Computation of standard errors for Bayes factors

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Description

Compute the standard errors for the Bayes factors estimates.

Usage

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bfse(pargrid, runs, nbatches, bfsize1 = 0.8, method = c("RL", "MW"),
  reference = 1, transf = FALSE, bmmcse.size = "sqroot")

Arguments

pargrid

A data frame with components "linkp", "phi", "omg", "kappa". Each row gives a combination of the parameters to compute the new standard errors.

runs

A list with outputs from the function mcsglmm or mcstrga.

nbatches

An integer scalar or vector of the same length as runs indicating the number of batches to create for computing the variance using the samples of the first stage.

bfsize1

A scalar or vector of the same length as runs with all integer values or all values in (0, 1]. How many samples (or what proportion of the sample) to use for estimating the Bayes factors at the first stage. The remaining sample will be used for estimating the standard errors in the second stage. Setting it to 1 will perform only the first stage.

method

Which method to use to calculate the Bayes factors: Reverse logistic or Meng-Wong.

reference

Which model goes in the denominator.

transf

Whether to use the transformed sample mu for the computations. Otherwise it uses z.

bmmcse.size

Size for computing the batch means Monte-Carlo variance using the samples of the second stage.

Details

Uses the batch means method to compute the standard errors for Bayes factors.

Value

A list with components

  • pargrid The inputted pargrid augmented with the computed standard errors.

  • bfEstimate The estimates of the Bayes factors

  • bfSigma The covariance matrix for the Bayes factors estimates.

References

Roy, V., Tan, A. and Flegal, J. (2015). Estimating standard errors for importance sampling estimators with multiple Markov chains. Technical report, Iowa State University. http://lib.dr.iastate.edu/stat_las_preprints/34