as.phylo: Conversion Among Tree Objects

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

as.phylo is a generic function which converts an object into a tree of class "phylo". There are currently two methods for this generic for objects of class "hclust" and of class "phylog" (implemented in the package ade4). as.hclust.phylo is a method of the generic as.hclust which converts an object of class "phylo" into one of class "hclust". This can used to convert an object of class "phylo" into one of class "dendrogram" (see examples).

old2new.phylo and new2old.phylo are utility functions for converting between the old and new coding of the class "phylo".

Usage

as.phylo(x, ...)
## S3 method for class 'hclust'
as.phylo(x, ...)
## S3 method for class 'phylog'
as.phylo(x, ...)
## S3 method for class 'phylo'
as.hclust(x, ...)
old2new.phylo(phy)
new2old.phylo(phy)

Arguments

x	an object to be converted into another class.
...	further arguments to be passed to or from other methods.
phy	an object of class "phylo".

Value

An object of class "hclust" or "phylo".

Author(s)

Emmanuel Paradis

See Also

hclust, as.hclust, dendrogram, phylog, as.phylo.formula

Examples

data(bird.orders)
hc <- as.hclust(bird.orders)
tr <- as.phylo(hc)
identical(bird.orders, tr) # FALSE, but...
all.equal(bird.orders, tr) # ... TRUE

### shows the three plots for tree objects:
dend <- as.dendrogram(hc)
layout(matrix(c(1:3, 3), 2, 2))
plot(bird.orders, font = 1)
plot(hc)
par(mar = c(8, 0, 0, 0)) # leave space for the labels
plot(dend)

### how to get (nearly) identical plots with
### plot.phylo and plot.dendrogram:
layout(matrix(1:2, 2, 1))
plot(bird.orders, font = 1, no.margin = TRUE)
par(mar = c(0, 0, 0, 8))
plot((dend), horiz = TRUE)
layout(matrix(1, 1, 1))

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.