Movement-based kernel density estimate (MKDE) in 3D using Rcpp
Provides a function for 3-dimensional MKDEs.
mkde3Dgrid(mkde.obj, move.dat, t.step, d.thresh)
mkde.obj |
A 3D MKDE object |
move.dat |
A move data object |
t.step |
An integration time step |
d.thresh |
A kernel density threshold |
This is lower-level function that call the C++ function. for
estimating the movement-based density in 3D. In practice, users
should call initializeDensity.
The argument d.thresh is a univariate probability density beyond which
the kernel contribution to the overall MKDE is assumed to be
negligible. Usually this is set at a very small value and is used to
prevent calculations from being performed in cells to which the kernel
makes a negligible contribution.
An array whose elements are the estimated utilization probabilities for each voxel.
Jeff A. Tracey, PhD
USGS Western Ecological Research Center, San Diego Field Station
jatracey@usgs.gov
James Sheppard, PhD
San Diego Zoo Institute for Conservation Research
jsheppard@sandiegozoo.org
Robert Sinkovits, PhD
San Diego Supercomputer Center
sinkovit@sdsc.edu
Glenn Lockwood, PhD
San Diego Supercomputer Center
glock@sdsc.edu
Jun Zhu, PhD
University of Wisconsin-Madison
jzhu@stat.wisc.edu
library(raster) data(condor) condor <- condor[1:10,] # simply to make example run more quickly mv.dat <- initializeMovementData(condor$time, condor$x, condor$y, z.obs=condor$z, sig2obs=25.0, sig2obs.z=81.0, t.max=65.0) data(condordem120) cell.sz <- mean(res(condordem120)) ext <- extent(condordem120) nx <- ncol(condordem120) ny <- nrow(condordem120) nz <- ceiling(3000.0/cell.sz) mkde.obj <- initializeMKDE3D(ext@xmin, cell.sz, nx, ext@ymin, cell.sz, ny, 0.0, cell.sz, nz) res <- mkde3Dgrid(mkde.obj, mv.dat, 5.0, 1e-20)
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