quartetTable: Produce table of counts of quartets displayed on trees

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Produce table of counts of quartets displayed on trees

Description

Compiles table of quartet count concordance factors (qcCFs) for topological quartets displayed on a collection of trees.

Usage

quartetTable(
  trees,
  taxonnames = NULL,
  epsilon = 0,
  random = 0,
  progressbar = FALSE
)

Arguments

trees	multiphylo object containing un/rooted metric/topological trees
taxonnames	vector of n names of taxa of interest; if NULL then taken from taxa on trees[[1]]
epsilon	minimum for branch lengths to be treated as non-zero (default 0)
random	number of random subsets of 4 taxa to consider; if 0, use all n choose 4 subsets
progressbar	FALSE, set to TRUE if want to see tally progress

Details

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.

This function calls an Rcpp function for tallying quartets, for much shorter computational time than can be achieved in R alone.

Value

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

See Also

quartetTableParallel, quartetTableResolved, quartetTableDominant, taxonNames

Examples

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)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.