phylosim (version 3.0.5)

BinarySubst: The BinarySubst class

Description

This is a class implementing a continuous-time Markov process acting on the state space defined by the BinaryAlphabet class.

Package: Class BinarySubst

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Process ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GeneralSubstitution ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--BinarySubst

Directly known subclasses:

public static class BinarySubst extends GeneralSubstitution

Usage

BinarySubst(name="Anonymous", rate.list=NA, equ.dist=NA, ...)

Arguments

name

The name of the object.

rate.list

A list of substitution rates (see setRateList.GeneralSubstitution).

equ.dist

Equilibrium distribution.

...

Additional arguments.

Fields and Methods

Methods:

	checkConsistency	-
	summary	-

Methods inherited from GeneralSubstitution: as.character, checkConsistency, clone, getAlphabet, getEquDist, getEventRate, getEventRateAtSite, getEventsAtSite, getQMatrix, getRate, getRateList, hasUndefinedRate, is, plot, rescaleQMatrix, sampleState, setAlphabet, setEquDist, setQMatrix, setRate, setRateList, summary

Methods inherited from Process: !=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, setWriteProtected, summary

Methods inherited from PSRoot: checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

See Also

GeneralSubstitution GTR WAG

Examples

# NOT RUN {
 	# The following code demonstrates
       # the use of the BinarySubst process  
       # during a simulation.
       p<-BinarySubst(rate=0.25,name="Binary",rate.list=list("0->1"=2,"1->0"=1))
       # create a sequence object, attach process p
       s<-BinarySequence(string="000000000000000000",processes=list(list(p)));
       # make the first five positions invariable
       setRateMultipliers(s,p,0,1:5)
       # get rate multipliers
       getRateMultipliers(s,p)
       # simulate
       sim<-PhyloSim(root.seq=s,phylo=rcoal(3))
       Simulate(sim)
       # print alignment
       sim$alignment
 
# }