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

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

Initialize.corPhyl: Initialize a `corPhyl' Structure Object

Description

Usage

Arguments

Value

See Also