mirror of https://github.com/msberends/AMR.git
113 lines
4.5 KiB
R
Executable File
113 lines
4.5 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/custom_microorganisms.R
|
|
\name{add_custom_microorganisms}
|
|
\alias{add_custom_microorganisms}
|
|
\alias{clear_custom_microorganisms}
|
|
\title{Add Custom Microorganisms}
|
|
\usage{
|
|
add_custom_microorganisms(x)
|
|
|
|
clear_custom_microorganisms()
|
|
}
|
|
\arguments{
|
|
\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, such the non-taxonomic outcome of laboratory analysis.
|
|
}
|
|
\details{
|
|
This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}.
|
|
|
|
\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:
|
|
|
|
\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 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")
|
|
}\if{html}{\out{</div>}}
|
|
|
|
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:
|
|
\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:
|
|
|
|
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
|
|
AMR::add_custom_microorganisms(
|
|
data.frame(genus = "Enterobacter",
|
|
species = "asburiae/cloacae")
|
|
)
|
|
}\if{html}{\out{</div>}}
|
|
}
|
|
|
|
Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to clear the previously added antimicrobials.
|
|
}
|
|
\examples{
|
|
\donttest{
|
|
# a combination of species is not formal taxonomy, so
|
|
# this will result in only "Enterobacter asburiae":
|
|
mo_name("Enterobacter asburiae/cloacae")
|
|
|
|
# now add a custom entry - it will be considered by as.mo() and
|
|
# all mo_*() functions
|
|
add_custom_microorganisms(
|
|
data.frame(
|
|
genus = "Enterobacter",
|
|
species = "asburiae/cloacae"
|
|
)
|
|
)
|
|
|
|
# E. asburiae/cloacae is now a new microorganism:
|
|
mo_name("Enterobacter asburiae/cloacae")
|
|
|
|
# its code:
|
|
as.mo("Enterobacter asburiae/cloacae")
|
|
|
|
# all internal algorithms will work as well:
|
|
mo_name("Ent asburia cloacae")
|
|
|
|
# and even the taxonomy was added based on the genus!
|
|
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 = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
|
|
SPECIES = "SPECIES"
|
|
)
|
|
)
|
|
mo_name("BACTEROIDES / PARABACTEROIDES")
|
|
mo_rank("BACTEROIDES / PARABACTEROIDES")
|
|
|
|
# taxonomy still works, although a slashline genus was given as input:
|
|
mo_family("Bacteroides/Parabacteroides")
|
|
|
|
|
|
# for groups and complexes, set them as species or subspecies:
|
|
add_custom_microorganisms(
|
|
data.frame(
|
|
genus = "Citrobacter",
|
|
species = c("freundii", "braakii complex"),
|
|
subspecies = c("complex", "")
|
|
)
|
|
)
|
|
mo_name(c("C. freundii complex", "C. braakii complex"))
|
|
mo_species(c("C. freundii complex", "C. braakii complex"))
|
|
mo_gramstain(c("C. freundii complex", "C. braakii complex"))
|
|
}
|
|
}
|
|
\seealso{
|
|
\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials.
|
|
}
|