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Fix for adding MO's

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dr. M.S. (Matthijs) Berends
2023-01-14 17:10:10 +01:00
parent 33f269e2f4
commit ca79068604
13 changed files with 147 additions and 86 deletions
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19
man/add_custom_microorganisms.Rd
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@ -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{