initializeMovementData: Initialize a movement data list

Description Usage Arguments Details Value Author(s) Examples

View source: R/mkdeFunctions.R

Description

This function sets up the movement data for use in other functions in the package.

Usage

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initializeMovementData(t.obs, x.obs, y.obs, z.obs=NULL, sig2obs=0.0,
sig2obs.z=NA, t.max=max(diff(t.obs), na.rm=TRUE))

Arguments

t.obs

A vector of times at which the animal locations were observed

x.obs

A vector of x-coordinates at which the animal locations were observed

y.obs

A vector of y-coordinates at which the animal locations were observed

z.obs

A vector of z-coordinates at which the animal locations were observed

sig2obs

Location error variance in the xy-dimensions

sig2obs.z

Location error variance in the z-dimension

t.max

The maximum time allowed between locations if the movement step is to be used in computing the density

Details

If only 2D or 2.5D MKDEs are to be calculated, then z.obs and sig2obs.z do not have to be provided.

Value

A move data object, in the form of a list, is returned.

dimension

The spatial dimension of the movement data. If z-coordinates are passed, the dimension will be 3; otherwise, the dimension will be 2.

t.obs

Times of the animal locations.

x.obs

x-coordinates of the animal locations.

y.obs

y-coordinates of the animal locations.

z.obs

z-coordinates of the animal locations.

a.obs

Altitude of the animal; that is, its z-coordinate minus the lower bound on the z-coordinate at the corresponding xy-coordinates of the animal location.

use.obs

A logical array that indicates whether each location should be used in the MKDE calculations. By default these values are set to TRUE.

t.max

The maximum time allowed between locations if the movement step is to be used in computing the density

sig2xy

A vector of movemenet variance paramters for the xy-dimensions, with NAs as placeholders. The functions estVarMKDE is provided to estimate these parameters, or they can be set manually to allow for different movement variances for each move step.

sig2z

A vector of movemenet variance paramters for the z-dimension, with NAs as placeholders. The functions estVarMKDE is provided to estimate these parameters, or they can be set manually to allow for different movement variances for each move step.

sig2obs

A vector of variances for the location observation error in the xy-dimensions. If only one value is provided for the variance parameters, the value is repeated to form a vector with one element for each location. Otherwise, a vector of location error variances can be passed to allow for different errors for each observed location.

sig2obs.z

A vector of variances for the location observation error in the z-dimension. If only one value is provided for the variance parameters, the value is repeated to form a vector with one element for each location. Otherwise, a vector of location error variances can be passed to allow for different errors for each observed location.

Author(s)

Jeff A. Tracey, PhD
USGS Western Ecological Research Center, San Diego Field Station
[email protected]
James Sheppard, PhD
San Diego Zoo Institute for Conservation Research
[email protected]

Examples

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data(condor)
mv.dat <- initializeMovementData(condor$time, condor$x,
condor$y, z.obs=condor$z, 65.0, 25.0, sig2obs.z=81.0)

mkde documentation built on May 2, 2019, 6:46 a.m.