consensus: Concensus Trees

In ape: Analyses of Phylogenetics and Evolution

Concensus Trees

Description

Given a series of trees, this function returns the consensus tree. By default, the strict-consensus tree is computed. To get the majority-rule consensus tree, use p = 0.5. Any value between 0.5 and 1 can be used.

Usage

consensus(..., p = 1, check.labels = TRUE, rooted = FALSE)

Arguments

...	either (i) a single object of class "phylo", (ii) a series of such objects separated by commas, or (iii) a list containing such objects.
p	a numeric value between 0.5 and 1 giving the proportion for a clade to be represented in the consensus tree.
check.labels	a logical specifying whether to check the labels of each tree. If FALSE (the default), it is assumed that all trees have the same tip labels, and that they are in the same order (see details).
rooted	a logical specifying whether the trees should be treated as rooted or not.

Details

Using check.labels = FALSE results in considerable decrease in computing times. This requires that all trees have the same tip labels, and these labels are ordered similarly in all trees (in other words, the element tip.label are identical in all trees).

Until ape 5.6-2, the trees passed to this function were implicitly treated as rooted, even when the option rooted = FALSE was used. This is now fixed (see PR65 on GitHub) so that, by default, the trees are explicitly treated as unrooted (even if is.rooted returns TRUE). Thus, it could be that results now differ from previous analyses (setting rooted = TRUE might help to replicate previous results).

Value

an object of class "phylo".

Author(s)

Emmanuel Paradis

References

Felsenstein, J. (2004) Inferring Phylogenies. Sunderland: Sinauer Associates.

See Also

prop.part, dist.topo

ape documentation built on May 29, 2024, 10:50 a.m.