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beast-dev / tracer

Posterior summarisation in Bayesian phylogenetics
https://beast.community/tracer
GNU Lesser General Public License v2.1
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What to do with categorical values with frequency 0? #128

Open GuyBaele opened 6 years ago

GuyBaele commented 6 years ago

When loading a trace with categorical values into Tracer, it may contain several categories that were only visited during the burn-in. When the burn-in is subsequently omitted, some categories will have frequency 0. I've committed a small fix that avoids a NullPointerException for those categories, but the question remains: should we still plot that category (in the marginal density panel) but with frequency 0, or should we not plot those categories at all?

rambaut commented 6 years ago

The other aspect of this is that a categorical value may not be visit even in burnin. Ideally all values should be shown even if zero frequency. Tracer has no way of knowing unvisited states exist. BEAST could define the set of categorical values in the log file's header (the initial lines prefixed with #).