Random local clock – rate change prior

This prior is over the number of internal nodes where a rate change takes place in the random local clock (Drummond & Suchard, 2010). When this is 0, the model behaves like the strict clock, and when it is the number of internal nodes it behaves like a relaxed clock (uncorrelated if ratesAreMultipliers=false and correlated if ratesAreMultipliers=true).

Usually, you want to encourage a low number of rate changes, so for example a Possion distribution with a low mean as prior would be appropriate. If the data indicates there are many rate changes, the random local clock will accomodate this if the prior is not too strong.

References

Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. BMC biology. 2010 Dec;8(1):1-2. doi:10.1186/s12862-020-01609-4.