all.equal.phylo: Global Comparison of two Phylogenies

Description

This function makes a global comparison of two phylogenetic trees.

Usage

## S3 method for class 'phylo':
all.equal(target, current, use.edge.length = TRUE,
                          use.tip.label = TRUE, index.return = FALSE,
                          tolerance = .Machine$double.eps ^ 0.5,
                          scale = NULL, \dots)

Arguments

target

an object of class "phylo".

current

an object of class "phylo".

use.edge.length

if FALSE only the topologies are compared; the default is TRUE.

use.tip.label

if FALSE the unlabelled trees are compared; the default is TRUE.

index.return

if TRUE the function returns a two-column matrix giving the correspondence between the nodes of both trees.

tolerance

the numeric tolerance used to compare the branch lengths.

scale

a positive number, comparison of branch lengths is made after scaling (i.e., dividing) them by this number.

...

further arguments passed to or from other methods.

Value

A logical value, or a two-column matrix.

encoding

latin1

Details

This function is meant to be an adaptation of the generic function all.equal for the comparison of phylogenetic trees.

A single phylogenetic tree may have several representations in the Newick format and in the "phylo" class of objects used in `ape'. One aim of the present function is to be able to identify whether two objects of class "phylo" represent the same phylogeny.

Only the labelled topologies are compared (i.e. branch lengths are not considered.

Examples

Run this code

### maybe the simplest example of two representations
### for the same rooted tree...:
t1 <- read.tree(text = "(a:1,b:1);")
t2 <- read.tree(text = "(b:1,a:1);")
all.equal(t1, t2)
### ... compare with this:
identical(t1, t2)
### one just slightly more complicated...:
t3 <- read.tree(text = "((a:1,b:1):1,c:2);")
t4 <- read.tree(text = "(c:2,(a:1,b:1):1);")
all.equal(t3, t4) # == all.equal.phylo(t3, t4)
### ... here we force the comparison as lists:
all.equal.list(t3, t4)
t5 <- read.tree(text = "(a:2,(c:1,b:1):1);")
### note that this does NOT return FALSE...:
all.equal(t3, t5)
### ... do this instead:
identical(all.equal(t3, t5), TRUE)

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