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Replace RSI with SIR

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Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
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parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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man/add_custom_microorganisms.Rd
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@ -22,7 +22,7 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
There are two ways to automate this process:
\strong{Method 1:} Using the , which is the preferred method. To use this method:
\strong{Method 1:} Using the option \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
\enumerate{
\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file: