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dr. M.S. (Matthijs) Berends
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10
man/count.Rd
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@ -56,16 +56,16 @@ Integer
\description{
These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
\code{count_resistant} should be used to count resistant isolates, \code{count_susceptible} should be used to count susceptible isolates.\cr
\code{count_resistant()} should be used to count resistant isolates, \code{count_susceptible()} should be used to count susceptible isolates.\cr
}
\details{
These functions are meant to count isolates. Use the \code{\link{resistance}}/\code{\link{susceptibility}} functions to calculate microbial resistance/susceptibility.
The function \code{count_resistant} is equal to the function \code{count_R}. The function \code{count_susceptible} is equal to the function \code{count_SI}.
The function \code{count_resistant()} is equal to the function \code{count_R()}. The function \code{count_susceptible()} is equal to the function \code{count_SI()}.
The function \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
The function \code{n_rsi()} is an alias of \code{count_all()}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the number of S's, I's and R's. The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
The function \code{count_df()} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}()}) and counts the number of S's, I's and R's. The function \code{rsi_df()} works exactly like \code{count_df()}, but adds the percentage of S, I and R.
}
\section{Interpretation of S, I and R}{
@ -79,7 +79,7 @@ In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link{susceptibility}} (equal to \code{\link{proportion_SI}}) to determine antimicrobial susceptibility and \code{\link{count_susceptible}} (equal to \code{\link{count_SI}}) to count susceptible isolates.
This AMR package honours this new insight. Use \code{\link{susceptibility}()} (equal to \code{\link{proportion_SI}()}) to determine antimicrobial susceptibility and \code{\link{count_susceptible}()} (equal to \code{\link{count_SI}()}) to count susceptible isolates.
}
\section{Combination therapy}{