R: Convert hierarchical HMM structure to a conventional HMM

formatHierHMM {momentuHMM}

R Documentation

Convert hierarchical HMM structure to a conventional HMM

Description

Convert hierarchical HMM structure to a conventional HMM

Usage

formatHierHMM(
  data,
  hierStates,
  hierDist,
  hierBeta = NULL,
  hierDelta = NULL,
  hierFormula = NULL,
  hierFormulaDelta = NULL,
  mixtures = 1,
  workBounds = NULL,
  betaCons = NULL,
  deltaCons = NULL,
  fixPar = NULL,
  checkData = TRUE
)

Arguments

`data`	`momentuHierHMMData` object or a data frame containing the data streams and covariates.
`hierStates`	A hierarchical data structure `Node` for the states ('state'). See `fitHMM`.
`hierDist`	A hierarchical data structure `Node` for the data streams ('dist'). See `fitHMM`.
`hierBeta`	A hierarchical data structure `Node` for the matrix of initial values for the regression coefficients of the transition probabilities at each level of the hierarchy ('beta'). See `fitHMM`.
`hierDelta`	A hierarchical data structure `Node` for the matrix of initial values for the regression coefficients of the initial distribution at each level of the hierarchy ('delta'). See `fitHMM`.
`hierFormula`	A hierarchical formula structure for the transition probability covariates for each level of the hierarchy ('formula'). See `fitHMM`. Default: `NULL` (only hierarchical-level effects, with no covariate effects).
`hierFormulaDelta`	A hierarchical formula structure for the initial distribution covariates for each level of the hierarchy ('formulaDelta'). See `fitHMM`. Default: `NULL` (no covariate effects and `fixPar$delta` is specified on the working scale).
`mixtures`	Number of mixtures for the state transition probabilities (i.e. discrete random effects sensu DeRuiter et al. 2017). See `fitHMM`. Default: `mixtures=1`.
`workBounds`	A list with elements named `'beta'` and/or `'delta'`, where each element is a hierarchical data structure `Node` indicating t.p.m. and initial distribution working parameter bounds ('workBounds') for parameters in `hierBeta` and `hierDelta`, respectively.
`betaCons`	A hierarchical data structure `Node` indicating t.p.m. constraints ('betaCons') among parameters in `hierBeta` at each level of the hierarchy.
`deltaCons`	A hierarchical data structure `Node` indicating initial distribution constraints ('deltaCons') among parameters in `hierDelta` at each level of the hierarchy.
`fixPar`	A list with elements named `'beta'` and/or `'delta'`, where each element is a hierarchical data structure `Node` indicating t.p.m. and initial distribution parameters in `hierBeta` and `hierDelta`, respectively, which are assumed known.
`checkData`	logical indicating whether or not to check the suitability of `data` for the specified hierarchy. Ignored unless `data` is provided. Default: TRUE.

Value

A list of arguments needed for specifying a hierarchical HMM as a conventional HMM in fitHMM or MIfitHMM, including:

`nbStates`	See `fitHMM`.
`dist`	See `fitHMM`.
`formula`	See `fitHMM`.
`formulaDelta`	See `fitHMM`.
`beta0`	See `fitHMM`.
`delta0`	See `fitHMM`.
`betaRef`	See `fitHMM`.
`betaCons`	See `fitHMM`.
`deltaCons`	See `fitHMM`.
`fixPar`	See `fitHMM`.
`workBounds`	See `fitHMM`.
`stateNames`	See `fitHMM`.

[Package momentuHMM version 1.5.5 Index]