getQMatrix.ToleranceSubstitution: Get the QMatrix object aggregated by a ToleranceSubstitution...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the QMatrix object aggregated by a ToleranceSubstitution object.

This method is mostly used internally.

Usage

## S3 method for class 'ToleranceSubstitution'
getQMatrix(this, ...)

Arguments

this	A ToleranceSubstitution object.
...	Not used.

Value

A QMatrix object.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see ToleranceSubstitution.

Examples

	# create a ToleranceSubstitution object
	# provide an Alphabet object and the rates
	p<-ToleranceSubstitution(alphabet=BinaryAlphabet(), rate.list=list("1->0"=1,"0->1"=1))
	# get the QMatrix object
	getQMatrix(p)
	# get the QMatrix object via virtual field
	q<-p$qMatrix
	# tweak with the QMatrix
	setRate(q,"0->1",2)
	# set a new QMatrix for p
	setQMatrix(p,q)
	summary(p)
	# set new QMatrix via virtual field
	setRate(q,"1->0",2)
	p$qMatrix<-q
	summary(p)
 

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