# ==================================================================== # # 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)) }