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Merge branch 'main' of https://github.com/msberends/AMR into main

# Conflicts:
#	DESCRIPTION
#	R/add_custom_antimicrobials.R
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dr. M.S. (Matthijs) Berends
2022-10-11 10:53:51 +02:00
parent 33227a5d90 57d66cd9d0
commit dfae4c7e7d
4 changed files with 15 additions and 11 deletions
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10
man/add_custom_antimicrobials.Rd
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@ -3,7 +3,7 @@
\name{add_custom_antimicrobials}
\alias{add_custom_antimicrobials}
\alias{clear_custom_antimicrobials}
\title{Add Manual Antimicrobials to This Package}
\title{Add Custom Antimicrobials to This Package}
\usage{
add_custom_antimicrobials(x)
@ -13,7 +13,7 @@ clear_custom_antimicrobials()
\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 manual antimicrobial codes to the \code{AMR} package.
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:
@ -38,15 +38,17 @@ suppressWarnings(
as.ab("test")
)
# now add a manual entry - it will be considered by as.ab() and
# 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:
# "test" is now a new antibiotic:
as.ab("test")
ab_name("test")
ab_group("test")