parDef: Parameters definition

In bmcclintock/momentuHMM: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

Parameters definition

Description

Parameters definition

Usage

parDef(
  dist,
  nbStates,
  estAngleMean,
  zeroInflation,
  oneInflation,
  DM,
  userBounds = NULL
)

Arguments

dist	Named list indicating the probability distributions of the data streams.
nbStates	Number of states of the HMM.
estAngleMean	Named list indicating whether or not to estimate the angle mean for data streams with angular distributions ('vm' and 'wrpcauchy').
zeroInflation	Named list of logicals indicating whether the probability distributions of the data streams should be zero-inflated.
oneInflation	Named list of logicals indicating whether the probability distributions of the data streams are one-inflated.
DM	An optional named list indicating the design matrices to be used for the probability distribution parameters of each data stream. Each element of DM can either be a named list of linear regression formulas or a matrix.
userBounds	An optional named list of 2-column matrices specifying bounds on the natural (i.e, real) scale of the probability distribution parameters for each data stream. For example, for a 2-state model using the wrapped Cauchy ('wrpcauchy') distribution for a data stream named 'angle' with estAngleMean$angle=TRUE), userBounds=list(angle=matrix(c(-pi,-pi,-1,-1,pi,pi,1,1),4,2)) specifies (-1,1) bounds for the concentration parameters instead of the default [0,1) bounds.

Value

A list of:

parSize	Named list indicating the number of natural parameters of the data stream probability distributions.
bounds	Named list of 2-column matrices specifying bounds on the natural (i.e, real) scale of the probability distribution parameters for each data stream.
parNames	Names of parameters of the probability distribution for each data stream.
Bndind	Named list indicating whether DM is NULL with default parameter bounds for each data stream.

Examples

## Not run: 
pD<-momentuHMM:::parDef(list(step="gamma",angle="wrpcauchy"),
    nbStates=2,list(step=FALSE,angle=FALSE),list(step=FALSE,angle=FALSE),
    list(step=FALSE,angle=FALSE),NULL,NULL)

## End(Not run)

bmcclintock/momentuHMM documentation built on Oct. 26, 2022, 1 a.m.