function(x,
like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE])
mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE])
# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
# be sure to comprise all coagulase-negative/-positive staphylococci when they are mentioned
if (mo_value %like% "coagulase" && any(x$genus == "Staphylococcus", na.rm = TRUE)) {
if (mo_value %like% "negative") {
eucast_rules_df[i, "this_value"] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "negative"),