ape (version 2.8)

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)

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.

See Also

all.equal for the generic Rfunction

Examples

### 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)