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(v1.5.0.9027) website update

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dr. M.S. (Matthijs) Berends
2021-02-26 12:11:29 +01:00
parent 1737d56ae4
commit 41f94cde97
45 changed files with 491 additions and 425 deletions
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18
man/plot.Rd
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@ -7,6 +7,7 @@
\alias{plot.disk}
\alias{ggplot.disk}
\alias{plot.rsi}
\alias{ggplot.rsi}
\title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
\usage{
\method{plot}{mic}(
@ -38,7 +39,7 @@
\method{plot}{disk}(
x,
main = paste("Disk zones values of", deparse(substitute(x))),
main = paste("Disk zones of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -52,7 +53,7 @@
\method{ggplot}{disk}(
data,
mapping = NULL,
title = paste("Disk zones values of", deparse(substitute(data))),
title = paste("Disk zones of", deparse(substitute(data))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -70,6 +71,16 @@
main = paste("Resistance Overview of", deparse(substitute(x))),
...
)
\method{ggplot}{rsi}(
data,
mapping = NULL,
title = paste("Resistance Overview of", deparse(substitute(data))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
...
)
}
\arguments{
\item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}
@ -121,9 +132,11 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
\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))
plot(some_mic_values)
plot(some_disk_values)
plot(some_rsi_values)
# when providing the microorganism and antibiotic, colours will show interpretations:
plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
@ -132,5 +145,6 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
if (require("ggplot2")) {
ggplot(some_mic_values)
ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
ggplot(some_rsi_values)
}
}