ape (version 1.2-7)

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, \dots)

Arguments

target
an object of class "phylo".
current
an object of class "phylo".
...
further arguments passed to or from other methods.

Value

  • If both trees are strictly similar, the logical TRUE is returned. Otherwise, the different elements of the trees (numbers of tips, numbers of nodes, tip labels, tree topologies) are compared, and the results of these comparisons are printed.

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 R function

Examples

Run this code
### maybe the simplest example of two representations
### for the same rooted tree
cat("((a:1,b:1):1,c:2);", file = "t1.tre")
cat("(c:2,(a:1,b:1):1);", file = "t2.tre")
t1 <- read.tree("t1.tre")
t2 <- read.tree("t2.tre")
all.equal(t1, t2)
### clean-up
unlink("t1.tre")
unlink("t2.tre")

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