consensus: Concensus Trees

Description Usage Arguments Details Value Author(s) References See Also

View source: R/dist.topo.R

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

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

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).

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).

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 April 5, 2018, 1:03 a.m.