phylosim (version 3.0.5)

cpREV: The cpREV empirical amino acid substitution model

Description

Package: Class cpREV

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Process ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GeneralSubstitution ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AminoAcidSubst ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--cpREV

Directly known subclasses:

public static class cpREV extends AminoAcidSubst

Usage

cpREV(equ.dist=NA, ...)

Arguments

equ.dist

Equilibrium distribution.

...

Not used.

Fields and Methods

Methods: No methods defined.

Methods inherited from AminoAcidSubst: buildFromPAML, checkConsistency, newAAMatrix, setEquDist, 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

References

Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa (2000) Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA - Journal of Molecular Evolution 50:348--358 DOI: 10.1007/s002399910038 http://bit.ly/bnBVLm

See Also

AminoAcidSubst GeneralSubstitution UNREST

Examples

# NOT RUN {
	# create substitution model object
	p<-cpREV()
	# get object summary
	summary(p)
	# display a bubble plot
	plot(p)

       # The following code demonstrates how to use
       # the process in a simulation.

	# create a sequence, attach process p
	s<-AminoAcidSequence(length=10,processes=list(list(p)) )
	# sample states
	sampleStates(s)
       # make the first three positions invariable
       setRateMultipliers(s,p,0,1:3)
       # get rate multipliers
       getRateMultipliers(s,p)
       # create a simulation object
       sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
       # run simulation
       Simulate(sim)
       # print alignment
       sim$alignment
 
# }