setOmegas.CodonSequence: Set the omegas for a collection of sites

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Set the omegas for a collection of sites.

Usage

## S3 method for class 'CodonSequence'
setOmegas(this, process, value, index, ...)

Arguments

this	A CodonSequence object.
process	A process object inheriting from GY94.
value	A vector containing the new values of the site-process specific parameter, recycled if shorter than the index vector.
index	A vector of positions. It is set to 1:seq$length if omitted.
...	Not used.

Value

A numeric vector.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see CodonSequence.

Examples

	# create a GY94 process
	p<-GY94()
	# create a CodonSequence object,
	# attach a process p
	s<-CodonSequence(length=20,processes=list(list(p)))
	# set omega values in range 1:5
	setOmegas(s,p,c(0.5,1,1.5),1:5)
	# get omega values from siutes 1,2,3,10, and 20
	getOmegas(s,p,c(1:3,10,20))
 

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