AutoCorrelatedLogRates distribution

AutoCorrelatedLogRates(TimeTree tree, Double sigma2, Double rootLogRate, Double[] nodeLogRates)

This parametric distribution generates node-specific log-rates by a Brownian increment process along the given time tree. The root node has a specified log-rate, and each child node’s log-rate is drawn from Normal( parentLogRate, sigma^2 * dt ), where dt is the time between parent and child. This leads to an auto-correlated relaxation of the molecular clock across lineages.

Parameters

• TimeTree tree -
• Double sigma2 -
• Double rootLogRate -
• Double[] nodeLogRates - (optional)

Return type

Double[]

Examples

• autoCorrelatedClock.lphy