Paint branches for Ornstein-Uhlenbeck analysis

Description

Paints branches with regimes changing at nodes specified. Called by regimeVectors.

Usage

1
  paintBranches(regimeShiftNodes, tree, regimeTitles)

Arguments

regimeShiftNodes

Either a vector of nodes (by number) at which the selective regime changes, or a list of taxa defining nodes. This allows you to use paintBranches with the same nodes you use to call runBatchHansen. This parameter may include the root but does not need to.

tree

An S4 ouchtree object, generated using ape2ouch or ouchtree. Old-style ouch trees (data frames) will not work but can be translated using ouchtree.

regimeTitles

Titles for the regimes.

Details

regimeTitles is a vector of titles for the regimes that begin at the root and at the nodes indicated in regimeShiftNodes in order of description in "regimeShiftNodes", except that the root is listed first in regimeTitles but may not be included at all in regimeShiftNodes.

Value

A regime in which shifts in optimum are coded as occuring at all nodes specified in regimeShiftNodes. The regime is formated to input directly into hansen

Author(s)

Andrew Hipp ahipp@mortonarb.org

See Also

regimeVectors, isMonophyletic