AMR/man/add_custom_antimicrobials.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_custom_antimicrobials.R
\name{add_custom_antimicrobials}
\alias{add_custom_antimicrobials}
\alias{clear_custom_antimicrobials}
\title{Add Custom Antimicrobials to This Package}
\usage{
add_custom_antimicrobials(x)

clear_custom_antimicrobials()
}
\arguments{
\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
}
\description{
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial codes to the \code{AMR} package.
}
\details{
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. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up:

\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
utils::file.edit("~/.Rprofile")

# Add custom antibiotic codes:
library(AMR)
add_custom_antimicrobials(
  data.frame(ab = "TEST",
             name = "Test Antibiotic",
             group = "Test Group")
)
}\if{html}{\out{</div>}}

Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
}
\examples{
\donttest{

# returns NA and throws a warning (which is now suppressed):
suppressWarnings(
  as.ab("test")
)

# now add a custom entry - it will be considered by as.ab() and
# all ab_*() functions
add_custom_antimicrobials(
  data.frame(ab = "TEST",
             name = "Test Antibiotic",
             # you can add any property present in the
             # 'antibiotics' data set, such as 'group':
             group = "Test Group")
)

# "test" is now a new antibiotic:
as.ab("test")
ab_name("test")
ab_group("test")

ab_info("test")


# Add Co-fluampicil, which is one of the many J01CR50 codes, see
# https://www.whocc.no/ddd/list_of_ddds_combined_products/
add_custom_antimicrobials(
  data.frame(ab = "COFLU",
             name = "Co-fluampicil",
             atc = "J01CR50",
             group = "Beta-lactams/penicillines")
)
ab_atc("Co-fluampicil")
ab_name("J01CR50")

# even antibiotic selectors work
x <- data.frame(random_column = "test",
                coflu = as.rsi("S"),
                ampicillin = as.rsi("R"))
x
x[, betalactams()]
}
}