ape (version 3.0-2)

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

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

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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