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(v0.8.0.9036) complete documentation rewrite
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#' Use predefined reference data set
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#'
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#' @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}}.
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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 \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package.
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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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#' @param path location of your reference file, see Details
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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 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.
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#' @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 `readxl` package installed.
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#'
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#' \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$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
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#' [set_mo_source()] will check the file for validity: it must be a [`data.frame`], must have a column named `"mo"` which contains values from [`microorganisms$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 export it to `"~/.mo_source.rds"`. This compressed data file will then be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location of the original file will be saved as option with `options(mo_source = path)`. Its timestamp will be saved with `options(mo_source_datetime = ...)`.
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#'
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#' \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.
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#' [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (the file defined with `path`), it will call [set_mo_source()] to update the data file automatically.
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#'
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#' 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).
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#' @section How it works:
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#' Reading an Excel file (`.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 [get_mo_source()] in only a couple of microseconds (a millionth of a second).
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#'
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#' ## How it works
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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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#' \preformatted{
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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_COL |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
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#' 4 | | |
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#' }
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#' ```
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#'
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#' We save it as \code{'home/me/ourcodes.xlsx'}. Now we have to set it as a source:
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#' \preformatted{
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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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#' set_mo_source("home/me/ourcodes.xlsx")
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#' # Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#' }
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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, but only the first column with foreign values and the 'mo' column will be kept.
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#' 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.
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#'
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#' And now we can use it in our functions:
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#' \preformatted{
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' [1] B_ESCHR_COL
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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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#' [1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
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#' }
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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 to, let's say, this:
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#' \preformatted{
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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_COL |
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#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
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#' 4 | lab_Staph_aureus | B_STPHY_AUR |
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#' 5 | | |
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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:
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#' \preformatted{
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#' ```
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#' as.mo("lab_mo_ecoli")
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#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#' [1] B_ESCHR_COL
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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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#'
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#' To remove the reference completely, just use any of these:
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#' \preformatted{
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#' ```
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#' set_mo_source("")
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#' set_mo_source(NULL)
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#' # Removed mo_source file '~/.mo_source.rds'.
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#' }
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#' ```
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#' @importFrom dplyr select everything
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#' @export
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#' @inheritSection AMR Read more on our website!
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