porpoise.hmm.pars: Harbour porpoise availability HMM parameters.

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

Harbour porpoise availability HMM parameters.

Description

Hidden Markov model (HMM) parameter estimates for harbour porpoise availability obtained the dive durations and proportons of time available of 7 tagged harbour porpoise, as reported by Westgate et al. (1995). HMM parameters were obtained using funtion make.hmm.pars.from.Et.

Usage

porpoise.hmm.pars

Format

A list with the following three elements.

Pi:

a 2x2x7 array containg the 7 HMM transition probability matrices (one for each tagged porpoise). 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.

pm:

a 2x7 matrix containing the 8 vectors of state-dependent Bernoulli availability parameters. pm[1,i] is the probability of porpoise i being available given state 1 (the less available behavoural state), and pm[1,i] is the probability of porpoise i being available given state 1 (the more available behavoural state).

delta:

the stationary distribution of Pi for each porpoise. So delta[1,i] is the probability that porpoise 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.

Source

Westgate et al. (1995).

References

Westgate, A. J., Read, A. J., Berggren, P., Koopman, H. N., and Gaskin, D. E. 1995. Diving behaviour of harbour porpoises, Phocoena phocoena. Canadian Journal of Fisheries and Aquatic Sciences 52, 1064-1073.

Examples

 data(porpoise.hmm.pars)

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