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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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Use a more natural parameterisation as done by `bdsky` #43

Closed aezarebski closed 2 years ago

aezarebski commented 2 years ago

Currently the model is parameterized in terms of rates, however we are often more interested in parameters such as R-naught and the net becoming noninfectious rate and the proportion of cases sequenced and observed. It would be nice to have an alternative parameterization for this. See for example https://github.com/BEAST2-Dev/bdsky/blob/ec2caf66a58b59cc82a7b8391dbd06b25fe67ca6/src/beast/evolution/speciation/BirthDeathSkylineModel.java#L251

aezarebski commented 2 years ago

This has been implemented, but the documentation is poor.