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)
)

Value

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

Arguments

theta: parameter values.
fixPar: values of parameters held fixed (contains NA for theta values).
y: 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. indicates 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

Author

Devin S. Johnson

Details

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

References

Johnson, D., J. London, M. -A. Lea, and J. Durban. 2008. Continuous-time model for animal telemetry data. Ecology 89:1208-1215.