Maximum clade credibility tree
maxCladeCred computes the maximum clade credibility tree from a
sample of trees.
maxCladeCred(x, tree = TRUE, part = NULL, rooted = TRUE) mcc(x, tree = TRUE, part = NULL, rooted = TRUE) allCompat(x)
x |
|
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 |
rooted |
logical, if FALSE the tree with highest maximum bipartition credibility is returned. |
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.
a tree (an object of class phylo) with the highest clade
credibility or a numeric vector of clade credibilities for each tree.
Klaus Schliep klaus.schliep@gmail.com
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
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