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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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14
man/ggplot_rsi.Rd
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@ -53,11 +53,7 @@ facet_rsi(facet = c("interpretation", "antibiotic"), nrow = NULL)
scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
scale_rsi_colours(
colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R =
"#ED553B"),
aesthetics = "fill"
)
scale_rsi_colours(..., aesthetics = "fill")
theme_rsi()
@ -100,7 +96,7 @@ labels_rsi_count(
\item{nrow}{(when using \code{facet}) number of rows}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} for standard \link[ggplot2:ggplot]{ggplot2} colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.}
\item{colours}{a named vactor with colour to be used for filling. The default colours are colour-blind friendly.}
\item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}}
@ -118,9 +114,9 @@ labels_rsi_count(
\item{y.title}{text to show as y axis description}
\item{...}{other arguments passed on to \code{\link[=geom_rsi]{geom_rsi()}}}
\item{...}{other arguments passed on to \code{\link[=geom_rsi]{geom_rsi()}} or, in case of \code{\link[=scale_rsi_colours]{scale_rsi_colours()}}, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See \emph{Examples}.}
\item{aesthetics}{aesthetics to apply the colours to, defaults to "fill" but can also be "colour" or "both"}
\item{aesthetics}{aesthetics to apply the colours to, defaults to "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"}
}
\description{
Use these functions to create bar plots for AMR data analysis. All functions rely on \link[ggplot2:ggplot]{ggplot2} functions.
@ -135,7 +131,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
\code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_y_continuous()}}.
\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2:scale_manual]{ggplot2::scale_fill_manual()}}.
\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
\code{\link[=theme_rsi]{theme_rsi()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.

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)
}
}