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cfta streptococci, codecov.yml

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dr. M.S. (Matthijs) Berends
2019-04-09 14:59:17 +02:00
parent cffb7787d8
commit 461eec9bac
18 changed files with 203 additions and 114 deletions
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9
R/rsi.R
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@ -25,7 +25,10 @@
#' @rdname as.rsi
#' @param x vector
#' @param threshold maximum fraction of \code{x} that is allowed to fail transformation, see Examples
#' @details The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
#' @details
#' \strong{NOTE:} This function does not translate MIC values to RSI values. If more than 50\% of the input resembles MIC values, it will warn about this.\cr You can use \code{\link{eucast_rules}} to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'
#' The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
#' @return Ordered factor with new class \code{rsi}
#' @keywords rsi
#' @export
@ -64,7 +67,7 @@ as.rsi <- function(x) {
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c('rsi', 'ordered', 'factor'))
} else {
if (mic_like(x) > 0.5) {
if (input_resembles_mic(x) > 0.5) {
warning("`as.rsi` is intended to clean antimicrobial interpretations - not to interpret MIC values.", call. = FALSE)
}
@ -109,7 +112,7 @@ as.rsi <- function(x) {
}
}
mic_like <- function(x) {
input_resembles_mic <- function(x) {
mic <- x %>%
gsub("[^0-9.,]+", "", .) %>%
unique()