AutoCorrelatedClock function

AutoCorrelatedClock(TimeTree tree, Double[] nodeLogRates, Double rootLogRate, Double sigma2, Double meanRate, Boolean normalize, Integer taylorOrder)

This deterministic function calculates the mean substitution rate on each branch of a phylogeny under an autocorrelated Brownian motion (log-rate) model. For each parent-child node pair, the average rate is computed via a bridging integral (the so-called MeanZ approach). Optionally, the average rates can be normalized so that the time-weighted mean rate over the entire tree is 1.0.

Parameters

• TimeTree tree -
• Double[] nodeLogRates -
• Double rootLogRate -
• Double sigma2 -
• Double meanRate - (optional)
• Boolean normalize - (optional)
• Integer taylorOrder - (optional)

Return type

Object

Examples

• autoCorrelatedClock.lphy