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133 lines
6.7 KiB
R
133 lines
6.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# 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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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Italicise Taxonomic Families, Genera, Species, Subspecies
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#'
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#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
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#' @inheritSection lifecycle Maturing Lifecycle
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#' @param string a [character] (vector)
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#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
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#' @details
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#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
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#'
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#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
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#'
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#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
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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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#' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
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#' italicise_taxonomy("An overview of S. aureus isolates")
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#'
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#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
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#'
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#' # since ggplot2 supports no markdown (yet), use
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#' # italicise_taxonomy() and the `ggtext` pkg for titles:
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#' \donttest{
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#' if (require("ggplot2") && require("ggtext")) {
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#' ggplot(example_isolates$AMC,
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#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
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#' theme(plot.title = ggtext::element_markdown())
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#' }
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#' }
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italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
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if (missing(type)) {
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type <- "markdown"
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}
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meet_criteria(string, allow_class = "character")
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
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if (type == "markdown") {
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before <- "*"
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after <- "*"
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} else if (type == "ansi") {
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if (!has_colour()) {
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return(string)
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}
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before <- "\033[3m"
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after <- "\033[23m"
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}
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vapply(FUN.VALUE = character(1),
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string,
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function(s) {
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s_split <- unlist(strsplit(s, " "))
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search_strings <- gsub("[^a-zA-Z-]", "", s_split)
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ind_species <- search_strings != "" &
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search_strings %in% MO_lookup[which(MO_lookup$rank %in% c("family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp.")),
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"species",
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drop = TRUE]
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ind_fullname <- search_strings != "" &
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search_strings %in% c(MO_lookup[which(MO_lookup$rank %in% c("family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp.")),
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"fullname",
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drop = TRUE],
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MO_lookup[which(MO_lookup$rank %in% c("family",
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"genus",
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"species",
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"subspecies",
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"infraspecies",
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"subsp.")),
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"subspecies",
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drop = TRUE])
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# also support E. coli, add "E." to indices
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has_previous_genera_abbr <- s_split[which(ind_species) - 1] %like_case% "^[A-Z][.]?$"
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ind_species <- c(which(ind_species), which(ind_species)[has_previous_genera_abbr] - 1)
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ind <- c(ind_species, which(ind_fullname))
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s_split[ind] <- paste0(before, s_split[ind], after)
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s_paste <- paste(s_split, collapse = " ")
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# clean up a bit
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s_paste <- gsub(paste0(after, " ", before), " ", s_paste, fixed = TRUE)
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s_paste
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},
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USE.NAMES = FALSE)
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}
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#' @rdname italicise_taxonomy
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#' @export
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italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
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if (missing(type)) {
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type <- "markdown"
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}
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italicise_taxonomy(string = string, type = type)
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}
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