mirror of https://github.com/msberends/AMR.git
40 lines
2.6 KiB
R
40 lines
2.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/isolate_identifier.R
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\name{isolate_identifier}
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\alias{isolate_identifier}
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\title{Create identifier of an isolate}
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\usage{
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isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
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}
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\arguments{
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\item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
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\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglysides]{aminoglysides()}}}
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}
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\description{
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This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
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}
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\section{Maturing lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
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}
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\examples{
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# automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi)
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x <- isolate_identifier(example_isolates)
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# ignore microorganism codes, only use antimicrobial results
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x <- isolate_identifier(example_isolates, col_mo = FALSE, cols_ab = c("AMX", "TZP", "GEN", "TOB"))
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# select antibiotics from certain antibiotic classes
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x <- isolate_identifier(example_isolates, cols_ab = c(carbapenems(), aminoglycosides()))
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}
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