formatHierHMM: 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
)

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.

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.