phangorn (version 2.11.1)

maxCladeCred: Maximum clade credibility tree

Description

maxCladeCred computes the maximum clade credibility tree from a sample of trees.

Usage

maxCladeCred(x, tree = TRUE, part = NULL, rooted = TRUE)
mcc(x, tree = TRUE, part = NULL, rooted = TRUE)
allCompat(x, rooted = FALSE)

Value

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

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.

Author

Klaus Schliep

Details

So far just the best tree is returned. No annotations or transformations of edge length are performed.

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.

See Also

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

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(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