phylosim (version 3.0.5)

rescaleQMatrix.GeneralSubstitution: Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object

Description

Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object.

The QMatrix objects aggregated by the GeneralSubstitution objects store two rate matrices: one containes the rates provided by the user (unscaled rate matrix), the other matrix (scaled rate matrix) is rescaled to have the expected number of subsitutions per unit time equal to one when the process is at equlibrium. This method performes the re-scaling of the scaled rate matrix in the associated QMatrix object based on the equlibrium distribution and the unscaled rate matrix.

This method is mainly used internally as the scaled matrix is rescaled every time the unscaled matrix is modifed.

Usage

# S3 method for GeneralSubstitution
rescaleQMatrix(this, ...)

Arguments

this

A GeneralSubstitution object.

...

Not used.

Value

Invisible TRUE.

See Also

For more information see GeneralSubstitution.

Examples

# NOT RUN {
	# create a GeneralSubstitution object
	# provide an Alphabet object and the rates
	p<-GeneralSubstitution(alphabet=BinaryAlphabet(), rate.list=list("1->0"=1,"0->1"=3))
	# rescale rate matrix
	rescaleQMatrix(p)
 
# }