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move object assignment to AMR_env

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dr. M.S. (Matthijs) Berends
2022-10-14 13:02:50 +02:00
parent dfae4c7e7d
commit 76bcd3528c
18 changed files with 116 additions and 127 deletions
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4
R/eucast_rules.R
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@ -435,11 +435,11 @@ eucast_rules <- function(x,
}
if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
all_staph <- MO_lookup[which(MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
all_staph <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
}
if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
all_strep <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), , drop = FALSE]
all_strep <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Streptococcus"), , drop = FALSE]
all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
}