mirror of https://github.com/msberends/AMR.git
100 lines
4.2 KiB
R
100 lines
4.2 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 to This Package}
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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 to the \code{AMR} package, 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 automate this process:
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\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). 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 \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:
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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:} Save the microorganism directly to your \code{.Rprofile} file. An important downside is that this requires to load the \code{AMR} package at every start-up. 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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library(AMR)
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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 antimicrobials.
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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 only "Enterobacter asburiae":
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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(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(GENUS = "ESCHERICHIA / KLEBSIELLA",
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SPECIES = "SPECIES"))
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mo_name("ESCHERICHIA / KLEBSIELLA")
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mo_family("Escherichia/Klebsiella")
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add_custom_microorganisms(
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data.frame(genus = "Citrobacter", species = "freundii complex"))
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mo_name("C. freundii complex")
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mo_gramstain("C. freundii 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 to this package.
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}
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