| initializeMovementData {mkde} | R Documentation |
Initialize a movement data list
Description
This function sets up the movement data for use in other functions in the package.
Usage
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
jatracey@usgs.gov
James Sheppard, PhD
San Diego Zoo Institute for Conservation Research
jsheppard@sandiegozoo.org
Examples
data(condor)
mv.dat <- initializeMovementData(condor$time, condor$x,
condor$y, z.obs=condor$z, 65.0, 25.0, sig2obs.z=81.0)