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(v0.8.0.9027) adding susceptibility() and resistance()

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dr. M.S. (Matthijs) Berends
2019-11-10 12:16:56 +01:00
parent 228a4245cb
commit 59ededa8dc
85 changed files with 1526 additions and 932 deletions
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6
R/availability.R
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@ -21,10 +21,10 @@
#' Check availability of columns
#'
#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. \code{\link{portion_R}}.
#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. \code{\link{resistance}}.
#' @param tbl a \code{data.frame} or \code{list}
#' @param width number of characters to present the visual availability, defaults to filling the width of the console
#' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
#' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{resistance}}.
#' @return \code{data.frame} with column names of \code{tbl} as row names
#' @inheritSection AMR Read more on our website!
#' @importFrom cleaner percentage
@ -48,7 +48,7 @@ availability <- function(tbl, width = NULL) {
1 - base::sum(base::is.na(x)) / base::length(x)
})
n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_R(x, minimum = 0), NA))
R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), resistance(x, minimum = 0), NA))
R_print <- character(length(R))
R_print[!is.na(R)] <- percentage(R[!is.na(R)])
R_print[is.na(R)] <- ""