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dr. M.S. (Matthijs) Berends
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@ -72,17 +72,18 @@ The function \code{\link[=n_rsi]{n_rsi()}} is an alias of \code{\link[=count_all
The function \code{\link[=count_df]{count_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and counts the number of S's, I's and R's. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=count_df]{count_df()}}, but adds the percentage of S, I and R.
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. 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.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
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]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}