maxCladeCred

0th

Percentile

Maximum clade credibility tree

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

Keywords
cluster
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.

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.

Value

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

See Also

consensus, consensusNet, prop.part

Aliases
  • maxCladeCred
  • mcc
  • allCompat
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)
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")

# 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

# }
Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)

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