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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Burn-in for GSS #1031

Closed maxbiostat closed 6 years ago

maxbiostat commented 6 years ago

Since currently in BEAUti there is not fill box for the number of burn-in iterations to use in the GSS, it just chucks in burnin="10000000" in the relevant block. I reckon this might be inappropriate if one chooses something different from the default, e.g. 250000 iterations, for which the current burn-in would be a bit much.

GuyBaele commented 6 years ago

Burn-in amounts to 10% of the selected chain length for the full analysis, so in the case of 250.000 iterations (for example), burn-in will equal 25.000 iterations and will be (or should be) adjusted automatically by BEAUti. Your report indicates that burn-in is always set to 10 million, is this the case?

maxbiostat commented 6 years ago

I believe this to be the case, yes.

On Fri, 28 Sep 2018 at 18:32, Guy Baele notifications@github.com wrote:

Burn-in amounts to 10% of the selected chain length per path step, so in the case of 250.000 iterations, burn-in will equal 25.000 iterations and will be (or should be) adjusted automatically by BEAUti. Your report indicates that burn-in is always set to 1 million, is this the case?

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GuyBaele commented 6 years ago

Working fine.