test.tree.preparation: data structure preparation for testing a population tree

In phylolm: Phylogenetic Linear Regression

data structure preparation for testing a population tree

Description

Takes a guide tree and quartet concordance factor data, and makes preliminary calculations to speed up the test of adequacy of a population tree with test.one.species.tree.

Usage

test.tree.preparation(cf, guidetree)

Arguments

cf	data frame containing one row for each 4-taxon set, with taxon names in columns 1-4.
guidetree	tree of class phylo on the same taxon set as those in cf.

Value

quartet2edge	matrix of booleans with as many rows as in cf (one row for each 4-taxon set) and with as many columns as edges in guidetree. For a given set of 4 taxa and for edge i, the corresponding entry is true if the guide tree pruned to the 4 taxa includes edge i as part of its internal edge.
dominant	Vector with as many entries as rows in cf, one for each 4-taxon set. Entries are 1, 2 or 3 depending on the quartet displayed in the guide tree: 1 for the quartet 12|34 (i.e. taxon1 + taxon2 versus taxon3 + taxon4), 2 for the quartet 13|24 and 3 for the quartet 14|23.

See Also

test.one.species.tree.

phylolm documentation built on Oct. 1, 2024, 1:09 a.m.