tidyst_kde_boundary | R Documentation |
Tidy and geospatial versions of kernel density estimates with boundary and truncated kernels for 1- and 2-dimensional data.
tidy_kde_boundary(data, ...)
tidy_kde_truncate(data, boundary, ...)
st_kde_boundary(x, ...)
st_kde_truncate(x, boundary, ...)
data |
data frame/tibble of data values |
x |
sf object with point geometry |
boundary |
data frame/sf point geometry of boundary |
... |
other parameters in |
A boundary kernel density estimate is a modification of the standard density estimate for bounded data. There are two main types: beta kernels (boundary.kernel="beta"
) and linear kernels (boundary.kernel="linear"
). For details of the computation of the boundary kernel estimates and of the bandwidth selector procedure, see ks::kde.boundary
. Currently only rectangular boundaries are supported, as defined by xmin
x xmax
.
A truncated kernel density estimate is a modification of the standard density estimate for bounded data. All the probability mass outside of boundary
is set to zero and re-assigned over the regions inside in the boundary. The boundary can be any polygon. For further details of the computation of the truncated kernel estimate, see ks::kde.truncate
.
For details of the computation of the boundary kernel estimates and the truncated kernel density estimates, and of the bandwidth selector procedure, see ks::kde.boundary
, ks::kde.truncate
.
The outputs from *_kde_boundary
, *_kde_truncate
have the same structure as the standard kernel density estimate from *_kde
.
## tidy boundary density estimates
library(ggplot2)
data(worldbank, package="ks")
worldbank <- dplyr::as_tibble(worldbank)
## percentage data is bounded on [0,100] x [0,100]
wb2 <- na.omit(worldbank[,c("internet", "ag.value")])
xmin <- c(0,0); xmax <- c(100,100)
rectb <- data.frame(x=c(0,100,100,0,0), y=c(0,0,100,100,0))
## standard density estimate
t1 <- tidy_kde(wb2)
## tidy truncated density estimate
t2 <- tidy_kde_truncate(wb2, boundary=rectb)
tt <- rbind(t1, t2, labels=c("Standard KDE", "Truncated KDE"))
tb <- contour_breaks(tt, group=FALSE)
## standard estimate exceeds boundary but not truncated estimate
gr <- geom_polygon(data=rectb, aes(x=x,y=y), inherit.aes=FALSE, fill=NA,
colour=1, linetype="dashed")
gt <- ggplot(tt, aes(x=internet, y=ag.value))
gt + geom_contour_filled_ks(colour=1, breaks=tb) + gr + facet_wrap(~group)
## linear boundary density estimate
## beta boundary density estimate
t3 <- tidy_kde_boundary(wb2, boundary.kernel="beta", xmin=xmin, xmax=xmax)
t4 <- tidy_kde_boundary(wb2, boundary.kernel="linear", xmin=xmin, xmax=xmax)
t5 <- rbind(t1, t2, t3, t4, labels=c("Standard KDE", "Truncated KDE",
"Beta bd KDE", "Linear bd KDE"))
tb <- contour_breaks(t5, group=FALSE)
## standard estimate exceeds boundary but not boundary or truncated estimates
gt + geom_contour_filled_ks(data=t5, colour=1, breaks=tb) + gr + facet_wrap(~group)
## geospatial boundary density estimates
data(wa)
data(grevilleasf)
hakeoides <- dplyr::filter(grevilleasf, species=="hakeoides")
hakeoides_bbox <- sf::st_bbox(c(xmin=4e5, xmax=5.7e5, ymin=6.47e6, ymax=7e6),
crs=sf::st_crs(hakeoides))
xminb <- hakeoides_bbox[1:2]; xmaxb <- hakeoides_bbox[3:4]
hakeoides_bbox <- sf::st_as_sfc(hakeoides_bbox)
hakeoides_crop <- sf::st_filter(hakeoides, hakeoides_bbox)
s1 <- st_kde(hakeoides_crop)
s2 <- st_kde_boundary(hakeoides_crop, boundary.kernel="beta",
xmin=xminb, xmax=xmaxb)
s3 <- st_kde_boundary(hakeoides_crop, boundary.kernel="linear",
xmin=xminb, xmax=xmaxb)
## geospatial truncated density estimate
s4 <- st_kde_truncate(x=hakeoides_crop, boundary=hakeoides_bbox)
s5 <- rbind(s1, s2, s3, s4, labels=c("Standard KDE", "Beta bd KDE",
"Linear bd KDE", "Truncated KDE"))
## base R plots
xlim <- c(1.2e5, 1.1e6); ylim <- c(6.1e6, 7.2e6)
cols <- colorspace::qualitative_hcl(n=4, palette="Set2")
layout(matrix(c(1,3,2,4), ncol=2))
plot(wa, xlim=xlim, ylim=ylim)
plot(hakeoides_bbox, add=TRUE, lty=3, lwd=2)
plot(s1, add=TRUE, border=cols[1], col=NA, legend=FALSE)
plot(wa, xlim=xlim, ylim=ylim)
plot(hakeoides_bbox, add=TRUE, lty=3, lwd=2)
plot(s2, add=TRUE, border=cols[2], col=NA, legend=FALSE)
plot(wa, xlim=xlim, ylim=ylim)
plot(hakeoides_bbox, add=TRUE, lty=3, lwd=2)
plot(s3, add=TRUE, border=cols[3], col=NA, legend=FALSE)
mapsf::mf_legend(type="symb", val=c("Standard KDE","Beta bd KDE",
"Linear bd KDE", "Truncated KDE"), pal=cols, cex=rep(3,4),
pch=rep("-",4), title="Density", pos="bottomleft")
plot(wa, xlim=xlim, ylim=ylim)
plot(hakeoides_bbox, add=TRUE, lty=3, lwd=2)
plot(s4, add=TRUE, border=cols[4], col=NA, legend=FALSE)
layout(1)
## geom_sf plots
gs <- ggplot() + geom_sf(data=wa, fill=NA) +
geom_sf(data=hakeoides_bbox, linetype="dotted", fill=NA) +
ggthemes::theme_map() +
colorspace::scale_colour_discrete_qualitative(palette="Set2")
gs + geom_sf(data=st_get_contour(s5), aes(colour=group), fill=NA) +
coord_sf(xlim=xlim, ylim=ylim) +
guides(colour=guide_legend(title="Density")) + facet_wrap(~group)
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