Estimate the marginal likelihood using the stepping stones
method from a sample of
n power posterior MCMC chains sampled
with mcmctree (or bpp).
stepping.stones(mcmcf = "mcmc.txt", betaf = "beta.txt")
character, mcmc output file name
character, file with beta values
The MCMC samples should be stored in a directory structure created
method = "step-stones". The function will
read the stored log-likelihood values and calculate the log-marginal
An approximation based on the Delta method is used to calculate the standard error (see Xie et al. 2011). Warnings are given if the approximation appears unreliable.
A list with components
logml, the log-marginal likelihood estimate;
se, the standard error of the estimate;
mean.logl, the mean of
log-likelihood values sampled for each beta; and
b, the beta values
Mario dos Reis
Xie et al. (2011) Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology, 60: 150–160.
make.bfctlf to prepare directories and mcmctree control files
to calculate the power posterior.
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