getRateList.QMatrix: Get a list of events and their unscaled rates from a QMatrix...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get a list of events and their unscaled rates from a QMatrix object.

This method returns the list of event rates from the unscaled rate matrix. The returned list contains the rates associated with the corresponding event names.

Usage

## S3 method for class 'QMatrix'
getRateList(this, ...)

Arguments

this	A GeneralSubstitution object.
...	Not used.

Value

A list of event rates.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see QMatrix.

Examples

       # create a GeneralSubstitution object
       # provide an Alphabet object and the rates
       p<-GeneralSubstitution(alphabet=BinaryAlphabet(), rate.list=list("1->0"=1,"0->1"=3))
	# get the QMatrix object from p
	m<-p$QMatrix
       # get the event rates from the unscaled Q matrix
       getRateList(m)
       # get rates from the unscaled rate matrix via virtual field
       m$rateList
       # set rates in the unscaled rate matrix
       setRateList(m, list("0->1"=1,"1->0"=1))
       m$rateList
       # set rates in the unscaled rate matrix via virtual field
       m$rateList<-list("0->1"=3,"1->0"=1);
	m$rateList
 

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