phylosim (version 3.0.5)

CodonUNREST: The CodonUNREST class

Description

This class implements a time-continuous Markov process acting on a state space defined by the symbol set of a CodonAlphabet object. The rate matrix of this model is unrestricted, so it can be used to implement empircal codon models or more restricted mechanistic models.

Package: Class CodonUNREST

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

Directly known subclasses: GY94

public static class CodonUNREST extends GeneralSubstitution

Usage

CodonUNREST(name="Anonymous", table.id=1, rate.list=NA, equ.dist=NA, ...)

Arguments

name

The name of the object.

table.id

The identifier of the genetic code table (see CodonAlphabet).

rate.list

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

equ.dist

Equilibrium distribution.

...

Additional arguments.

Fields and Methods

Methods:

	checkConsistency	-
	is	-

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 GY94

Examples

# NOT RUN {
	# create a CodonUNREST object
	p<-CodonUNREST(table.id=2)
	# get object summary
	summary(p)
 
# }