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AMR/R/mo_source.R

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# ==================================================================== #
# 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.gitlab.io/AMR. #
# ==================================================================== #
#' Use predefined reference data set
#'
#' @description These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
#'
#' This is \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package.
#' @param path location of your reference file, see Details
#' @rdname mo_source
#' @name mo_source
#' @aliases set_mo_source get_mo_source
#' @details The reference file can be a text file seperated 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 need to have the \code{readxl} package installed.
#'
#' \code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
#'
#' \code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
#'
#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
#' @section How it works:
#' 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:
#' \preformatted{
#' | A | B |
#' --|--------------------|-------------|
#' 1 | Organisation XYZ | mo |
#' 2 | lab_mo_ecoli | B_ESCHR_COL |
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
#' 4 | | |
#' }
#'
#' We save it as \code{'home/me/ourcodes.xlsx'}. Now we have to set it as a source:
#' \preformatted{
#' set_mo_source("home/me/ourcodes.xlsx")
#' # Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' }
#'
#' It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.
#'
#' And now we can use it in our functions:
#' \preformatted{
#' as.mo("lab_mo_ecoli")
#' [1] B_ESCHR_COL
#'
#' mo_genus("lab_mo_kpneumoniae")
#' [1] "Klebsiella"
#'
#' # other input values still work too
#' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
#' [1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
#' }
#'
#' If we edit the Excel file to, let's say, this:
#' \preformatted{
#' | A | B |
#' --|--------------------|-------------|
#' 1 | Organisation XYZ | mo |
#' 2 | lab_mo_ecoli | B_ESCHR_COL |
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
#' 4 | lab_Staph_aureus | B_STPHY_AUR |
#' 5 | | |
#' }
#'
#' ...any new usage of an MO function in this package will update your data:
#' \preformatted{
#' as.mo("lab_mo_ecoli")
#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' [1] B_ESCHR_COL
#'
#' mo_genus("lab_Staph_aureus")
#' [1] "Staphylococcus"
#' }
#'
#' To remove the reference completely, just use any of these:
#' \preformatted{
#' set_mo_source("")
#' set_mo_source(NULL)
#' # Removed mo_source file '~/.mo_source.rds'.
#' }
#' @importFrom dplyr select everything
#' @export
#' @inheritSection AMR Read more on our website!
set_mo_source <- function(path) {
file_location <- path.expand('~/mo_source.rds')
if (!is.character(path) | length(path) > 1) {
stop("`path` must be a character of length 1.")
}
if (path %in% c(NULL, "")) {
options(mo_source = NULL)
options(mo_source_timestamp = NULL)
if (file.exists(file_location)) {
unlink(file_location)
message("Removed mo_source file '", file_location, "'.")
}
return(invisible())
}
if (!file.exists(path)) {
stop("File not found: ", path)
}
if (path %like% '[.]rds$') {
df <- readRDS(path)
} else if (path %like% '[.]xlsx?$') {
# is Excel file (old or new)
if (!"readxl" %in% utils::installed.packages()) {
stop("Install the 'readxl' package first.")
}
df <- readxl::read_excel(path)
} else if (path %like% '[.]tsv$') {
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
} else {
# try comma first
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!mo_source_isvalid(df)) {
# try tab
try(
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
silent = TRUE)
}
if (!mo_source_isvalid(df)) {
# try pipe
try(
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
silent = TRUE)
}
}
if (!mo_source_isvalid(df)) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
df <- df %>% filter(!is.na(mo))
# keep only first two columns, second must be mo
if (colnames(df)[1] == "mo") {
df <- df[, c(2, 1)]
} else {
df <- df[, c(1, 2)]
}
df <- as.data.frame(df, stringAsFactors = FALSE)
# success
if (file.exists(file_location)) {
action <- "Updated"
} else {
action <- "Created"
}
saveRDS(df, file_location)
options(mo_source = path)
options(mo_source_timestamp = as.character(file.info(path)$mtime))
message(action, " mo_source file '", file_location, "' from '", path, "'.")
}
#' @rdname mo_source
#' @export
get_mo_source <- function() {
if (is.null(getOption("mo_source", NULL))) {
NULL
} else {
old_time <- as.POSIXct(getOption("mo_source_timestamp"))
new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
if (is.na(new_time)) {
# source file was deleted, remove reference too
set_mo_source("")
return(NULL)
}
if (new_time != old_time) {
# set updated source
set_mo_source(getOption("mo_source"))
}
file_location <- path.expand('~/mo_source.rds')
readRDS(file_location)
}
}
mo_source_isvalid <- function(x) {
if (deparse(substitute(x)) == "get_mo_source()") {
return(TRUE)
}
if (identical(x, get_mo_source())) {
return(TRUE)
}
if (is.null(x)) {
return(TRUE)
}
if (!is.data.frame(x)) {
return(FALSE)
}
if (!"mo" %in% colnames(x)) {
return(FALSE)
}
all(x$mo %in% c("", AMR::microorganisms$mo))
}
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