Maximum Clade Information Tree

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)

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.

Value

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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

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

# Maximum Clade Information tree
mci <- MCITree(trees)
SplitwiseInfo(mci)
#> [1] 133.8514
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)
#> [1] 128.5908
# }