Description Usage Arguments Details Value Author(s) References See Also

Estimate marginal likelihood by thermodynamic integration and Gauss-Legendre
quadrature from a sample of `n`

power posterior MCMC chains sampled
with mcmctree (or bpp).

1 | ```
gauss.quad(mcmcf = "mcmc.txt", betaf = "beta.txt")
``` |

`mcmcf` |
character, mcmc output file name |

`betaf` |
character, file with beta values |

The MCMC samples should be stored in a directory structure created
by `make.bfctlf`

with `method = "gauss-quad"`

. The function
will read the stored log-likelihood values and calculate the log-marginal
likelihood.

Numerical integration is done using Gauss-Legendre quadrature. See Rannala and Yang (2017) for details (also dos Reis et al. 2017, Appendix 2).

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
used.

Mario dos Reis

Rannala B and Yang Z. (2017) Efficient Bayesian species tree inference under
the multispecies coalescent. *Systematic Biology* 66: 823-842.

dos Reis et al. (2017) Using phylogenomic data to explore the effects of
relaxed clocks and calibration strategies on divergence time estimation:
Primates as a test case. *bioRxiv*

`make.bfctlf`

to prepare directories and mcmctree control files
to calculate the power posterior.

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