formatHierHMM: Convert hierarchical HMM structure to a conventional HMM

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

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.

momentuHMM documentation built on Oct. 19, 2022, 1:07 a.m.