mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
99 lines
4.2 KiB
R
99 lines
4.2 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' Check Availability of Columns
|
|
#'
|
|
#' Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. [susceptibility()] and [resistance()].
|
|
#' @param tbl a [data.frame] or [list]
|
|
#' @param width number of characters to present the visual availability, defaults to filling the width of the console
|
|
#' @details The function returns a [data.frame] with columns `"resistant"` and `"visual_resistance"`. The values in that columns are calculated with [resistance()].
|
|
#' @return [data.frame] with column names of `tbl` as row names
|
|
#' @export
|
|
#' @examples
|
|
#' availability(example_isolates)
|
|
#' \donttest{
|
|
#' if (require("dplyr")) {
|
|
#' example_isolates %>%
|
|
#' filter(mo == as.mo("Escherichia coli")) %>%
|
|
#' select_if(is.rsi) %>%
|
|
#' availability()
|
|
#' }
|
|
#' }
|
|
availability <- function(tbl, width = NULL) {
|
|
meet_criteria(tbl, allow_class = "data.frame")
|
|
meet_criteria(width, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
|
|
|
|
tbl <- as.data.frame(tbl, stringsAsFactors = FALSE)
|
|
|
|
x <- vapply(FUN.VALUE = double(1), tbl, function(x) {
|
|
1 - sum(is.na(x)) / length(x)
|
|
})
|
|
n <- vapply(FUN.VALUE = double(1), tbl, function(x) length(x[!is.na(x)]))
|
|
R <- vapply(FUN.VALUE = double(1), tbl, function(x) ifelse(is.rsi(x), resistance(x, minimum = 0), NA_real_))
|
|
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,
|
|
stringsAsFactors = FALSE
|
|
)
|
|
if (length(R[is.na(R)]) == ncol(tbl)) {
|
|
df[, 1:3, drop = FALSE]
|
|
} else {
|
|
df
|
|
}
|
|
}
|