BEASTObject that performs calculations based on the State.
A node that can be part of the state.
Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.
Create initial beast.tree by hierarchical clustering, either through one of the classic link methods or by neighbor joining. The following link methods are supported:
o single link,
o complete link,
o UPGMA=average link,
o mean link,
o Ward and
o adjusted complete link
o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining
Logable: yes, this can be used in a log.
clusterType, taxa, distance, clock.rate, initial, trait, taxonset, nodetype, estimate
|type of clustering algorithm used for generating initial beast.tree. Should be one of [single, average, complete, upgma, mean, centroid, ward, adjcomplete, neighborjoining, neighborjoining2] (default average)|
|alignment data used for calculating distances for clustering|
|method for calculating distance between two sequences (default Jukes Cantor)|
|the clock rate parameter, used to divide all divergence times by, to convert from substitutions to times. (default 1.0)|
|tree to start with|
|trait information for initializing traits (like node dates) in the tree|
|set of taxa that correspond to the leafs in the tree|
|type of the nodes in the beast.tree|
|Optional input. Default: beast.evolution.tree.Node|
|whether to estimate this item or keep constant to its initial value|
|Optional input. Default: true|