mirror of https://github.com/msberends/AMR.git
89 lines
4.7 KiB
R
89 lines
4.7 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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\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, 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_locale(),
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minimum = 30,
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combine_SI = TRUE,
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combine_IR = FALSE,
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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}{data with antibiotic columns, like e.g. \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{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \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 character of length 1 containing column names of the \link{antibiotics} data set}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("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 Source.}
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\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}.}
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\item{combine_IR}{logical to indicate whether values R and I should be summed}
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\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
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\item{remove_intrinsic_resistant}{logical to indicate that rows 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 \code{\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 publicable/printable format, see 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. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
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The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
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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, translate_ab = "name (atc)")
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# Use FUN to change to transformation of microorganism codes
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x <- bug_drug_combinations(example_isolates,
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FUN = mo_gramstain)
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x <- bug_drug_combinations(example_isolates,
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FUN = function(x) ifelse(x == "B_ESCHR_COLI",
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"E. coli",
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"Others"))
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}
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}
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