# ==================================================================== # # 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! #' @export #' @examples #' availability(septic_patients) #' #' library(dplyr) #' septic_patients %>% availability() #' #' septic_patients %>% #' select_if(is.rsi) %>% #' availability() #' #' septic_patients %>% #' 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)] <- percent(R[!is.na(R)], round = 1, force_zero = TRUE) 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 = percent(x, round = 1, force_zero = TRUE), 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 } }