mirror of https://github.com/msberends/AMR.git
64 lines
3.1 KiB
R
64 lines
3.1 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mo_source.R
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\name{mo_source}
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\alias{mo_source}
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\alias{set_mo_source}
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\alias{get_mo_source}
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\title{Use predefined reference data set}
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\usage{
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set_mo_source(path)
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get_mo_source()
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}
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\arguments{
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\item{path}{location of your reference file, see Details}
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}
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\description{
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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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}
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\details{
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The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new '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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\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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\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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Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file 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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}
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\section{Read more on our website!}{
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\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
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}
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\examples{
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\dontrun{
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# imagine this Excel file (mo codes looked up in `microorganisms` data set):
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# A B
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# 1 our code 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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# 1. We save it as 'home/me/ourcodes.xlsx'
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# 2. We use it for input:
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set_mo_source("C:\\path\\ourcodes.xlsx")
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#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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# 3. And use it in our functions:
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as.mo("lab_mo_ecoli")
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#> B_ESCHR_COL
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mo_genus("lab_mo_kpneumoniae")
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#> "Klebsiella"
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# 4. It will look for changes itself:
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# (add new row to the Excel file and save it)
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mo_genus("lab_mo_kpneumoniae")
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#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#> "Klebsiella"
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}
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}
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