phylosim (version 3.0.5)

UNREST: The UNREST class

Description

This class implements the UNRESTricted nucleotide substitution model. UNREST objects are basically a GeneralSubstitution process acting on a nucleotide alphabet.

Package: Class UNREST

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

Directly known subclasses: F81, F84, GTR, HKY, JC69, K80, K81, T92, TN93

public static class UNREST extends GeneralSubstitution

Usage

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

Arguments

name

Object name.

rate.list

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

equ.dist

Equlibrium 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

References

Yang, Z (1994) Estimating the pattern of nucleotide substitution - Journal of Molecular Evolution 39:105-111 http://bit.ly/aFO0cq

See Also

GeneralSubstitution GTR

Examples

# NOT RUN {
       p<-UNREST(rate.list=list(
		"T->C"=1, "T->A"=2, "T->G"=3, "C->T"=4, "C->A"=1,
		"C->G"=2, "A->T"=3, "A->C"=4, "A->G"=1, "G->T"=2,
		"G->C"=3, "G->A"=4
	))
       # 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
 
# }