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96 lines
3.9 KiB
R
96 lines
3.9 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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#' Check availability of columns
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#'
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#' 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()].
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#' @inheritSection lifecycle Stable lifecycle
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#' @param tbl a [`data.frame`] or [`list`]
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#' @param width number of characters to present the visual availability, defaults to filling the width of the console
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#' @details The function returns a [`data.frame`] with columns `"resistant"` and `"visual_resistance"`. The values in that columns are calculated with [resistance()].
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#' @return [`data.frame`] with column names of `tbl` as row names
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#' @inheritSection AMR Read more on our website!
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#' @export
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#' @examples
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#' availability(example_isolates)
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#'
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#' \dontrun{
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#' library(dplyr)
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#' example_isolates %>% availability()
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#'
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#' example_isolates %>%
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#' select_if(is.rsi) %>%
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#' availability()
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#'
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#' example_isolates %>%
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#' filter(mo == as.mo("E. coli")) %>%
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#' select_if(is.rsi) %>%
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#' availability()
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#' }
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availability <- function(tbl, width = NULL) {
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stop_ifnot(is.data.frame(tbl), "`tbl` must be a data.frame")
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x <- base::sapply(tbl, function(x) {
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1 - base::sum(base::is.na(x)) / base::length(x)
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})
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n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
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R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), resistance(x, minimum = 0), NA))
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R_print <- character(length(R))
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R_print[!is.na(R)] <- percentage(R[!is.na(R)])
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R_print[is.na(R)] <- ""
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if (is.null(width)) {
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width <- options()$width -
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(max(nchar(colnames(tbl))) +
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# count col
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8 +
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# available % column
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10 +
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# resistant % column
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10 +
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# extra margin
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5)
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width <- width / 2
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}
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if (length(R[is.na(R)]) == ncol(tbl)) {
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width <- width * 2 + 10
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}
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x_chars_R <- strrep("#", round(width * R, digits = 2))
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x_chars_SI <- strrep("-", width - nchar(x_chars_R))
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vis_resistance <- paste0("|", x_chars_R, x_chars_SI, "|")
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vis_resistance[is.na(R)] <- ""
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x_chars <- strrep("#", round(x, digits = 2) / (1 / width))
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x_chars_empty <- strrep("-", width - nchar(x_chars))
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df <- data.frame(count = n,
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available = percentage(x),
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visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"),
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resistant = R_print,
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visual_resistance = vis_resistance)
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if (length(R[is.na(R)]) == ncol(tbl)) {
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df[, 1:3]
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} else {
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df
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}
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}
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