Spatial kernel density estimate
A weighted or unweighted Gaussian Kernel Density estimate for spatial data
sp.kde( x, y = NULL, bw = NULL, newdata = NULL, nr = NULL, nc = NULL, standardize = FALSE, scale.factor = NULL, mask = TRUE )
x |
sp SpatialPointsDataFrame object |
y |
Optional values, associated with x coordinates, to be used as weights |
bw |
Distance bandwidth of Gaussian Kernel, must be units of projection |
newdata |
A Rasterlayer, any sp class object or c[xmin,xmax,ymin,ymax] vector to estimate the kde extent |
nr |
Number of rows used for creating grid. If not defined a value based on extent or existing raster will be used |
nc |
Number of columns used for creating grid. If not defined a value based on extent or existing raster will be used |
standardize |
Standardize results to 0-1 (FALSE/TRUE) |
scale.factor |
Optional numeric scaling factor for the KDE (eg., 10000), to account for small estimate values |
mask |
(TRUE/FALSE) mask resulting raster if newdata is provided |
Raster class object containing kernel density estimate
Jeffrey S. Evans <jeffrey_evans@tnc.org>
library(sp)
library(raster)
data(meuse)
coordinates(meuse) <- ~x+y
# Unweighted KDE (spatial locations only)
pt.kde <- sp.kde(x = meuse, bw = 1000, standardize = TRUE,
nr=104, nc=78, scale.factor = 10000 )
# Plot results
plot(pt.kde, main="Unweighted kde")
points(meuse, pch=20, col="red")
#### Using existing raster(s) to define grid ####
# Weighted KDE using cadmium and extent with row & col to define grid
e <- c(178605, 181390, 329714, 333611)
cadmium.kde <- sp.kde(x = meuse, y = meuse$cadmium, bw = 1000,
nr = 104, nc = 78, newdata = e,
standardize = TRUE,
scale.factor = 10000 )
plot(cadmium.kde)
points(meuse, pch=19)
# Weighted KDE using cadmium and raster object to define grid
r <- raster::raster(raster::extent(c(178605, 181390, 329714, 333611)),
nrow=104, ncol=78)
r[] <- rep(1,ncell(r))
cadmium.kde <- sp.kde(x = meuse, y = meuse$cadmium, bw = 1000,
newdata = r, standardize = TRUE,
scale.factor = 10000 )
plot(cadmium.kde)
points(meuse, pch=19)
# Weighted KDE using cadmium and SpatialPixelsDataFrame object to define grid
data(meuse.grid)
coordinates(meuse.grid) = ~x+y
proj4string(meuse.grid) <- CRS("+init=epsg:28992")
gridded(meuse.grid) = TRUE
cadmium.kde <- sp.kde(x = meuse, y = meuse$cadmium, bw = 1000,
newdata = meuse.grid, standardize = TRUE,
scale.factor = 10000 )
plot(cadmium.kde)
points(meuse, pch=19)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.