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check for 2.0

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dr. M.S. (Matthijs) Berends
2023-03-12 13:02:37 +01:00
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25 changed files with 127 additions and 134 deletions
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6
man/add_custom_microorganisms.Rd
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@ -20,7 +20,7 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
\strong{Important:} Due to how \R works, the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
There are two ways to automate this process:
There are two ways to circumvent this and automate the process of adding microorganisms:
\strong{Method 1:} Using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
\enumerate{
@ -34,7 +34,7 @@ options(AMR_custom_mo = "~/my_custom_mo.rds")
Upon package load, this file will be loaded and run through the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function.
}
\strong{Method 2:} Loading the microorganism directly from your \code{.Rprofile} file. An important downside is that this requires the \code{AMR} package to be installed or else this method will fail. To use this method:
\strong{Method 2:} Loading the microorganism directly from your \code{.Rprofile} file. Note that the definitions will be stored in a user-specific \R file, which is a suboptimal workflow. To use this method:
\enumerate{
\item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}.
\item Add a text like below and save the file:
@ -47,7 +47,7 @@ Upon package load, this file will be loaded and run through the \code{\link[=add
}\if{html}{\out{</div>}}
}
Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to clear the previously added antimicrobials.
Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to clear the previously added microorganisms.
}
\examples{
\donttest{