Initialize.corPhyl

An object inheriting from class <code>corPhyl</code>.

object

The data to use. If it contains rownames, they are matched with the tree tip labels, otherwise data are supposed to be in the same order than tip labels and a warning is sent.

data

some methods for this generic require additional arguments. None are used in this method.

Initialize a <code>corPhyl</code> correlation structure object.
	Does the same as <code>Initialize.corStruct</code>, but also checks the row names of data and builds an index.

manip

models

Ape provides functions for reading, writing, plotting,
  and manipulating phylogenetic trees, analyses of comparative data
  in a phylogenetic framework, analyses of diversification and
  macroevolution, computing distances from allelic and nucleotide
  data, reading nucleotide sequences, and several tools such as
  Mantel's test, computation of minimum spanning tree, the population
  parameter theta based on various approaches, nucleotide diversity,
  generalized skyline plots, estimation of absolute evolutionary rates
  and clock-like trees using non-parametric rate smoothing, conversion
  of APE trees to and from hclust objects and for classifying genes in
  trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation
  can be done with the NJ and ML methods.

Initialize.corPhyl: Initialize a 'corPhyl' Structure Object

Description

Usage

Arguments

Value

See Also