P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 14:21:57 +02:00
Code Releases Activity

Replace RSI with SIR

Browse Source
This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
Download Patch File Download Diff File Expand all files Collapse all files

36
man/plot.Rd
View File

@ -8,10 +8,10 @@
\alias{plot.disk}
\alias{autoplot.disk}
\alias{fortify.disk}
\alias{plot.rsi}
\alias{autoplot.rsi}
\alias{fortify.rsi}
\title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
\alias{plot.sir}
\alias{autoplot.sir}
\alias{fortify.sir}
\title{Plotting for Classes \code{sir}, \code{mic} and \code{disk}}
\usage{
\method{plot}{mic}(
x,
@ -21,7 +21,7 @@
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...
@ -35,7 +35,7 @@
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...
@ -51,7 +51,7 @@
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...
@ -65,7 +65,7 @@
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...
@ -73,7 +73,7 @@
\method{fortify}{disk}(object, ...)
\method{plot}{rsi}(
\method{plot}{sir}(
x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
@ -82,20 +82,20 @@
...
)
\method{autoplot}{rsi}(
\method{autoplot}{sir}(
object,
title = deparse(substitute(object)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
...
)
\method{fortify}{rsi}(object, ...)
\method{fortify}{sir}(object, ...)
}
\arguments{
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.rsi]{as.rsi()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
@ -107,7 +107,7 @@
\item{xlab, ylab}{axis title}
\item{colours_RSI}{colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.}
\item{colours_SIR}{colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
@ -121,7 +121,7 @@ The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} mo
The \code{fortify()} functions return a \link{data.frame} as an extension for usage in the \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} function.
}
\description{
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
}
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
@ -133,11 +133,11 @@ Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select
\examples{
some_mic_values <- random_mic(size = 100)
some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
some_rsi_values <- random_rsi(50, prob_RSI = c(0.30, 0.55, 0.05))
some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
plot(some_mic_values)
plot(some_disk_values)
plot(some_rsi_values)
plot(some_sir_values)
# when providing the microorganism and antibiotic, colours will show interpretations:
plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
@ -152,7 +152,7 @@ if (require("ggplot2")) {
autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
}
if (require("ggplot2")) {
autoplot(some_rsi_values)
autoplot(some_sir_values)
}
}
}