crwN2ll: -2 * log-likelihood for CTCRW models

Description

This function is designed for primary use within the crwMLE model fitting function. But, it can be accessed for advanced R and crawl users. Uses the state-space parameterization and Kalman filter method presented in Johnson et al. (2008).

Usage

crwN2ll(theta, fixPar, y, noObs, delta, mov.mf, err.mfX, err.mfY, rho = NULL,
  activity = NULL, n.errX, n.errY, n.mov, driftMod, prior, need.hess,
  constr = list(lower = -Inf, upper = Inf))

Arguments

theta

parameter values.

fixPar

values of parameters held fixed (contains NA for theta values).

N by 2 matrix of coordinates with the longitude coordinate in the first column.

noObs

vector with 1 for unobserved locations, and 0 for observed locations.

delta

time difference to next location.

mov.mf

Movement covariate data.

err.mfX

longitude error covariate data.

err.mfY

latitude error covariate data.

rho

A vector of known correlation coefficients for the error model, typically used for modern ARGOS data.

activity

Stopping covariate (= 0 if animal is not moving).

n.errX

number or longitude error parameters.

n.errY

number of latitude error parameters.

n.mov

number or movement parameters.

driftMod

Logical. inicates whether a drift model is specified.

prior

Function of theta that returns the log-density of the prior

need.hess

Whether or not the Hessian will need to be calculated from this call

constr

Named list giving the parameter constraints

Value

-2 * log-likelihood value for specified CTCRW model.

Details

This function calls compiled C++ code which can be viewed in the src directory of the crawl source package.

References