getEventRateAtSite.GeneralSubstitution: Get the site spcific rate of an event from a...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the site spcific rate of an event from a GeneralSubstitution object.

This method return the element from the associated QMatrix object corresponding to a given event multiplied by the "rate.multiplier" site-process specific parameter stored in the specified site object. 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.

Usage

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

Arguments

this	A GeneralSubstitution object. It must be attached to the provided Site object.
site	A Site 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))
	# create a Site object
	s<-Site(alphabet=BinaryAlphabet())
	# attach process p to site s
	s$processes<-list(p)
	# set the rate multiplier for s and p
       setParameterAtSite(p,s,id="rate.multiplier",value=2)
	# get the site specific rate of "0->1" by name
	getEventRateAtSite(p,s,"0->1")
	# get the site specific rate of "0->1" by states
	getEventRateAtSite(p,s,from="0",to="1")
 

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