PhyloOU(TimeTree tree, Double diffRate, Double theta, Double alpha, Double y0, Double[] branchThetas)

The phylogenetic Ornstein-Ulhenbeck distribution. A continous trait is simulated for every leaf node, and every direct ancestor node with an id.

Parameters

  • TimeTree tree - the time tree.
  • Double diffRate - the variance of the underlying Brownian process. This is not the equilibrium variance of the OU process.
  • Double theta - (optional) the ‘optimal’ value that the long-term process is centered around.
  • Double alpha - the drift term that determines the rate of drift towards the optimal value.
  • Double y0 - the value of continuous trait at the root.
  • Double[] branchThetas - (optional) the ‘optimal’ value for each branch in the tree.

Return type

ContinuousCharacterData

Examples

  • simplePhyloOU.lphy

Reference

Felsenstein J. (1973). Maximum-likelihood estimation of evolutionary trees from continuous characters. American journal of human genetics, 25(5), 471–492.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762641/