phylosim (version 3.0.5)

HKY: The HKY class

Description

This class implements the HKY GTR-submodel.

The rate parameters are the following: "Alpha", "Beta". Package: Class HKY

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Process ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GeneralSubstitution ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--UNREST ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--GTR ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HKY

Directly known subclasses:

public static class HKY extends GTR

Usage

HKY(name="Anonymous", rate.params=list(Alpha = 1, Beta = 1),
  base.freqs=c(0.25, 0.25, 0.25, 0.25), ...)

Arguments

name

Object name.

rate.params

Rate parameters.

base.freqs

Base frequency parameters.

...

Not used.

Fields and Methods

Methods:

	checkConsistency	-
	getBaseFreqs	-
	getRateParam	-
	getRateParamList	-
	setBaseFreqs	-
	setRateParam	-
	setRateParamList	-
	summary	-

Methods inherited from GTR: checkConsistency, getBaseFreqs, getRateParam, getRateParamList, setBaseFreqs, setRateParam, setRateParamList, summary

Methods inherited from UNREST: 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

References

Hasegawa, M Kishino, H and Yano, T (1985) Dating of human-ape splitting by a molecular clock of mitochondrial DNA Journal of Molecular Evolution 22:160-174 http://bit.ly/a9AxKm

See Also

GTR UNREST GeneralSubstitution TN93

Examples

# NOT RUN {
	# create substitution process object
       p<-HKY(rate.params=list( "Alpha"=10,"Beta"=2),
		base.freqs=c(4,3,2,1)/10
	)
       # get a 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<-NucleotideSequence(length=20,processes=list(list(p)))
	# sample states
	sampleStates(s)
	# make the first five positions invariable
	setRateMultipliers(s,p,0,1:5)
	# 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
 
# }