R: Concensus Trees

consensus {ape} | R Documentation

## 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).

### 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`

[Package ape version 5.6-2 Index]