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(v0.7.1.9059) bug_drug_combinations

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dr. M.S. (Matthijs) Berends
2019-08-25 22:53:22 +02:00
parent 7c069145ac
commit e46cb0399f
23 changed files with 1081 additions and 230 deletions
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5
man/availability.Rd
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@ -15,7 +15,10 @@ availability(tbl, width = NULL)
\code{data.frame} with column names of \code{tbl} as row names
}
\description{
Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. \code{\link{portion_R}}.
}
\details{
The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
}
\section{Read more on our website!}{

33
man/bug_drug_combinations.Rd Normal file
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% 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}
\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, minimum = 30)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\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}}.}
\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.}
}
\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 printable format, see Examples.
}
\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(septic_patients)
x
format(x)
}
}

16
man/reexports.Rd Normal file
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@ -0,0 +1,16 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/freq.R
\docType{import}
\name{reexports}
\alias{reexports}
\alias{freq}
\title{Objects exported from other packages}
\keyword{internal}
\description{
These objects are imported from other packages. Follow the links
below to see their documentation.
\describe{
\item{clean}{\code{\link[clean]{freq}}}
}}