tidyst_ksupp {eks}

Tidy and geospatial kernel support estimate

Description

Tidy and geospatial versions of a kernel support estimate for 2-dimensional data.

Usage

tidy_ksupp(data, cont=95, convex_hull=TRUE, ...)
st_ksupp(x, cont=95, convex_hull=TRUE, ...)

Arguments

data

tidy kernel density estimate (output from tidy_kde)

x

spatial kernel density estimate (output from st_kde)

cont

scalar contour level. Default is 95.

convex_hull

flag to compute convex hull of contour region. Default is TRUE.

...

other parameters in ks::ksupp function

Details

The kernel support estimate is considered to be the cont% probability contour of the kernel density estimate, with an additional convex hull calculation if convex_hull=TRUE. For details of the computation of the kernel support estimate, see ?ks::ksupp.

Value

The output from *_ksupp have the same structure as the kernel density estimate from *_kde, except that x,y indicate the boundary of the density support estimate (if convex.hull=TRUE) or the grid points inside the density support (if convex.hull=FALSE), rather than the complete grid points themselves.

For st_kdr, the density support estimate is stored as a (multi)polygon sf object.

Examples

## tidy density support estimate
data(crabs, package="MASS")
crabs2 <- dplyr::select(crabs, FL, CW)
t1 <- tidy_kde(crabs2)
t2 <- tidy_ksupp(t1)
gt <- ggplot2::ggplot(t1, ggplot2::aes(x=FL, y=CW)) 
gt + geom_contour_filled_ks(cont=c(25,50,75,95), colour=1) +
    ggplot2::geom_polygon(data=t2, ggplot2::aes(linetype=label), fill=NA, colour=1,
    linewidth=1.2) + colorspace::scale_fill_discrete_sequential() +
    ggplot2::scale_linetype_manual(values="dashed", name="Support\nconvex hull")

gt + ggplot2::geom_polygon(data=t2, ggplot2::aes(colour=label), fill=NA,
    linetype="dashed") + geom_point_ks(data=t1, colour=3) +
    ggplot2::scale_colour_manual(values=1)

## geospatial density support estimate
data(wa)
data(grevilleasf)
hakeoides <- dplyr::filter(grevilleasf, species=="hakeoides")
s1 <- st_kde(hakeoides)
s2 <- st_ksupp(s1)

## base R plot
xlim <- c(1.2e5, 1.1e6); ylim <- c(6.1e6, 7.2e6)
plot(wa, xlim=xlim, ylim=ylim)
plot(s1, cont=c(25,50,75,95), add=TRUE)
plot(sf::st_geometry(hakeoides), add=TRUE, pch=16, col=1)
plot(s2, add=TRUE, lty=2, lwd=2)

## geom_sf plot
gs1 <- ggplot2::ggplot(s1) + ggplot2::geom_sf(data=wa, fill=NA)  + 
    ggthemes::theme_map()
gs1 + ggplot2::geom_sf(data=st_get_contour(s1, cont=c(25,50,75,95)),
    ggplot2::aes(fill=label_percent(contlabel))) +
    ggplot2::geom_sf(data=st_get_contour(s2,cont=95), 
    ggplot2::aes(linetype=contlabel), fill=NA, colour=1) + 
    ggplot2::geom_sf(data=hakeoides, ggplot2::aes(colour=species)) +
    colorspace::scale_fill_discrete_sequential(palette="Heat2") +
    ggplot2::scale_colour_manual(values=1) + 
    ggplot2::guides(colour=ggplot2::guide_legend(title="Locations")) +
    ggplot2::scale_linetype_manual(values="dashed", name="Support\nconvex hull") +
    ggplot2::coord_sf(xlim=xlim, ylim=ylim)