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(v1.3.0.9026) eucast expert rules 3.2

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-24 00:30:11 +02:00
parent a1411ddafc
commit c19095a3d5
107 changed files with 48638 additions and 3953 deletions
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19
R/mdro.R
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@ -141,7 +141,7 @@ mdro <- function(x,
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
}
if (is.null(col_mo) & guideline$code == "tb") {
message(font_blue("NOTE: No column found as input for `col_mo`,",
@ -303,7 +303,9 @@ mdro <- function(x,
"TCY",
"DOX",
"MNO"),
verbose = verbose, ...)
verbose = verbose,
info = info,
...)
} else if (guideline$code == "tb") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("CAP",
@ -314,7 +316,9 @@ mdro <- function(x,
"RIF",
"RIB",
"RFP"),
verbose = verbose, ...)
info = info,
verbose = verbose,
...)
} else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("PIP",
@ -323,9 +327,14 @@ mdro <- function(x,
"IPM",
"MEM",
"CIP"),
verbose = verbose, ...)
verbose = verbose,
info = info,
...)
} else {
cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
cols_ab <- get_column_abx(x = x,
verbose = verbose,
info = info,
...)
}
AMC <- cols_ab["AMC"]