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dr. M.S. (Matthijs) Berends
2019-05-13 12:21:57 +02:00
parent 38a4421450
commit 0dc0715dc6
21 changed files with 137 additions and 68 deletions
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72
R/mdro.R
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@ -374,42 +374,42 @@ eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
mdro(x = x, country = "EUCAST", ...)
}
is_ESBL <- function(x, col_mo = NULL, ...) {
col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
cols_ab <- get_column_abx(tbl = x,
soft_dependencies = c("AMX", "AMP"),
hard_dependencies = c("CAZ"),
...)
if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
# both ampicillin and amoxicillin are missing
generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
return(rep(NA, nrow(x)))
}
ESBLs <- rep(NA, nrow(x))
# first make all eligible cases FALSE
ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
& x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
)] <- FALSE
# now make the positives cases TRUE
ESBLs[which(!is.na(ESBLs)
& x[, get_ab_col(cols_ab, "AMX")] == "R"
& x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
ESBLs
}
is_3MRGN <- function(x, ...) {
}
is_4MRGN <- function(x, ...) {
}
# is_ESBL <- function(x, col_mo = NULL, ...) {
# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
# cols_ab <- get_column_abx(tbl = x,
# soft_dependencies = c("AMX", "AMP"),
# hard_dependencies = c("CAZ"),
# ...)
#
# if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
# # both ampicillin and amoxicillin are missing
# generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
# return(rep(NA, nrow(x)))
# }
#
# ESBLs <- rep(NA, nrow(x))
#
# # first make all eligible cases FALSE
# ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# )] <- FALSE
# # now make the positives cases TRUE
# ESBLs[which(!is.na(ESBLs)
# & x[, get_ab_col(cols_ab, "AMX")] == "R"
# & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
# ESBLs
#
# }
#
# is_3MRGN <- function(x, ...) {
#
# }
#
# is_4MRGN <- function(x, ...) {
#
# }
get_column_mo <- function(tbl, col_mo = NULL) {
# throws a blue note about which column will be used if guessed