Paint all possible regimes

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Description

Creates all regimes possible for the nodes specified on the trees provided, returning for each tree only those regimes that are present on that tree, and

Usage

1
  regimeVectors(ouchTrees, cladeMembersList, maxNodes = NULL)

Arguments

ouchTrees

A list of S4 ouchtree objects

cladeMembersList

A list of taxa defining nodes.

maxNodes

The maximum number of nodes at which a regime may change.

Details

regimeVectors is the basic call to get all regime permutations for analysis in batchHansen.

Value

A list with three items:

regList

A list (by tree) of lists of regimes that can be input directly into hansen.

nodeMatrix

A matrix indicating which nodes are presentin each tree.

regMatrix

A list (by tree) of matrices indicating which nodes are present in each model.

Author(s)

Andrew Hipp ahipp@mortonarb.org

See Also

paintBranches, link{regimeMatrix}, link{regimeMaker}