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328 lines
14 KiB
R
Executable File
328 lines
14 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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#' Add Custom Microorganisms
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#'
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#' With [add_custom_microorganisms()] you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
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#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing column "genus" (case-insensitive)
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#' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
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#'
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#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
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#'
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#' There are two ways to circumvent this and automate the process of adding microorganisms:
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#'
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#' **Method 1:** Using the package option [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
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#'
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#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
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#'
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#' 2. Set the file location to the package option [`AMR_custom_mo`][AMR-options]: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
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#'
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#' ```r
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#' # Add custom microorganism codes:
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#' options(AMR_custom_mo = "~/my_custom_mo.rds")
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#' ```
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#'
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#' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function.
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#'
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#' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. Note that the definitions will be stored in a user-specific \R file, which is a suboptimal workflow. To use this method:
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#'
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#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
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#'
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#' 2. Add a text like below and save the file:
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#'
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#' ```r
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#' # Add custom antibiotic drug codes:
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#' AMR::add_custom_microorganisms(
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#' data.frame(genus = "Enterobacter",
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#' species = "asburiae/cloacae")
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#' )
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#' ```
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#'
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#' Use [clear_custom_microorganisms()] to clear the previously added microorganisms.
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#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials.
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#' @rdname add_custom_microorganisms
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#' @export
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#' @examples
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#' \donttest{
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#' # a combination of species is not formal taxonomy, so
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#' # this will result in "Enterobacter cloacae cloacae",
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#' # since it resembles the input best:
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#' mo_name("Enterobacter asburiae/cloacae")
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#'
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#' # now add a custom entry - it will be considered by as.mo() and
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#' # all mo_*() functions
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#' add_custom_microorganisms(
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#' data.frame(
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#' genus = "Enterobacter",
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#' species = "asburiae/cloacae"
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#' )
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#' )
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#'
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#' # E. asburiae/cloacae is now a new microorganism:
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#' mo_name("Enterobacter asburiae/cloacae")
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#'
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#' # its code:
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#' as.mo("Enterobacter asburiae/cloacae")
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#'
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#' # all internal algorithms will work as well:
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#' mo_name("Ent asburia cloacae")
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#'
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#' # and even the taxonomy was added based on the genus!
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#' mo_family("E. asburiae/cloacae")
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#' mo_gramstain("Enterobacter asburiae/cloacae")
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#'
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#' mo_info("Enterobacter asburiae/cloacae")
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#'
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#'
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#' # the function tries to be forgiving:
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#' add_custom_microorganisms(
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#' data.frame(
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#' GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
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#' SPECIES = "SPECIES"
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#' )
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#' )
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#' mo_name("BACTEROIDES / PARABACTEROIDES")
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#' mo_rank("BACTEROIDES / PARABACTEROIDES")
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#'
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#' # taxonomy still works, even though a slashline genus was given as input:
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#' mo_family("Bacteroides/Parabacteroides")
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#'
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#'
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#' # for groups and complexes, set them as species or subspecies:
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#' add_custom_microorganisms(
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#' data.frame(
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#' genus = "Citrobacter",
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#' species = c("freundii", "braakii complex"),
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#' subspecies = c("complex", "")
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#' )
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#' )
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#' mo_name(c("C. freundii complex", "C. braakii complex"))
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#' mo_species(c("C. freundii complex", "C. braakii complex"))
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#' mo_gramstain(c("C. freundii complex", "C. braakii complex"))
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#' }
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add_custom_microorganisms <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
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add_MO_lookup_to_AMR_env()
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# remove any extra class/type, such as grouped tbl, or data.table:
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- tolower(colnames(x))
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# rename 'name' to 'fullname' if it's in the data set
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if ("name" %in% colnames(x) && !"fullname" %in% colnames(x)) {
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colnames(x)[colnames(x) == "name"] <- "fullname"
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}
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# keep only columns available in the microorganisms data set
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x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE]
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# clean the input ----
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for (col in c("genus", "species", "subspecies")) {
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if (!col %in% colnames(x)) {
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x[, col] <- ""
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}
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if (is.factor(x[, col, drop = TRUE])) {
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x[, col] <- as.character(x[, col, drop = TRUE])
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}
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col_ <- x[, col, drop = TRUE]
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col_ <- tolower(col_)
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col_ <- gsub("slashline", "", col_, fixed = TRUE)
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col_ <- trimws2(col_)
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col_[col_ %like% "(sub)?species"] <- ""
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col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
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# groups are in our taxonomic table with a capital G
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col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
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col_[is.na(col_)] <- ""
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if (col == "genus") {
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substr(col_, 1, 1) <- toupper(substr(col_, 1, 1))
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col_ <- gsub("/([a-z])", "/\\U\\1", col_, perl = TRUE)
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stop_if(any(col_ == ""), "the 'genus' column cannot be empty")
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stop_if(any(col_ %like% " "), "the 'genus' column must not contain spaces")
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}
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x[, col] <- col_
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}
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# if subspecies is a group or complex, add it to the species and empty the subspecies
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x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(
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x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
