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aezarebski / timtam2

This repository is an implementation of the TimTam likelihood as a BEAST2 package.
https://aezarebski.github.io/timtam/
MIT License
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It is very difficult to set up a boom-bust style analysis that only uses sequence data #53

Closed aezarebski closed 1 year ago

aezarebski commented 1 year ago

It is very difficult to set up a boom-bust style analysis that only uses sequence data because the most appropraite parameterisation is missing a fxtemplate file

https://github.com/aezarebski/timtam2/blob/6da605bd6e2ae430575286092c594d54d9327ea6/src/timtam/TimTam.java#L163

A nice solution would be to put together a "sequence only" fxtemplate for the cases where people do not want to worry about the time series. There is also some fiddling around with change times in this setting that would be a pretty big barrier to usage of the model.

aezarebski commented 1 year ago

This has been merged into dev-v2.7 and a couple of example XML files have been included to demonstrate the results