The site concordance factor (Minh et al. 2020) is a measure of the strength of support that the dataset presents for a given split in a tree.

QuartetConcordance(tree, dataset = NULL)

ClusteringConcordance(tree, dataset)

PhylogeneticConcordance(tree, dataset)

MutualClusteringConcordance(tree, dataset)

SharedPhylogeneticConcordance(tree, dataset)

Arguments

tree

A tree of class phylo.

dataset

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree.

Details

QuartetConcordance() is the proportion of quartets (sets of four leaves) that are decisive for a split which are also concordant with it. For example, a quartet with the characters 0 0 0 1 is not decisive, as all relationships between those leaves are equally parsimonious. But a quartet with characters 0 0 1 1 is decisive, and is concordant with any tree that groups the first two leaves together to the exclusion of the second.

NOTE: These functions are under development, and may be incompletely tested or change without notice. Complete documentation and discussion will follow soon.

References

Minh BQ, Hahn MW, Lanfear R (2020). “New methods to calculate concordance factors for phylogenomic datasets.” Molecular Biology and Evolution, 37(9), 2727--2733. doi:10.1093/molbev/msaa106 .

See also

Other split support functions: JackLabels(), Jackknife(), MaximizeParsimony()

Examples

data('congreveLamsdellMatrices', package = 'TreeSearch')
dataset <- congreveLamsdellMatrices[[1]][, 1:20]
tree <- referenceTree
qc <- QuartetConcordance(tree, dataset)
cc <- ClusteringConcordance(tree, dataset)
pc <- PhylogeneticConcordance(tree, dataset)
spc <- SharedPhylogeneticConcordance(tree, dataset)
mcc <- MutualClusteringConcordance(tree, dataset)

oPar <- par(mar = rep(0, 4), cex = 0.8)
plot(tree)
TreeTools::LabelSplits(tree, signif(qc, 3))
TreeTools::LabelSplits(tree, signif(cc, 3))
TreeTools::LabelSplits(tree, signif(pc, 3))

par(oPar)

pairs(cbind(qc, cc, pc, spc, mcc))