getBigRate.Sequence: Get the sum of all active event rates from a Sequence object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the sum of all active event rates from a Sequence object. The sum of active event rates depends on all Site object states and on the attached Process objects. It basically returns the last element of the cumulative site rates vector.

Usage

## S3 method for class 'Sequence'
getBigRate(this, ...)

Arguments

this	A Sequence object.
...	Not used.

Value

A numeric vector of length one.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see Sequence.

Examples

	# create a nucleotide sequence attach a process
	s<-NucleotideSequence(length=5);
	s$processes<-list(list(JC69()))
	# get the sum of active event rates
	getBigRate(s)	# returns NA because site states are undefined
	# set site states
	s$states<-c("A","T")
	# get big rate via virtual field
	s$bigRate
 

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