(v0.7.1.9063) septic_patients -> example_isolates

man/bug_drug_combinations.Rd

@@ -15,10 +15,15 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30)
 \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.}
+
+\item{combine_RI}{logical to indicate whether values R and I should be summed}
 }
 \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.
 }
+\details{
+The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_RI = FALSE} (default) to test R vs. S+I and \code{combine_RI = TRUE} to test R+I vs. S.
+}
 \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}.
@@ -26,7 +31,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 
 \examples{
 \donttest{
-x <- bug_drug_combinations(septic_patients)
+x <- bug_drug_combinations(example_isolates)
 x
 format(x)
 }