mirror of https://github.com/msberends/AMR.git
39 lines
2.1 KiB
R
39 lines
2.1 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/bug_drug_combinations.R
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\name{bug_drug_combinations}
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\alias{bug_drug_combinations}
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\title{Determine bug-drug combinations}
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\source{
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\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
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}
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\usage{
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bug_drug_combinations(x, col_mo = NULL, minimum = 30)
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}
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\arguments{
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\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
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\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
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\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
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\item{combine_RI}{logical to indicate whether values R and I should be summed}
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}
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\description{
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Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
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}
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\details{
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The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_RI = FALSE} (default) to test R vs. S+I and \code{combine_RI = TRUE} to test R+I vs. S.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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\donttest{
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x <- bug_drug_combinations(example_isolates)
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x
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format(x)
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}
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}
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