phangorn (version 2.8.1)

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)

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.

Value

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

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 compatible splits similar to the option allcompat in MrBayes.

See Also

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

Examples

# NOT RUN {

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

# }