phylosim (version 3.0.5)

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

Description

Get the QMatrix object aggregated by a ToleranceSubstitution object.

This method is mostly used internally.

Usage

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

Arguments

this

A ToleranceSubstitution object.

...

Not used.

Value

A QMatrix object.

See Also

For more information see ToleranceSubstitution.

Examples

# NOT RUN {
	# 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)
 
# }