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