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(v2.1.1.9122) fix documentation

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dr. M.S. (Matthijs) Berends
2024-12-20 10:52:44 +01:00
parent 15fc72fc66
commit 2e31ec19c3
13 changed files with 160 additions and 77 deletions
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45
man/plot.Rd
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@ -123,7 +123,7 @@ facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
scale_y_percent(
breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
limits = NULL
limits = c(0, NA)
)
scale_sir_colours(
@ -175,6 +175,28 @@ labels_sir_count(
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
\item{facet}{variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable}
\item{nrow}{(when using \code{facet}) number of rows}
\item{breaks}{a \link{numeric} vector of positions}
\item{limits}{a \link{numeric} vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
\item{aesthetics}{aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"}
\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} or \code{"dodge"}}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
\item{combine_SI}{a \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
\item{datalabels.size}{size of the datalabels}
\item{datalabels.colour}{colour of the datalabels}
}
\value{
The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
@ -219,7 +241,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
# Plotting using scale_x_mic()
# Plotting using scale_x_mic() ---------------------------------------------
\donttest{
if (require("ggplot2")) {
mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
@ -259,5 +281,24 @@ if (require("ggplot2")) {
if (require("ggplot2")) {
autoplot(some_sir_values)
}
# Plotting using scale_y_percent() -----------------------------------------
if (require("ggplot2")) {
p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
counts = c(1, 1, 2, 2, 3, 3)),
aes(mics, counts / sum(counts))) +
geom_col()
print(p)
p2 <- p +
scale_y_percent() +
theme_sir()
print(p2)
p +
scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
limits = c(0, 1)) +
theme_sir()
}
}
}