mirror of https://github.com/msberends/AMR.git
85 lines
3.9 KiB
R
85 lines
3.9 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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\alias{format.bug_drug_combinations}
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\title{Determine Bug-Drug Combinations}
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\usage{
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bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
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\method{format}{bug_drug_combinations}(
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x,
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translate_ab = "name (ab, atc)",
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language = get_AMR_locale(),
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minimum = 30,
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combine_SI = TRUE,
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add_ab_group = TRUE,
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remove_intrinsic_resistant = FALSE,
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decimal.mark = getOption("OutDec"),
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big.mark = ifelse(decimal.mark == ",", ".", ","),
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...
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)
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}
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\arguments{
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\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
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\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{FUN}{the function to call on the \code{mo} column to transform the microorganism codes - the default is \code{\link[=mo_shortname]{mo_shortname()}}}
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\item{...}{arguments passed on to \code{FUN}}
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\item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antibiotics} data set}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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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 \emph{Source}.}
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\item{combine_SI}{a \link{logical} to indicate whether values S and I should be summed, so resistance will be based on only R - the default is \code{TRUE}}
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\item{add_ab_group}{a \link{logical} to indicate where the group of the antimicrobials must be included as a first column}
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\item{remove_intrinsic_resistant}{\link{logical} to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
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\item{decimal.mark}{the character to be used to indicate the numeric
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decimal point.}
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\item{big.mark}{character; if not empty used as mark between every
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\code{big.interval} decimals \emph{before} (hence \code{big}) the
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decimal point.}
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}
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\value{
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The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
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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{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.
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}
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\details{
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The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use \code{combine_SI = TRUE} (default) to test R vs. S+I and \code{combine_SI = FALSE} to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. \code{\link[knitr:kable]{knitr::kable()}}.
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}
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\examples{
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# example_isolates is a data set available in the AMR package.
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# run ?example_isolates for more info.
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example_isolates
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\donttest{
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x <- bug_drug_combinations(example_isolates)
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head(x)
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format(x, translate_ab = "name (atc)")
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# Use FUN to change to transformation of microorganism codes
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bug_drug_combinations(example_isolates,
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FUN = mo_gramstain
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)
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bug_drug_combinations(example_isolates,
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FUN = function(x) {
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ifelse(x == as.mo("Escherichia coli"),
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"E. coli",
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"Others"
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)
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}
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)
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}
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}
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