getEquDist.ToleranceSubstitution: Get the equilibrium distribution from a ToleranceSubstitution...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the equilibrium distribution from a ToleranceSubstitution object.

Usage

## S3 method for class 'ToleranceSubstitution'
getEquDist(this, dummy=NA, ...)

Arguments

this	A ToleranceSubstitution object.
dummy	Not used.
...	Not used.

Value

The new equlibrium distribution (invisible).

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 equlibrium distribution
	getEquDist(p)
	# get equilibrium distribution via virtual field
	p$equDist
	# re-set the equilibrium distribution
	dist<-p$equDist * 3
	dist
	setEquDist(p,dist)
	p$equDist
	# re-set equilibrium distribution via virtual field
	p$equDist<-p$equDist * 2
	p$equDist
 

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