R: Maximum clade credibility tree

maxCladeCred {phangorn} | R Documentation

## 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.

### 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.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### See Also

`consensus`, `consensusNet`, `prop.part`

### 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

[Package phangorn version 2.6.2 Index]