formatHierHMM: Convert hierarchical HMM structure to a conventional HMM

Description Usage Arguments Value

View source: R/formatHierHMM.R

Description

Convert hierarchical HMM structure to a conventional HMM

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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 July 7, 2021, 9:06 a.m.