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(v0.7.1.9059) bug_drug_combinations

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dr. M.S. (Matthijs) Berends
2019-08-25 22:53:22 +02:00
parent 7c069145ac
commit e46cb0399f
23 changed files with 1081 additions and 230 deletions
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25
R/availability.R
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@ -21,9 +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 antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
#' 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}}.
#' @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}}.
#' @return \code{data.frame} with column names of \code{tbl} as row names
#' @inheritSection AMR Read more on our website!
#' @export
@ -44,10 +45,10 @@
availability <- function(tbl, width = NULL) {
x <- base::sapply(tbl, function(x) { 1 - base::sum(base::is.na(x)) / base::length(x) })
n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
IR <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_IR(x, minimum = 0), NA))
IR_print <- character(length(IR))
IR_print[!is.na(IR)] <- percent(IR[!is.na(IR)], round = 1, force_zero = TRUE)
IR_print[is.na(IR)] <- ""
R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_R(x, minimum = 0), NA))
R_print <- character(length(R))
R_print[!is.na(R)] <- percent(R[!is.na(R)], round = 1, force_zero = TRUE)
R_print[is.na(R)] <- ""
if (is.null(width)) {
width <- options()$width -
@ -63,14 +64,14 @@ availability <- function(tbl, width = NULL) {
width <- width / 2
}
if (length(IR[is.na(IR)]) == ncol(tbl)) {
if (length(R[is.na(R)]) == ncol(tbl)) {
width <- width * 2 + 10
}
x_chars_IR <- strrep("#", round(width * IR, digits = 2))
x_chars_S <- strrep("-", width - nchar(x_chars_IR))
vis_resistance <- paste0("|", x_chars_IR, x_chars_S, "|")
vis_resistance[is.na(IR)] <- ""
x_chars_R <- strrep("#", round(width * R, digits = 2))
x_chars_SI <- strrep("-", width - nchar(x_chars_R))
vis_resistance <- paste0("|", x_chars_R, x_chars_SI, "|")
vis_resistance[is.na(R)] <- ""
x_chars <- strrep("#", round(x, digits = 2) / (1 / width))
x_chars_empty <- strrep("-", width - nchar(x_chars))
@ -78,9 +79,9 @@ availability <- function(tbl, width = NULL) {
df <- data.frame(count = n,
available = percent(x, round = 1, force_zero = TRUE),
visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"),
resistant = IR_print,
resistant = R_print,
visual_resistance = vis_resistance)
if (length(IR[is.na(IR)]) == ncol(tbl)) {
if (length(R[is.na(R)]) == ncol(tbl)) {
df[,1:3]
} else {
df