Produce table of counts of quartets displayed on trees
Compiles table of quartet count concordance factors (qcCFs) for topological quartets displayed on a collection of trees.
quartetTable(trees, taxonnames = NULL, epsilon = 0, random = 0)
trees |
multiphylo object containing un/rooted metric/topological trees |
taxonnames |
vector of |
epsilon |
minimum for branch lengths to be treated as non-zero |
random |
number of random subsets of 4 taxa to consider; if 0, use all |
The names in taxonnames may be any subset of those on the trees.
Branch lengths of non-negative size less than or equal to epsilon
are treated as zero, giving polytomies.
In the returned table, columns are labeled by taxon names and quartet names ("12|34", etc.). 1s and 0s in taxon columns indicate the taxa in a quartet. Quartet 12|34 means the first and second indicated taxa form a cherry, 13|24 means the first and third form a cherry, 14|23 means the first and fourth form a cherry, and 1234 means the quartet is unresolved.
An error occurs if any branch length is negative.
Warnings are given if some of taxonnames are missing on some trees, or
if some 4-taxon set is not on any tree.
If random>0, then for efficiency random should be much smaller then
the number of possible 4 taxon subsets.
an (n choose 4)x(n+4) matrix (or (random)x(n+4) matrix) encoding
4 taxon subsets of taxonnames and counts of each of the
quartets 12|34, 13|24, 14|23, 1234 across the trees
gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
DQT=quartetTableDominant(RQT)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.