regimeVectors: Paint all possible regimes

Description Usage Arguments Details Value Author(s) See Also

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}



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