SetModel4M-class: An S4 class to hold model definition and fitting parameters.

In lawlerem/markmodmover: Analyze animal movement data using the Markov-modulated movement model.

Description

An S4 class to hold model definition and fitting parameters.

Slots

N.States

The number of states n used in the model.

Use.HMM

If TRUE fixes autocorrelation to zero.

Distribution

Distribution for step length. Can be one of gamma or log-normal.

Zero.Inflation

A named logical vector with entries Step.Length and Deflection.Angle. A TRUE entry enables zero inflation.

Starting.Values

A named list giving the starting values of the working parameters with the following entries:

Tpm.Working.Pars

An n by n matrix.

Theta.Working.Pars

An n by 2 matrix. The first column is untransformed center, the second is the logit of concentration.

Step.Working.Pars

An n by 3 matrix. The first column is the log of the reversion level, the second is the logit of the autocorrelation, the third is the log of the standard deviation.

Logit.Step.Zero.Probs

A length n vector.

Logit.Angle.Zero.Probs

A length n vector.

Angle.Zero.Working.Pars

An n by 2 matrix.

Parameter.Mapping

A named list with the same structure as Starting.Values. Controls TMB parameter mapping. See details of MakeADFun.

See Also

Other 4M-classes: Data4M-class, Model4M-class, SetSim4M-class, Simulate4M-class

lawlerem/markmodmover documentation built on Feb. 12, 2020, 8:30 p.m.