beaked.hmm.pars: Alboran sea beaked whale availability HMM parameters.

In david-borchers/hmltm: Line transect estimation with hidden Markov availability models

Alboran sea beaked whale availability HMM parameters.

Description

Hidden Markov model (HMM) parameter estimates for beaked whale availability obtained from mean times available and unavailable observed by Ana Canadas (pers commn.) in thge Alboran sea. This dataset was used in the analyses of Borchers et al. (2013).

Usage

beaked.hmm.pars

Format

A list with the following five elements.

pm:

a 2x1 matrix containing the vector of state-dependent Bernoulli availability parameters. pm[1,i] is the probability of whale i being available given state 1 (the less available behavoural state), and pm[1,i] is the probability of whale i being available given state 1 (the more available behavoural state).

Pi:

a 2x2x1 array containg the transition probability matrix. States can be interpreted as behavioural states, one of which being a state in which the animal is more likely to be available than when in the other state.

delta:

a 2x1 matrix containing the stationary distribution of Pi for each whale. So delta[1,i] is the probability that whale i is in behavioural state 1 when observation starts, and delta[2,i] is the probability that it is in behavioural state 2 when observation starts.

Et:

a 2x1 matrix containing the expected times animals are available and unavailable (in seconds).

Sigma.Et:

a 2x2 matrix containing variance-covariance matrix of the expected times animals are available and unavailable.

Source

Canadas (pers commn.).

References

Borchers, D.L., Zucchini, W., Heide-Jorgenssen, M.P., Canadas, A. and Langrock, R. 2013. Using hidden Markov models to deal with availability bias on line transect surveys. Biometrics.

Examples

 data(beaked.hmm.pars)

david-borchers/hmltm documentation built on Oct. 29, 2023, 9:07 p.m.