setAlphabet.QMatrix: Set the Alphabet object for a QMatrix object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Set the Alphabet object for a QMatrix object.

This method rebuilds the scaled and unscaled rate matrices and so sets all rates to NA.

Usage

## S3 method for class 'QMatrix'
setAlphabet(this, value, ...)

Arguments

this	A QMatrix object.
value	An Alphabet object.
...	Not used.

Value

The Alphabet object.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see QMatrix.

Examples

	# create a QMatrix object
	m<-QMatrix()
	# set the alphabet
	setAlphabet(m,NucleotideAlphabet())
	# get the alphabet
	getAlphabet(m)
	# set alphabet via virtual field
	m$alphabet<-BinaryAlphabet()
	summary(m)
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.