maxCladeCred: Maximum clade credibility tree

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Maximum clade credibility tree

Description

maxCladeCred computes the maximum clade credibility tree from a sample of trees. So far just the best tree is returned. No annotations or transformations of edge length are performed and the edge length are taken from the tree.

Usage

maxCladeCred(x, tree = TRUE, part = NULL, rooted = TRUE)

mcc(x, tree = TRUE, part = NULL, rooted = TRUE)

allCompat(x, rooted = FALSE)

Arguments

x	x is an object of class multiPhylo or phylo
tree	logical indicating whether return the tree with the clade credibility (default) or the clade credibility score for all trees.
part	a list of partitions as returned by prop.part
rooted	logical, if FALSE the tree with highest maximum bipartition credibility is returned.

Details

If a list of partition is provided then the clade credibility is computed for the trees in x.

allCompat returns a 50% majority rule consensus tree with added compatible splits similar to the option allcompat in MrBayes. This tree has no edge length.

add_edge_length can be used to add edge lengths computed from the sample of trees.

Value

a tree (an object of class phylo) with the highest clade credibility or a numeric vector of clade credibilities for each tree.

Author(s)

Klaus Schliep [e-mail]

See Also

consensus, consensusNet, prop.part, bootstrap.pml, plotBS, transferBootstrap, add_edge_length, add_boxplot

Examples

data(Laurasiatherian)
set.seed(42)
bs <- bootstrap.phyDat(Laurasiatherian,
  FUN = function(x)upgma(dist.hamming(x)), bs=100)

strict_consensus <- consensus(bs)
majority_consensus <- consensus(bs, p=.5)
all_compat <- allCompat(bs)
max_clade_cred <- maxCladeCred(bs)

old.par <- par(no.readonly = TRUE)
par(mfrow = c(2,2), mar = c(1,4,1,1))
plot(strict_consensus, main="Strict consensus tree")
plot(majority_consensus, main="Majority consensus tree")
plot(all_compat, main="Majority consensus tree with compatible splits")
plot(max_clade_cred, main="Maximum clade credibility tree")

par(mfrow = c(2,1))
plot(max_clade_cred, main="Edge length from tree")
add_boxplot(max_clade_cred, bs)
max_clade_cred_2 <- add_edge_length(max_clade_cred, bs)
plot(max_clade_cred_2, main="Edge length computed from sample")
add_boxplot(max_clade_cred_2, bs)

par(old.par)

# compute clade credibility for trees given a prop.part object
pp <- prop.part(bs)
tree <- rNNI(bs[[1]], 20)
maxCladeCred(c(tree, bs[[1]]), tree=FALSE, part = pp)
# first value likely be -Inf

KlausVigo/phangorn documentation built on June 23, 2024, 10:49 p.m.