getEventRate.GeneralSubstitution: Get the scaled rate of an event from a GeneralSubstitution...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the scaled rate of an event from a GeneralSubstitution object.

This method return the element from the scaled rate matrix stored in the associated QMatrix object corresponding to a given event. The event can be specified by the inital and target states ("from" and "to" arguments), or by the event name ("from->to"). The event name takes precedence over the "from" and "to" arguments.

This method doesn't take into account the site specific rate multipliers in any way.

Usage

## S3 method for class 'GeneralSubstitution'
getEventRate(this, name=NA, from=NA, to=NA, ...)

Arguments

this	A GeneralSubstitution object.
name	The name of the event.
from	The initial state.
to	Target state.
...	Not used.

Value

A Numeric vector of length one.

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"=1))
	# get the scaled rate of "0->1" by name
	getEventRate(p,"0->1")
	# get the scaled rate of "0->1" by states
	getEventRate(p,from="0",to="1")
 

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