AMR/man/bug_drug_combinations.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bug_drug_combinations.R
\name{bug_drug_combinations}
\alias{bug_drug_combinations}
\alias{format.bug_drug_combinations}
\title{Determine bug-drug combinations}
\source{
\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/}.
}
\usage{
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)

\method{format}{bug_drug_combinations}(x,
  translate_ab = "name (ab, atc)", language = get_locale(),
  minimum = 30, combine_SI = TRUE, combine_IR = FALSE,
  add_ab_group = TRUE, remove_intrinsic_resistant = FALSE,
  decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark ==
  ",", ".", ","), ...)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}

\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}

\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}}

\item{...}{arguments passed on to \code{FUN}}

\item{translate_ab}{a character of length 1 containing column names of the \code{\link{antibiotics}} data set}

\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}

\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.}

\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}

\item{combine_IR}{logical to indicate whether values R and I should be summed}

\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}

\item{remove_intrinsic_resistant}{logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table}

\item{decimal.mark}{the character to be used to indicate the numeric
    decimal point.}

\item{big.mark}{character; if not empty used as mark between every
    \code{big.interval} decimals \emph{before} (hence \code{big}) the
    decimal point.}
}
\value{
The function \code{bug_drug_combinations} returns a \code{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
}
\description{
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 publicable/printable format, see Examples.
}
\details{
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. 

The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
}
\section{Read more on our website!}{

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}.
}

\examples{
\donttest{
x <- bug_drug_combinations(example_isolates)
x
format(x, translate_ab = "name (atc)")

# Use FUN to change to transformation of microorganism codes
x <- bug_drug_combinations(example_isolates, 
                           FUN = mo_gramstain)
                           
x <- bug_drug_combinations(example_isolates,
                           FUN = function(x) ifelse(x == "B_ESCHR_COLI",
                                                    "E. coli",
                                                    "Others"))
}
}