R: Compare Two "phylo" Objects

comparePhylo {ape} | R Documentation

## Compare Two "phylo" Objects

### Description

This function compares two phylogenetic trees, rooted or unrooted, and returns a detailed report of this comparison.

### Usage

    comparePhylo(x, y, plot = FALSE, force.rooted = FALSE,
                 use.edge.length = FALSE, commons = TRUE,
                 location = "bottomleft", ...)
    ## S3 method for class 'comparePhylo'
    print(x, ...)

### Arguments

`x, y` | two objects of class `"phylo"`.
`plot` | a logical value. If `TRUE`, the two trees are plotted on the same device and their similarities are shown.
`force.rooted` | a logical value. If `TRUE`, the trees are considered rooted even if `is.rooted` returns `FALSE`.
`use.edge.length` | a logical value passed to `plot.phylo` (see below).
`commons` | whether to show the splits (the default), or the splits specific to each tree (applies only for unrooted trees).
`location` | location of where to position the `legend`.
`...` | further parameters used by `plot.phylo`, in function `print.comparePhylo` unused.

### Details

In all cases, the numbers of tips and of nodes and the tip labels are compared.

If both trees are rooted, or if `force.rooted = TRUE`, the clade compositions of each tree are compared. If both trees are also ultrametric, their branching times are compared.

If both trees are unrooted and have the same number of nodes, the bipartitions (aka splits) are compared.

If `plot = TRUE`, the edge lengths are not used by default because in some situations with unrooted trees, some splits might not be visible if the corresponding internal edge length is very short. To use edge lengths, set `use.edge.length = TRUE`.

### Value

an object of class `"comparePhylo"` which is a list with messages from the comparison and, optionally, tables comparing branching times.

### Author(s)

Emmanuel Paradis, Klaus Schliep

### See Also

`all.equal.phylo`

### Examples

    ## two unrooted trees but force comparison as rooted:
    a <- read.tree(text = "(a,b,(c,d));")
    b <- read.tree(text = "(a,c,(b,d));")
    comparePhylo(a, b, plot = TRUE, force.rooted = TRUE)
    ## two random unrooted trees:
    c <- rtree(5, rooted = FALSE)
    d <- rtree(5, rooted = FALSE)
    comparePhylo(c, d, plot = TRUE)

[Package ape version 5.6-2 Index]