ape (version 4.0)

as.matching: Conversion Between Phylo and Matching Objects

Description

These functions convert objects between the classes "phylo" and "matching".

Usage

as.matching(x, ...)
"as.matching"(x, labels = TRUE, ...)
"as.phylo"(x, ...)

Arguments

x

an object to convert as an object of class "matching" or of class "phylo".

labels

a logical specifying whether the tip and node labels should be included in the returned matching.

...

further arguments to be passed to or from other methods.

Value

as.matching returns an object of class "matching" with the following component:as.phylo.matching returns an object of class "phylo".

Details

A matching is a representation where each tip and each node are given a number, and sibling groups are grouped in a ``matching pair'' (see Diaconis and Holmes 1998, for details). This coding system can be used only for binary (fully dichotomous) trees.

Diaconis and Holmes (1998) gave some conventions to insure that a given tree has a unique representation as a matching. I have tried to follow them in the present functions.

References

Diaconis, P. W. and Holmes, S. P. (1998) Matchings and phylogenetic trees. Proceedings of the National Academy of Sciences USA, 95, 14600--14602.

See Also

as.phylo

Examples

data(bird.orders)
m <- as.matching(bird.orders)
str(m)
m
tr <- as.phylo(m)
all.equal(tr, bird.orders, use.edge.length = FALSE)