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105 lines
4.0 KiB
R
105 lines
4.0 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/custom_antimicrobials.R
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\name{add_custom_antimicrobials}
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\alias{add_custom_antimicrobials}
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\alias{clear_custom_antimicrobials}
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\title{Add Custom Antimicrobials}
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\usage{
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add_custom_antimicrobials(x)
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clear_custom_antimicrobials()
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}
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\arguments{
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\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
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}
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\description{
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug names and codes.
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}
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\details{
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\strong{Important:} Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials 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 antimicrobials:
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\strong{Method 1:} Using the package option \code{\link[=AMR-options]{AMR_custom_ab}}, 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{antibiotics} data set (containing at the very least columns "ab" and "name") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_ab.rds"}, or any remote location.
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\item Set the file location to the package option \code{\link[=AMR-options]{AMR_custom_ab}}: \code{options(AMR_custom_ab = "~/my_custom_ab.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 antimicrobial codes:
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options(AMR_custom_ab = "~/my_custom_ab.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_antimicrobials]{add_custom_antimicrobials()}} function.
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}
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\strong{Method 2:} Loading the antimicrobial additions 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_antimicrobials(
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data.frame(ab = "TESTAB",
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name = "Test Antibiotic",
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group = "Test Group")
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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_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
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}
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\examples{
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\donttest{
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# returns NA and throws a warning (which is suppressed here):
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suppressWarnings(
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as.ab("testab")
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)
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# now add a custom entry - it will be considered by as.ab() and
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# all ab_*() functions
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add_custom_antimicrobials(
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data.frame(
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ab = "TESTAB",
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name = "Test Antibiotic",
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# you can add any property present in the
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# 'antibiotics' data set, such as 'group':
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group = "Test Group"
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)
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)
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# "testab" is now a new antibiotic:
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as.ab("testab")
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ab_name("testab")
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ab_group("testab")
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ab_info("testab")
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# Add Co-fluampicil, which is one of the many J01CR50 codes, see
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# https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/
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add_custom_antimicrobials(
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data.frame(
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ab = "COFLU",
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name = "Co-fluampicil",
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atc = "J01CR50",
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group = "Beta-lactams/penicillins"
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)
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)
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ab_atc("Co-fluampicil")
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ab_name("J01CR50")
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# even antibiotic selectors work
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x <- data.frame(
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random_column = "some value",
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coflu = as.sir("S"),
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ampicillin = as.sir("R")
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)
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x
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x[, betalactams()]
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}
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}
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\seealso{
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\code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} to add custom microorganisms.
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}
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