getEventsAtSite.Process: Generate the list of active Event objects given a Site object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Generate the list of active Event objects given a Site object. The Process object must be attached to the specified Site object.

This method is crucial for the simulations. For the Process class it returns an empty list. Descendant classes should implement meaningful getEventsAtSite methods.

Usage

## S3 method for class 'Process'
getEventsAtSite(this, site, position, ...)

Arguments

this	A Process object.
site	A valid Site object.
position	The position of the site in the enclosing Sequence object (if any).
...	Not used.

Value

An empty list.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see Process.

Examples

	# create objects
	a<-NucleotideAlphabet()
	p<-Process(alphabet=a)
	s<-Site(alphabet=a)
	# attach Process p to Site s
	s$processes<-list(p)
	# get active Event objects (empty list)
	getEventsAtSite(p,s)

 

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