mkde (version 0.2)

initializeMKDE3D: 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)

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.

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

Author

Jeff A. Tracey, PhD
USGS Western Ecological Research Center, San Diego Field Station

James Sheppard, PhD
San Diego Zoo Institute for Conservation Research

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.

Examples

library(raster)
data(condordem)
cell.sz <- mean(res(condordem))
ext <- extent(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)