getRate.GeneralSubstitution: Get an unscaled rate of an event from a GeneralSubstitution...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get an unscaled rate of an event from a GeneralSubstitution object.

This method gets the element corresponding to a given event form the unscaled Q matrix. 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.

The rescaled rates (used during simulations) are returned by the getEventRate method.

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

Usage

## S3 method for class 'GeneralSubstitution'
getRate(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 unscaled rate of "0->1" by name
	getRate(p,"0->1")
	# get the unscaled rate of "0->1" by states
	getRate(p,from="0",to="1")
 

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