regimeVectors {maticce} | R Documentation |
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
regimeVectors(ouchTrees, cladeMembersList, maxNodes = NULL)
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. |
regimeVectors
is the basic call to get all regime permutations for analysis in batchHansen.
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. |
Andrew Hipp ahipp@mortonarb.org
paintBranches
, link{regimeMatrix}
, link{regimeMaker}