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(v0.7.1.9100) bug_drug speed, MIC levels

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dr. M.S. (Matthijs) Berends
2019-10-08 22:21:33 +02:00
parent 683d226fd3
commit c8f6b97847
22 changed files with 117 additions and 70 deletions
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10
man/bug_drug_combinations.Rd
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@ -8,8 +8,7 @@
\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,
FUN = mo_shortname, ...)
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\method{format}{bug_drug_combinations}(x,
translate_ab = "name (ab, atc)", language = get_locale(),
@ -23,8 +22,6 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\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{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{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}}
@ -33,6 +30,8 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\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}
@ -48,6 +47,9 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\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.
}