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(v2.1.1.9079) fix for uti in as.sir()

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dr. M.S. (Matthijs) Berends
2024-09-24 15:34:12 +02:00
parent 127892430d
commit 1ca40e8d67
32 changed files with 98 additions and 109 deletions
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4
man/add_custom_microorganisms.Rd
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@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
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:
\strong{Method 1:} Using the package 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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_mo}}: \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:
\item Set the file location to the package option \code{\link[=AMR-options]{AMR_custom_mo}}: \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:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
options(AMR_custom_mo = "~/my_custom_mo.rds")