setRateList.GeneralSubstitution: Setting the rates for a GeneralSubstitution object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Setting the rates for a GeneralSubstitution object.

This method set the rates in the unscaled Q matrix based on the provided list containing even names and the associated rates. The rate must be specified for every event!

Usage

## S3 method for class 'GeneralSubstitution'
setRateList(this, value, ...)

Arguments

this	A GeneralSubstitution object.
value	A list with the events names and the associated rates.
...	Not used.

Value

The GeneralSubstitution object (invisible).

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see GeneralSubstitution.

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 event rates from the unscaled Q matrix
	getRateList(p)
	# get rates from the unscaled rate matrix via virtual field
	p$rateList
	# set rates in the unscaled rate matrix
	setRateList(p, list("0->1"=1,"1->0"=1))
	p$rateList
	# set rates in the unscaled rate matrix via virtual field
	p$rateList<-list("0->1"=3,"1->0"=1);
	# check the contenst of the associated QMatrix object
	summary(p$QMatrix)
 

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