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63 lines
3.0 KiB
R
63 lines
3.0 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://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.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 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}}.
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#' @param tbl a \code{data.frame} or \code{list}
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#' @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}.
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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(septic_patients)
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#'
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#' library(dplyr)
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#' septic_patients %>% availability()
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#'
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#' septic_patients %>%
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#' select_if(is.rsi) %>%
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#' availability()
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#'
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#' septic_patients %>%
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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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availability <- function(tbl) {
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x <- base::sapply(tbl, function(x) { 1 - base::sum(base::is.na(x)) / base::length(x) })
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n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
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IR <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), base::round(portion_IR(x, minimum = 0) * 100, 1), "NaN"))
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IR <- paste0(IR, "%")
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IR <- gsub("NaN%", "", IR)
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max_chars <- 50
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x_chars <- strrep("#", round(x, digits = 2) / (1 / max_chars))
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x_chars_empty <- strrep("-", max_chars - nchar(x_chars))
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# x_abnames <- character(length(x))
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# for (i in 1:length(x)) {
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# if (tbl %>% pull(i) %>% is.rsi()) {
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# x_abnames[i] <- atc_name(colnames(tbl)[i])
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# }
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# }
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data.frame(percent_IR = IR,
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count = n,
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percent = paste0(round(x * 100, 1), "%"),
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visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"))
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}
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