writeToXDMF: Write 3D MKDE to XDMF XML wrapper and binary data file.

In mkde: 2D and 3D Movement-Based Kernel Density Estimates (MKDEs)

Write 3D MKDE to XDMF XML wrapper and binary data file.

Description

Write the MKDE to a XDMF files.

Usage

writeToXDMF(mkde.obj, fname, nodat="NA", cumprob=FALSE)	

Arguments

mkde.obj	3D MKDE object created with initialize3DMKDE and density initialized with initializeDensity
fname	The path and base file name for output XDMF files
nodat	A no data character string that will be written in place of no data values.
cumprob	Indicate whether to write the voxel probabilities of cumulative probabilities.

Details

This function writes XDMF XML wrapper and binary data file.

Value

No value is returned

Author(s)

Jeff A. Tracey, PhD
USGS Western Ecological Research Center, San Diego Field Station
[e-mail]
James Sheppard, PhD
San Diego Zoo Institute for Conservation Research
[e-mail]
Amit Chourasia, MS
San Diego Supercomputer Center
[e-mail]

Examples

library(terra)
data(condor)
condor <- condor[1:20,] # 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)

fpath <- system.file("extdata", "condordem120.RDS", package="mkde")
condordem120 <- terra::readRDS(fpath)
cell.sz <- mean(res(condordem120))
ext <- ext(condordem120)
nx <- ncol(condordem120)
ny <- nrow(condordem120)
mkde.obj <- initializeMKDE3D(ext$xmin, cell.sz, nx, ext$ymin, cell.sz,
ny, min(values(condordem120), na.rm=TRUE), cell.sz, 25)

# note: we use a raster coarse integration time step so the
# example runs faster
dens.res <- initializeDensity(mkde.obj, mv.dat, integration.step=10.0)
mkde.obj <- dens.res$mkde.obj
mv.dat <- dens.res$move.dat

# Write file (note no file extension!)
writeToXDMF(mkde.obj, "condor_3dMKDE")

# Clean up files
unlink("condor_3dMKDE.dat")
unlink("condor_3dMKDE.xdmf")

mkde documentation built on April 3, 2025, 11:44 p.m.