R: Perform a single step of the MCMC sampling process for...

sampleStep {skipTrack}

R Documentation

Perform a single step of the MCMC sampling process for skipTrack

Description

This function performs a single step of the Markov Chain Monte Carlo (MCMC) algorithm to update parameters in a hierarchical model used for identifying skips in menstrual cycle tracking.

Usage

sampleStep(
  ijDat,
  iDat,
  rho,
  pi,
  Xi,
  Zi,
  Beta,
  Gamma,
  priorAlphas,
  indFirst,
  rhoBeta,
  rhoGamma,
  phi,
  rhoPhi,
  fixedSkips
)

Arguments

`ijDat`	A data.frame with individual-observation level parameters: Individual, ys, cijs, muis, tauis.
`iDat`	A data.frame with individual level parameters: Individual, mus, taus, thetas.
`rho`	Updated value of the global parameter rho.
`pi`	Updated value of the global parameter pi.
`Xi`	A matrix (numIndividuals x length(Beta)) of covariates for cycle length mean. Default is a vector of 1's. NOTE THE DIFFERENCE (from skipTrack.MCMC) IN EXPECTED DIMENSION OF X
`Zi`	A matrix (numIndividuals x length(Gamma)) of covariates for cycle length precision. Default is a vector of 1's. NOTE THE DIFFERENCE (from skipTrack.MCMC) IN EXPECTED DIMENSION OF Z
`Beta`	Matrix (1 x length(Beta)) of coefficients for cycle length mean.
`Gamma`	Matrix of (1 x length(Gamma)) coefficients for cycle length precision.
`priorAlphas`	Vector of prior alpha values for updating pi.
`indFirst`	A logical vector indicating the first occurrence of each individual.
`rhoBeta`	Updated value of the global parameter rhoBeta.
`rhoGamma`	Value of the proposal parameter rhoGamma.
`phi`	Value of the parameter phi.
`rhoPhi`	Value of the proposal parameter rhoPhi.
`fixedSkips`	Logical. If TRUE cycle skip information (cijs) is not updated in sample steps and the inputs are instead assumed to be true.

Value

A list containing updated parameters after performing a single MCMC step. The list includes:

ijDat: A data.frame with updated parameters at the individual-observation level: Individual, ys, cijs, muis, tauis.
iDat: A data.frame with updated parameters at the individual level: Individual, mus, taus, thetas.
rho: Updated value of the global parameter rho.
pi: Updated value of the global parameter pi.
Xi: Matrix of covariates for cycle length mean.
Zi: Matrix of covariates for cycle length precision.
Beta: Updated matrix of coefficients for cycle length mean.
Gamma: Updated matrix of coefficients for cycle length precision.
priorAlphas: Vector of prior alpha values for updating pi.
indFirst: A logical vector indicating the first occurrence of each individual.
rhoBeta: Hyperprior parameter rhoBeta, used to update Beta.
rhoGamma: Value of the proposal parameter rhoGamma.
phi: Updated value of the parameter phi.
rhoPhi: Value of the proposal parameter rhoPhi.
fixedSkips: Logical. Indicates if skips were fixed.

[Package skipTrack version 0.1.0 Index]