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.
consensus(..., p = 1, check.labels = TRUE, rooted = FALSE)an object of class "phylo".
either (i) a single object of class "phylo", (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects.
a numeric value between 0.5 and 1 giving the proportion for a clade to be represented in the consensus tree.
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).
a logical specifying whether the trees should be treated as rooted or not.
Emmanuel Paradis
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).
Felsenstein, J. (2004) Inferring Phylogenies. Sunderland: Sinauer Associates.
prop.part, dist.topo