mirror of https://github.com/msberends/AMR.git
309 lines
13 KiB
R
309 lines
13 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) 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) 2018-2020 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 analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' User-defined reference data set for microorganisms
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#'
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#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
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#'
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#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
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#' @inheritSection lifecycle Stable lifecycle
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#' @param path location of your reference file, see Details. Can be `""`, `NULL` or `FALSE` to delete the reference file.
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#' @param destination destination of the compressed data file, default to the user's home directory.
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#' @rdname mo_source
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#' @name mo_source
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#' @aliases set_mo_source get_mo_source
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#' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
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#'
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#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` parameter and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds)`.
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#'
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#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an attribute to the compressed data file.
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#'
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#' The function [get_mo_source()] will return the data set by reading `"mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the location and timestamp of the original file), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
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#'
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#' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file created with [set_mo_source()] will then have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (millionths of a second).
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#'
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#' @section How to setup:
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#'
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#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
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#'
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#' ```
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#' | A | B |
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#' --|--------------------|--------------|
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#' 1 | Organisation XYZ | mo |
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#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
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#' 4 | | |
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#' ```
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#'
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#' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
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#'
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#' ```
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#' set_mo_source("home/me/ourcodes.xlsx")
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#' #> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
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#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
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#' #> "Organisation XYZ" and "mo"
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#' ```
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#'
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#' It has now created a file `"~/mo_source.rds"` with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
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#'
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#' And now we can use it in our functions:
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#'
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' #> Class <mo>
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#' #> [1] B_ESCHR_COLI
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' #> [1] "Klebsiella"
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#'
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#' # other input values still work too
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#' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
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#' #> NOTE: Translation to one microorganism was guessed with uncertainty.
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#' #> Use mo_uncertainties() to review it.
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#' #> Class <mo>
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#' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
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#' ```
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#'
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#' If we edit the Excel file by, let's say, adding row 4 like this:
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#'
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#' ```
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#' | A | B |
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#' --|--------------------|--------------|
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#' 1 | Organisation XYZ | mo |
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#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
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#' 4 | lab_Staph_aureus | B_STPHY_AURS |
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#' 5 | | |
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#' ```
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#'
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#' ...any new usage of an MO function in this package will update your data file:
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#'
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
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#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
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#' #> "Organisation XYZ" and "mo"
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#' #> Class <mo>
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#' #> [1] B_ESCHR_COLI
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#'
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#' mo_genus("lab_Staph_aureus")
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#' #> [1] "Staphylococcus"
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#' ```
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#'
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#' To delete the reference data file, just use `""`, `NULL` or `FALSE` as input for [set_mo_source()]:
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#'
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#' ```
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#' set_mo_source(NULL)
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#' #> Removed mo_source file '/Users/me/mo_source.rds'
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#' ```
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#'
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#' If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of [as.mo()].
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#' @export
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#' @inheritSection AMR Read more on our website!
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set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
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meet_criteria(path, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(destination, allow_class = "character", has_length = 1)
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stop_ifnot(destination %like% "[.]rds$", "the `destination` must be a file location with file extension .rds")
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mo_source_destination <- path.expand(destination)
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stop_ifnot(interactive(), "This function can only be used in interactive mode, since it must ask for the user's permission to write a file to their home folder.")
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if (is.null(path) || path %in% c(FALSE, "")) {
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mo_env$mo_source <- NULL
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if (file.exists(mo_source_destination)) {
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unlink(mo_source_destination)
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message_("Removed mo_source file '", font_bold(mo_source_destination), "'",
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add_fn = font_red,
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as_note = FALSE)
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}
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return(invisible())
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}
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stop_ifnot(file.exists(path), "file not found: ", path)
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if (path %like% "[.]rds$") {
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df <- readRDS(path)
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} else if (path %like% "[.]xlsx?$") {
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# is Excel file (old or new)
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read_excel <- import_fn("read_excel", "readxl")
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df <- read_excel(path)
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} else if (path %like% "[.]tsv$") {
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df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
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} else {
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# try comma first
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try(
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df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
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silent = TRUE)
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if (!mo_source_isvalid(df, stop_on_error = FALSE)) {
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# try tab
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try(
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df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
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silent = TRUE)
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}
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if (!mo_source_isvalid(df, stop_on_error = FALSE)) {
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# try pipe
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try(
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df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
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silent = TRUE)
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}
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}
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# check integrity
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mo_source_isvalid(df)
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df <- subset(df, !is.na(mo))
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# keep only first two columns, second must be mo
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if (colnames(df)[1] == "mo") {
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df <- df[, c(colnames(df)[2], "mo")]
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} else {
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df <- df[, c(colnames(df)[1], "mo")]
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}
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df <- as.data.frame(df, stringAsFactors = FALSE)
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df[, "mo"] <- set_clean_class(df[, "mo", drop = TRUE], c("mo", "character"))
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# success
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if (file.exists(mo_source_destination)) {
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action <- "Updated"
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} else {
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action <- "Created"
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# only ask when file is created, not when it is updated
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txt <- paste0(word_wrap(paste0("This will write create the new file '",
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mo_source_destination,
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"', for which your permission is needed.")),
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"\n\n",
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word_wrap("Do you agree that this file will be created?"))
