nLogLike_rcpp {moveHMM}

Negative log-likelihood

Description

Computation of the negative log-likelihood (forward algorithm - written in C++)

Usage

nLogLike_rcpp(
  nbStates,
  beta,
  covs,
  data,
  stepDist,
  angleDist,
  stepPar,
  anglePar,
  delta,
  aInd,
  zeroInflation,
  stationary,
  knownStates
)

Arguments

nbStates

Number of states

beta

Matrix of regression coefficients for the transition probabilities

covs

Covariates

data

A moveData object of the observations

stepDist

The name of the step length distribution

angleDist

The name of the turning angle distribution

stepPar

State-dependent parameters of the step length distribution

anglePar

State-dependent parameters of the turning angle distribution

delta

Stationary distribution

aInd

Vector of indices of the rows at which the data switches to another animal

zeroInflation

true if zero-inflation is included in the step length distribution, false otherwise.

stationary

false if there are covariates. If true, the initial distribution is considered equal to the stationary distribution.

knownStates

Vector of values of the state process which are known prior to fitting the model (if any). Default: NULL (states are not known). This should be a vector with length the number of rows of 'data'; each element should either be an integer (the value of the known states) or NA if the state is not known.

Value

Negative log-likelihood