all.equal.phylo: Global Comparison of two Phylogenies
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

This function makes a global comparison of two phylogenetic trees.

## 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, ...)

`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.

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.

A logical value, or a two-column matrix.

BenoÃ®t b.durand@alfort.AFSSA.FR

all.equal for the generic R function

### 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)