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if ("rsasdtudioapi" %in% rownames(utils::installed.packages())) {
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showQuestion <- import_fn("showQuestion", "rstudioapi")
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q_continue <- showQuestion("Create new file in home directory", txt)
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} else {
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q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
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}
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if (q_continue %in% c(FALSE, 2)) {
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return(invisible())
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}
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}
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attr(df, "mo_source_location") <- path
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attr(df, "mo_source_timestamp") <- file.mtime(path)
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saveRDS(df, mo_source_destination)
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mo_env$mo_source <- df
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message_(action, " mo_source file '", font_bold(mo_source_destination),
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"' (", formatted_filesize(mo_source_destination),
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") from '", font_bold(path),
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"' (", formatted_filesize(path),
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'), columns "', colnames(df)[1], '" and "', colnames(df)[2], '"')
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}
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#' @rdname mo_source
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#' @export
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get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
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if (!file.exists(path.expand(destination))) {
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if (interactive()) {
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# source file might have been deleted, update reference
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set_mo_source("")
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}
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return(NULL)
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}
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if (is.null(mo_env$mo_source)) {
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mo_env$mo_source <- readRDS(path.expand(destination))
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}
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old_time <- attributes(mo_env$mo_source)$mo_source_timestamp
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new_time <- file.mtime(attributes(mo_env$mo_source)$mo_source_location)
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if (interactive() && !identical(old_time, new_time)) {
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# source file was updated, also update reference
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set_mo_source(attributes(mo_env$mo_source)$mo_source_location)
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}
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mo_env$mo_source
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}
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mo_source_isvalid <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
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check_dataset_integrity()
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if (paste(deparse(substitute(x)), collapse = "") == "get_mo_source()") {
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return(TRUE)
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}
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if (is.null(mo_env$mo_source) && (identical(x, get_mo_source()))) {
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return(TRUE)
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}
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if (is.null(x)) {
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if (stop_on_error == TRUE) {
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stop_(refer_to_name, " cannot be NULL", call = FALSE)
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} else {
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return(FALSE)
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}
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}
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if (!is.data.frame(x)) {
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if (stop_on_error == TRUE) {
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stop_(refer_to_name, " must be a data.frame", call = FALSE)
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} else {
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return(FALSE)
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}
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}
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if (!"mo" %in% colnames(x)) {
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if (stop_on_error == TRUE) {
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stop_(refer_to_name, " must contain a column 'mo'", call = FALSE)
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} else {
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return(FALSE)
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}
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}
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if (!all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)) {
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if (stop_on_error == TRUE) {
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invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old)), , drop = FALSE]
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if (nrow(invalid) > 1) {
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plural <- "s"
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} else {
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plural <- ""
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}
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stop_("Value", plural, " ", paste0("'", invalid[, 1, drop = TRUE], "'", collapse = ", "),
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" found in ", tolower(refer_to_name),
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", but with invalid microorganism code", plural, " ", paste0("'", invalid$mo, "'", collapse = ", "),
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call = FALSE)
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} else {
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return(FALSE)
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}
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}
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if (colnames(x)[1] != "mo" & nrow(x) > length(unique(x[, 1, drop = TRUE]))) {
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if (stop_on_error == TRUE) {
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stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[1], "'", call = FALSE)
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} else {
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return(FALSE)
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}
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}
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if (colnames(x)[2] != "mo" & nrow(x) > length(unique(x[, 2, drop = TRUE]))) {
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if (stop_on_error == TRUE) {
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stop_(refer_to_name, " contains duplicate values in column '", colnames(x)[2], "'", call = FALSE)
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} else {
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return(FALSE)
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}
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}
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return(TRUE)
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}
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