update

man/AMR-deprecated.Rd

@@ -1,14 +1,57 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/aa_deprecated.R
+% Please edit documentation in R/zz_deprecated.R
+\docType{data}
 \name{AMR-deprecated}
 \alias{AMR-deprecated}
+\alias{NA_rsi_}
 \alias{as.rsi}
+\alias{facet_rsi}
+\alias{geom_rsi}
+\alias{ggplot_rsi}
+\alias{ggplot_rsi_predict}
+\alias{is.rsi}
 \alias{is.rsi.eligible}
+\alias{labels_rsi_count}
+\alias{n_rsi}
+\alias{random_rsi}
+\alias{rsi_df}
+\alias{rsi_predict}
+\alias{scale_rsi_colours}
+\alias{theme_rsi}
 \title{Deprecated Functions}
+\format{
+An object of class \code{rsi} (inherits from \code{ordered}, \code{factor}) of length 1.
+}
 \usage{
-as.rsi(...)
+NA_rsi_
+
+as.rsi(x, ...)
+
+facet_rsi(...)
+
+geom_rsi(...)
+
+ggplot_rsi(...)
+
+ggplot_rsi_predict(...)
+
+is.rsi(x, ...)
 
 is.rsi.eligible(...)
+
+labels_rsi_count(...)
+
+n_rsi(...)
+
+random_rsi(...)
+
+rsi_df(...)
+
+rsi_predict(...)
+
+scale_rsi_colours(...)
+
+theme_rsi(...)
 }
 \description{
 These functions are so-called '\link{Deprecated}'. \strong{They will be removed in a future release.} Using the functions will give a warning with the name of the function it has been replaced by (if there is one).

man/as.sir.Rd

@@ -163,16 +163,19 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU
 
 \code{NA_sir_} is a missing value of the new \code{sir} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
 }
-\section{Interpretation of R and S/I}{
+\section{Interpretation of SIR}{
 
-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{https://www.eucast.org/newsiandr/}).
+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{https://www.eucast.org/newsiandr/}):
 \itemize{
+\item \strong{S - Susceptible, standard dosing regimen}\cr
+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} \emph{\cr
+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}\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 = Susceptible, Increased exposure}\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.
+A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
+\itemize{
+\item \emph{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 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.

man/count.Rd

@@ -69,16 +69,19 @@ The function \code{\link[=n_sir]{n_sir()}} 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{sir}} class (created with \code{\link[=as.sir]{as.sir()}}) and counts the number of S's, I's and R's. It also supports grouped variables. The function \code{\link[=sir_sf]{sir_sf()}} works exactly like \code{\link[=count_df]{count_df()}}, but adds the percentage of S, I and R.
 }
-\section{Interpretation of R and S/I}{
+\section{Interpretation of SIR}{
 
-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{https://www.eucast.org/newsiandr/}).
+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{https://www.eucast.org/newsiandr/}):
 \itemize{
+\item \strong{S - Susceptible, standard dosing regimen}\cr
+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} \emph{\cr
+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}\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 = Susceptible, Increased exposure}\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.
+A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
+\itemize{
+\item \emph{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 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.

man/proportion.Rd

@@ -141,16 +141,19 @@ and that, in combination therapies, for \code{only_all_tested = FALSE} applies t
 Using \code{only_all_tested} has no impact when only using one antibiotic as input.
 }
 
-\section{Interpretation of R and S/I}{
+\section{Interpretation of SIR}{
 
-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{https://www.eucast.org/newsiandr/}).
+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{https://www.eucast.org/newsiandr/}):
 \itemize{
+\item \strong{S - Susceptible, standard dosing regimen}\cr
+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} \emph{\cr
+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}\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 = Susceptible, Increased exposure}\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.
+A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
+\itemize{
+\item \emph{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 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.

man/resistance_predict.Rd

@@ -110,16 +110,19 @@ Valid options for the statistical model (argument \code{model}) are:
 \item \code{"lin"} or \code{"linear"}: a linear regression model
 }
 }
-\section{Interpretation of R and S/I}{
+\section{Interpretation of SIR}{
 
-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{https://www.eucast.org/newsiandr/}).
+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{https://www.eucast.org/newsiandr/}):
 \itemize{
+\item \strong{S - Susceptible, standard dosing regimen}\cr
+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} \emph{\cr
+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}\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 = Susceptible, Increased exposure}\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.
+A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
+\itemize{
+\item \emph{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 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.