TreeDist (version 2.14.1)

MCITree: Maximum Clade Information Tree

Description

Analogous to the Maximum Clade Credibility tree: select the tree from a posterior distribution whose clades have the highest information content. Generate the MCC tree by specifying info = "credibility".

Usage

MCITree(trees, info = "phylogenetic", check.tips = TRUE)

Value

MCITree() returns the tree with the highest information content, selected from trees.

Arguments

trees

List of phylo objects, optionally with class multiPhylo.

info

Abbreviation of "phylogenetic" or "clustering", specifying the concept of information to employ.

check.tips

Logical specifying whether to renumber leaves such that leaf numbering is consistent in all trees.

Author

Martin R. Smith ()

See Also

Other summary trees: TransferConsensus()

Examples

library("TreeTools", quietly = TRUE)
trees <- as.phylo(24:40, 16)

# Maximum Clade Information tree
mci <- MCITree(trees)
SplitwiseInfo(mci)
plot(mci)
p <- SplitFrequency(mci, trees) / length(trees)
LabelSplits(mci, round(p * 100), "%", bg = SupportColor(p))

# \donttest{
# Compare with Maximum Clade Credibility tree
mcc <- MCITree(trees, "credibility")
plot(mcc)
p <- SplitFrequency(mcc, trees) / length(trees)
LabelSplits(mcc, round(p * 100), "%", bg = SupportColor(p))
SplitwiseInfo(mcc)
# }