is.rsi.eligible update

2025-07-12 04:21:49 +02:00 · 2019-02-04 12:24:07 +01:00
parent cd07d65734
commit 587e00b7be
25 changed files with 1115 additions and 491 deletions
--- a/R/availability.R
+++ b/R/availability.R
@ -0,0 +1,61 @@
+# ==================================================================== #
+# 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.gitab.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 antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
+#' @param tbl a \code{data.frame} or \code{list}
+#' @return \code{data.frame} with column names of \code{tbl} as row names and columns: \code{percent_IR}, \code{count}, \code{percent}, \code{visual_availability}.
+#' @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) {
+  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), base::round(portion_IR(x, minimum = 0) * 100, 1), "NaN"))
+  IR <- paste0(IR, "%")
+  IR <- gsub("NaN%", "", IR)
+  max_chars <- 50
+  x_chars <- strrep("#", round(x, digits = 2) / (1 / max_chars))
+  x_chars_empty <- strrep("-", max_chars - nchar(x_chars))
+  # x_abnames <- character(length(x))
+  # for (i in 1:length(x)) {
+  #   if (tbl %>% pull(i) %>% is.rsi()) {
+  #     x_abnames[i] <- atc_name(colnames(tbl)[i])
+  #   }
+  # }
+  data.frame(percent_IR = IR,
+             count = n,
+             percent = paste0(round(x * 100, 1), "%"),
+             visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"))
+}