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

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

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

The QMatrix objects aggregated by the ToleranceSubstitution 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 class 'ToleranceSubstitution'
rescaleQMatrix(this, ...)

Arguments

this	A ToleranceSubstitution object.
...	Not used.

Value

Invisible TRUE.

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"=3))
	# rescale rate matrix
	rescaleQMatrix(p)
 

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