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x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))]
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)
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x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))] <- ""
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if ("rank" %in% colnames(x)) {
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stop_ifnot(
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all(x$rank %in% AMR_env$MO_lookup$rank),
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"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank)
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)
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} else {
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x$rank <- ifelse(x$subspecies != "", "subspecies",
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ifelse(x$species != "", "species",
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ifelse(x$genus != "", "genus",
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stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
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call. = FALSE
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)
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)
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)
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)
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}
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x$source <- "Added by user"
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if (!"fullname" %in% colnames(x)) {
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x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies))
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}
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if (!"kingdom" %in% colnames(x)) x$kingdom <- ""
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if (!"phylum" %in% colnames(x)) x$phylum <- ""
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if (!"class" %in% colnames(x)) x$class <- ""
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if (!"order" %in% colnames(x)) x$order <- ""
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if (!"family" %in% colnames(x)) x$family <- ""
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x$kingdom[is.na(x$kingdom)] <- ""
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x$phylum[is.na(x$phylum)] <- ""
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x$class[is.na(x$class)] <- ""
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x$order[is.na(x$order)] <- ""
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x$family[is.na(x$family)] <- ""
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for (col in colnames(x)) {
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if (is.factor(x[, col, drop = TRUE])) {
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x[, col] <- as.character(x[, col, drop = TRUE])
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}
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if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
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x[, col] <- as.list(x[, col, drop = TRUE])
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}
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}
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# fill in taxonomy based on genus
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genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE)
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x$kingdom[which(x$kingdom == "" & genus_to_check != "")] <- AMR_env$MO_lookup$kingdom[match(genus_to_check[which(x$kingdom == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$phylum[which(x$phylum == "" & genus_to_check != "")] <- AMR_env$MO_lookup$phylum[match(genus_to_check[which(x$phylum == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$class[which(x$class == "" & genus_to_check != "")] <- AMR_env$MO_lookup$class[match(genus_to_check[which(x$class == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$order[which(x$order == "" & genus_to_check != "")] <- AMR_env$MO_lookup$order[match(genus_to_check[which(x$order == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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# fill in other columns that are used in internal algorithms
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x$prevalence <- NA_real_
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x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$prevalence[is.na(x$prevalence)] <- 1.25
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x$status <- "accepted"
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x$ref <- paste("Self-added,", format(Sys.Date(), "%Y"))
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x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
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# complete missing kingdom index, so mo_matching_score() will not return NA
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x$kingdom_index[is.na(x$kingdom_index)] <- 1
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x$fullname_lower <- tolower(x$fullname)
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x$full_first <- substr(x$fullname_lower, 1, 1)
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x$species_first <- tolower(substr(x$species, 1, 1))
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x$subspecies_first <- tolower(substr(x$subspecies, 1, 1))
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if (!"mo" %in% colnames(x)) {
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# create the mo code
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x$mo <- NA_character_
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}
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x$mo <- trimws2(as.character(x$mo))
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x$mo[x$mo == ""] <- NA_character_
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current <- sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE)
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x$mo[is.na(x$mo)] <- paste0(
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"CUSTOM",
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seq.int(from = current + 1, to = current + nrow(x), by = 1),
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"_",
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trimws(
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paste(abbreviate_mo(x$genus, 5),
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abbreviate_mo(x$species, 4, hyphen_as_space = TRUE),
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abbreviate_mo(x$subspecies, 4, hyphen_as_space = TRUE),
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sep = "_"),
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whitespace = "_"))
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stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
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# add to package ----
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AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
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class(AMR_env$MO_lookup$mo) <- "character"
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new_df <- AMR_env$MO_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
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rownames(new_df) <- NULL
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list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
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for (l in which(list_cols)) {
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# prevent binding NULLs in lists, replace with NA
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new_df[, l] <- as.list(NA_character_)
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}
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for (col in colnames(x)) {
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# assign new values
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new_df[, col] <- x[, col, drop = TRUE]
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}
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# clear previous coercions
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suppressMessages(mo_reset_session())
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AMR_env$MO_lookup <- unique(rbind_AMR(AMR_env$MO_lookup, new_df))
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class(AMR_env$MO_lookup$mo) <- c("mo", "character")
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if (nrow(x) <= 3) {
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message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.")
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} else {
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message_("Added ", nr2char(nrow(x)), " records to the internal `microorganisms` data set.")
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}
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}
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#' @rdname add_custom_microorganisms
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#' @export
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clear_custom_microorganisms <- function() {
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n <- nrow(AMR_env$MO_lookup)
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# reset
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AMR_env$MO_lookup <- NULL
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add_MO_lookup_to_AMR_env()
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# clear previous coercions
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suppressMessages(mo_reset_session())
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n2 <- nrow(AMR_env$MO_lookup)
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AMR_env$custom_mo_codes <- character(0)
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AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
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AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE]
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message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.")
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}
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abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE, ...) {
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if (hyphen_as_space == TRUE) {
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x <- gsub("-", " ", x, fixed = TRUE)
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}
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# keep a starting Latin ae
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suppressWarnings(
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gsub("(\u00C6|\u00E6)+",
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"AE",
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toupper(
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paste0(prefix,
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abbreviate(
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gsub("^ae",
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"\u00E6\u00E6",
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x,
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ignore.case = TRUE),
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minlength = minlength,
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use.classes = TRUE,
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method = "both.sides",
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...
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))))
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)
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}
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