mirror of https://github.com/msberends/AMR.git
93 lines
3.8 KiB
R
93 lines
3.8 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' 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}}.
|
|
#' @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!
|
|
# @importFrom clean percentage
|
|
#' @export
|
|
#' @examples
|
|
#' availability(example_isolates)
|
|
#'
|
|
#' library(dplyr)
|
|
#' example_isolates %>% availability()
|
|
#'
|
|
#' example_isolates %>%
|
|
#' select_if(is.rsi) %>%
|
|
#' availability()
|
|
#'
|
|
#' example_isolates %>%
|
|
#' filter(mo == as.mo("E. coli")) %>%
|
|
#' select_if(is.rsi) %>%
|
|
#' availability()
|
|
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)]))
|
|
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)] <- percentage(R[!is.na(R)])
|
|
R_print[is.na(R)] <- ""
|
|
|
|
if (is.null(width)) {
|
|
width <- options()$width -
|
|
(max(nchar(colnames(tbl))) +
|
|
# count col
|
|
8 +
|
|
# available % column
|
|
10 +
|
|
# resistant % column
|
|
10 +
|
|
# extra margin
|
|
5)
|
|
width <- width / 2
|
|
}
|
|
|
|
if (length(R[is.na(R)]) == ncol(tbl)) {
|
|
width <- width * 2 + 10
|
|
}
|
|
|
|
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))
|
|
|
|
df <- data.frame(count = n,
|
|
available = percentage(x),
|
|
visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"),
|
|
resistant = R_print,
|
|
visual_resistance = vis_resistance)
|
|
if (length(R[is.na(R)]) == ncol(tbl)) {
|
|
df[, 1:3]
|
|
} else {
|
|
df
|
|
}
|
|
}
|