initializeMKDE3D {mkde} | R Documentation |
Set up a 3D MKDE object.
Description
Define the spatial extent and resolution of a 3D MKDE and create an 3D MKDE list object for use in other functions in the package.
Usage
initializeMKDE3D(xLL, xCellSize, nX, yLL, yCellSize, nY,
zLL, zCellSize, nZ)
Arguments
xLL |
Lower bounds of the grid in the x-dimension |
xCellSize |
Cell size in the x-dimension |
nX |
Number of cells in the x-dimension |
yLL |
Lower bounds of the grid in the y-dimension |
yCellSize |
Cell size in the y-dimension |
nY |
Number of cells in the y-dimension |
zLL |
Lower bounds of the grid in the z-dimension |
zCellSize |
Cell size in the z-dimension |
nZ |
Number of cells in the z-dimension |
Details
It is strongly recommended that the same value is used for xCellSize
and
yCellSize
. The grid should be defined so that it covers the volume that
the animal used, plus a sufficient buffer so that the density is
negligable beyond the grid.
Value
A list representing an MKDE object is returned with the following elements:
dimension |
The dimension of the MKDE; that is, 3. |
x |
A grid of points along the x-axis where the voxel centers occur. |
y |
A grid of points along the y-axis where the voxel centers occur. |
z |
A grid of points along the z-axis where the voxel centers occur. |
z.min |
A 2D array representing the lower bounds of space in the z-dimension at each x and y coordinate. Defaults to a constant value based on the arguments zLL, zCellSize,and nZ. |
z.max |
A 2D array representing the upper bounds of space in the z-dimension at each x and y coordinate. Defaults to a constant value based on the arguments zLL, zCellSize,and nZ. |
nx |
Number of cells in the x-dimension. |
ny |
Number of cells in the y-dimension. |
nz |
Number of cells in the z-dimension. |
d |
A 3D array with dimensions (nx, ny, nz) that stores the density. The elements are initialized toNA. |
Author(s)
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
Examples
library(terra)
fpath <- system.file("extdata", "condordem.RDS", package="mkde")
condordem <- terra::readRDS(fpath)
cell.sz <- mean(res(condordem))
ext <- ext(condordem)
nx <- ncol(condordem)
ny <- nrow(condordem)
zmin <- min(values(condordem), na.rm=TRUE)
nz <- 30
mkde.obj <- initializeMKDE3D(ext$xmin, cell.sz, nx, ext$ymin, cell.sz,
ny, zmin, cell.sz, nz)