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(v3.0.1.9034) Add amr_course()

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dr. M.S. (Matthijs) Berends
2026-03-11 16:07:31 +01:00
parent 353eaa3f38
commit 4dc3ec0008
8 changed files with 110 additions and 17 deletions
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36
man/amr_course.Rd Normal file
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/amr_course.R
\name{amr_course}
\alias{amr_course}
\title{Download and Unpack an AMR Course Repository}
\usage{
amr_course(github_repo, branch = "main", ...)
}
\arguments{
\item{github_repo}{A character string specifying the GitHub repository with username and repo name, e.g. \code{"https://github.com/username/repo"}.}
\item{branch}{A character string specifying the branch to download. Defaults to \code{"main"}.}
\item{...}{Additional arguments passed on to \code{\link[usethis:zip-utils]{usethis::use_course()}}.}
}
\value{
Called for its side effect. \code{\link[usethis:zip-utils]{usethis::use_course()}} will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever \code{\link[usethis:zip-utils]{usethis::use_course()}} returns.
}
\description{
Downloads and unpacks a GitHub repository containing course materials, using \code{\link[usethis:zip-utils]{usethis::use_course()}}. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
}
\details{
This function constructs a ZIP archive URL from the provided \code{github_repo} and \code{branch}, then delegates to \code{\link[usethis:zip-utils]{usethis::use_course()}} to handle the download and extraction.
The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
}
\examples{
\dontrun{
# Let this run by users, e.g., webinar participants
amr_course("https://github.com/my_user_name/our_AMR_course")
}
}
\seealso{
\code{\link[usethis:zip-utils]{usethis::use_course()}}
}

4
man/interpretive_rules.Rd
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@@ -76,10 +76,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
\strong{WORK IN PROGRESS}
\strong{The \code{interpretive_rules()} function is new, to allow CLSI 'rules' too. The old \code{eucast_rules()} function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.}
Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}.