setRateMultipliers.Sequence

Sequence.setRateMultipliers

setRateMultipliers,Sequence-method

this

process

A numeric vector containing the new values of the site-process specific parameter, recycled if shorter than the index vector.

value

An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.

index

Set the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object.
	This method just calls <code>setParameterAtSites(this=this,process=process,id="rate.multiplier",value=value,index=index)</code> See setParameterAtSites.Sequence for details.

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment <doi:10.1186/1471-2105-12-104>.

Botond Sipos

phylosim

Flexible Simulations of Biological Sequence Evolution

setRateMultipliers.Sequence function

Set the values of the rate multiplier parameters for a given Process object and a collection of Site  object aggregated by a Sequence object — setRateMultipliers.Sequence

setRateMultipliers.Sequence: Set the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object

Description

Usage

Arguments

Value

See Also