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114 lines
4.6 KiB
R
114 lines
4.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/custom_microorganisms.R
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\name{add_custom_microorganisms}
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\alias{add_custom_microorganisms}
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\alias{clear_custom_microorganisms}
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\title{Add Custom Microorganisms}
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\usage{
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add_custom_microorganisms(x)
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clear_custom_microorganisms()
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}
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\arguments{
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\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing column "genus" (case-insensitive)}
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}
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\description{
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With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
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}
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\details{
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This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}.
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\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.
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There are two ways to circumvent this and automate the process of adding microorganisms:
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\strong{Method 1:} Using the package option \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
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\enumerate{
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\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.
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\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:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
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options(AMR_custom_mo = "~/my_custom_mo.rds")
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}\if{html}{\out{</div>}}
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Upon package load, this file will be loaded and run through the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function.
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}
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\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:
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\enumerate{
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\item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}.
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\item Add a text like below and save the file:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
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AMR::add_custom_microorganisms(
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data.frame(genus = "Enterobacter",
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species = "asburiae/cloacae")
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)
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}\if{html}{\out{</div>}}
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}
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Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to clear the previously added microorganisms.
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}
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\examples{
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\donttest{
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# a combination of species is not formal taxonomy, so
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# this will result in "Enterobacter cloacae cloacae",
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# since it resembles the input best:
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mo_name("Enterobacter asburiae/cloacae")
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# now add a custom entry - it will be considered by as.mo() and
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# all mo_*() functions
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add_custom_microorganisms(
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data.frame(
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genus = "Enterobacter",
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species = "asburiae/cloacae"
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)
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)
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# E. asburiae/cloacae is now a new microorganism:
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mo_name("Enterobacter asburiae/cloacae")
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# its code:
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as.mo("Enterobacter asburiae/cloacae")
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# all internal algorithms will work as well:
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mo_name("Ent asburia cloacae")
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# and even the taxonomy was added based on the genus!
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mo_family("E. asburiae/cloacae")
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mo_gramstain("Enterobacter asburiae/cloacae")
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mo_info("Enterobacter asburiae/cloacae")
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# the function tries to be forgiving:
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add_custom_microorganisms(
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data.frame(
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GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
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SPECIES = "SPECIES"
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)
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)
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mo_name("BACTEROIDES / PARABACTEROIDES")
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mo_rank("BACTEROIDES / PARABACTEROIDES")
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# taxonomy still works, even though a slashline genus was given as input:
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mo_family("Bacteroides/Parabacteroides")
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# for groups and complexes, set them as species or subspecies:
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add_custom_microorganisms(
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data.frame(
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genus = "Citrobacter",
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species = c("freundii", "braakii complex"),
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subspecies = c("complex", "")
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)
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)
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mo_name(c("C. freundii complex", "C. braakii complex"))
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mo_species(c("C. freundii complex", "C. braakii complex"))
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mo_gramstain(c("C. freundii complex", "C. braakii complex"))
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}
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}
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\seealso{
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\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials.
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}
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