mirror of
https://github.com/msberends/AMR.git
synced 2025-07-11 07:01:57 +02:00
Fix for adding MO's
This commit is contained in:
@ -1,5 +1,5 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/add_custom_microorganisms.R
|
||||
% Please edit documentation in R/custom_microorganisms.R
|
||||
\name{add_custom_microorganisms}
|
||||
\alias{add_custom_microorganisms}
|
||||
\alias{clear_custom_microorganisms}
|
||||
@ -10,7 +10,7 @@ add_custom_microorganisms(x)
|
||||
clear_custom_microorganisms()
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
|
||||
\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing column "genus" (case-insensitive)}
|
||||
}
|
||||
\description{
|
||||
With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms to the \code{AMR} package, such the non-taxonomic outcome of laboratory analysis.
|
||||
@ -24,7 +24,7 @@ There are two ways to automate this process:
|
||||
|
||||
\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
|
||||
\enumerate{
|
||||
\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "genus" and "species") 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 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 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:
|
||||
@ -79,6 +79,19 @@ mo_family("E. asburiae/cloacae")
|
||||
mo_gramstain("Enterobacter asburiae/cloacae")
|
||||
|
||||
mo_info("Enterobacter asburiae/cloacae")
|
||||
|
||||
|
||||
# the function tries to be forgiving:
|
||||
add_custom_microorganisms(
|
||||
data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
|
||||
SPECIES = "SPECIES"))
|
||||
mo_name("ESCHERICHIA / KLEBSIELLA")
|
||||
mo_family("Escherichia/Klebsiella")
|
||||
|
||||
add_custom_microorganisms(
|
||||
data.frame(genus = "Citrobacter", species = "freundii complex"))
|
||||
mo_name("C. freundii complex")
|
||||
mo_gramstain("C. freundii complex")
|
||||
}
|
||||
}
|
||||
\seealso{
|
||||
|
Reference in New Issue
Block a user