Preprocessed Trees. — PPtree • entropart

Methods for objects of type "PPtree".

Usage

is.PPtree(x)
# S3 method for class 'PPtree'
plot(x, ...)

Arguments

x: An object to be tested or plotted
...: Additional arguments to be passed to the generic methods.

Value

An object of class PPtree is a list:

phyTree: A "phylo" (see read.tree) tree
hTree: A hclust tree
Height: The height of the tree, that is to say the distance between root and leaves
Cuts: A vector. Cut times of the tree (the distance from nodes to leaves)
Intervals: A vector. The lengths of intervals between cuts

is.PPtree returns TRUE if the object is of class PPtree.

plot.PPtree plots it.

Note

Versions up to 1.3 contained a phylog tree, now deprecated in ade4. A "phylo" (see read.tree) tree is now used.

See the dedicated vignette (vignette("Phylogenies", package="entropart")) for more details.

Examples

data(Paracou618)
# Preprocess a phylog object
ppt <- Preprocess.Tree(EightSpTree)
# Is it a preprocessed tree?
is.PPtree(ppt)
#> [1] TRUE
# Plot it
plot(ppt, hang=-1)

# Alternative plot
ade4::radial.phylog(EightSpTree)