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rlang dependency, new fungi
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@ -15,6 +15,8 @@ get_mo_source()
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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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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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}
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\details{
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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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@ -25,38 +27,66 @@ The reference file can be a text file seperated with commas (CSV) or tabs or pip
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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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}
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\section{How it works}{
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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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| 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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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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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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It has now created a file "~/.mo_source.rds" with the contents of our Excel file. It it an R specific format with great compression.
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And now we can use it in our functions:
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\preformatted{
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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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}
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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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...any new usage of an MO function in this package will update your data:
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\preformatted{
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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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# B_ESCHR_COL
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mo_genus("lab_Staph_aureus")
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# "Staphylococcus"
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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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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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\section{Read more on our website!}{
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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 comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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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("home/me/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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