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(v1.5.0.9016) only_rsi_columns update, documentation

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dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
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18
R/eucast_rules.R
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@ -78,7 +78,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param ... column name of an antibiotic, see section *Antibiotics* below
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
#' @param administration route of administration, either `r vector_or(dosage$administration)`
#' @param only_rsi_columns a logical to indicate whether only antibiotic columns must be detected that were [transformed to class `<rsi>`]([rsi]) on beforehand. Defaults to `TRUE` if any column of `x` is of class `<rsi>`.
#' @param only_rsi_columns a logical to indicate whether only antibiotic columns must be detected that were [transformed to class `<rsi>`]([rsi]) on beforehand (defaults to `FALSE`)
#' @inheritParams first_isolate
#' @details
#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
@ -167,7 +167,7 @@ eucast_rules <- function(x,
version_breakpoints = 11.0,
version_expertrules = 3.2,
ampc_cephalosporin_resistance = NA,
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...) {
meet_criteria(x, allow_class = "data.frame")
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
@ -282,17 +282,7 @@ eucast_rules <- function(x,
info = info,
only_rsi_columns = only_rsi_columns,
...)
if (only_rsi_columns == TRUE && !paste0(sys.calls()[1], collapse = "") %like% "only_rsi_columns") {
cols_rsi_eligible <- colnames(x[, is.rsi.eligible(x), drop = FALSE])
if (length(cols_rsi_eligible) > 0) {
message_("These columns might be eligible for EUCAST rules, but are ignored since `only_rsi_columns` is `TRUE`: ",
vector_and(cols_rsi_eligible, quotes = TRUE, sort = FALSE),
as_note = TRUE, add_fn = font_red)
}
}
AMC <- cols_ab["AMC"]
AMK <- cols_ab["AMK"]
AMP <- cols_ab["AMP"]
@ -850,7 +840,7 @@ eucast_rules <- function(x,
# is new rule within group, print its name
cat(markup_italics_where_needed(word_wrap(rule_current,
width = getOption("width") - 30,
extra_indent = 4)))
extra_indent = 6)))
warned <- FALSE
}
}