phylosim (version 3.0.5)

AminoAcidSubst: The AminoAcidSubst class

Description

This is a class implementing a continuous-time Markov process acting on the state-space defined by the AminoAcidAlphabet class. The rate matrix of this model is completely unrestricted.

The rate matrix can be built from PAML files specified by the paml.file argument. Alternatively the rates can be specified as a list through the rate.list parameter.

Package: Class AminoAcidSubst

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

Directly known subclasses: JTT, JTT.dcmut, LG, MtZoa, PAM, PAM.dcmut, WAG, cpREV, mtArt, mtMam, mtREV24

public static class AminoAcidSubst extends GeneralSubstitution

Usage

AminoAcidSubst(name="Anonymous", paml.file=NA, rate.list=NA, equ.dist=NA, ...)

Arguments

name

The name of the object.

paml.file

The name of the PAML file used to construct the rate matrix.

rate.list

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

equ.dist

Equilibrium distribution.

...

Additional arguments.

Fields and Methods

Methods:

	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

See Also

For more information see AminoAcidSubst.

Examples

# NOT RUN {
	# create an object
	p<-AminoAcidSubst()
	# build rate matrix from paml file
	# buildFromPAML(p,"path_to_paml_file")	# do not run this
	# set a rate
	setRate(p,"A->D",2)
	# get object summary
	summary(p)
 
# }