Author: de Silva, Eric; Ferguson, Neil M.; Fraser, Christophe
Title: Inferring pandemic growth rates from sequence data Document date: 2012_8_7
ID: 1piyoafd_30
Snippet: The tuning parameters that control the speed and efficiency with which the MCMC chain used to sample tree space in BEAST equilibriates are automatically optimized. Required MCMC chain lengths are determined via evaluation of the effective sample sizes (ESSs) for the parameters of interest, and depend strongly on the number of sampled sequences. The ESS is the number of effectively independent draws from a marginal posterior distribution of a para.....
Document: The tuning parameters that control the speed and efficiency with which the MCMC chain used to sample tree space in BEAST equilibriates are automatically optimized. Required MCMC chain lengths are determined via evaluation of the effective sample sizes (ESSs) for the parameters of interest, and depend strongly on the number of sampled sequences. The ESS is the number of effectively independent draws from a marginal posterior distribution of a parameter that a particular length of MCMC chain is equivalent to. A low ESS for a given parameter implies high correlation between MCMC samples and that the posterior distribution will be poor. The software package 'TRACER' (http://tree.bio.ed.ac.uk/software/tracer/) is used to check ESSs and examine the trace for any trends that may indicate lack of convergence, or any long-range fluctuations indicative of poor mixing.
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