setParameterAtSites.Sequence: Set the values of a site-process specific paramater for a...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Set the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object.

Usage

## S3 method for class 'Sequence'
setParameterAtSites(this, process, id, value, index, ...)

Arguments

this	A Sequence object.
process	A valid Process object.
id	The identifier of the site-process specific parameter.
value	A vector containing the new values of the site-process specific parameter, recycled if shorter than the index vector. It should be consistent with the type of the parameter.
index	An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.
...	Not used.

Value

The Sequence object (invisible).

Author(s)

Botond Sipos, Gregory Jordan

See Also

Site Process For more information see Sequence.

Examples

	# create a sequence, attach a process
	p<-K80()
	s<-Sequence(length=6,alphabets=list(NucleotideAlphabet()),processes=list(list(p)))
	# set a new pattern of rate multipliers in the range 1:3,
   # the default value is 1.0 by the way
	setParameterAtSites(s,p,"rate.multiplier",c(2,3),1:3)
	# get rate multipliers
	getParameterAtSites(s,p,"rate.multiplier")
	# set a new value for the whole sequence
	setParameterAtSites(s,p,"rate.multiplier",0.5)
	# get rate multipliers
	getParameterAtSites(s,p,"rate.multiplier")
 

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