Man pages for phylosim
Flexible Simulations of Biological Sequence Evolution

000==.AlphabetCheck if two alaphabet objects have the same symbol set
000==.ProcessCheck whether the two supplied Process objects are identical
AlphabetThe Alphabet class
AminoAcidAlphabetThe AminoAcidAlphabet class
AminoAcidSequenceThe AminoAcidSequence class
AminoAcidSubstThe AminoAcidSubst class
AnyAlphabetThe AnyAlphabet class
areSynonymous.CodonAlphabetCheck whether two codons are synonymous
as.character.AlphabetGet the character representation of an Alphabet object
as.character.EventGet the character representation of an Event object
as.character.GeneralSubstitutionReturn the character representation of a GeneralSubstitution...
as.character.PhyloSimReturn the character representation of a PhyloSim object
as.character.ProcessGet the character representation of a Process object
as.character.QMatrixReturn the character representation of a QMatrix object
as.character.SequenceGet the string representation of a Sequence object
as.character.SiteGet the character representation of a Site object
as.character.ToleranceSubstitutionReturn the character representation of a...
attachHookToNode.PhyloSimAttach a callback function to a given node of a phylo object...
attachProcess.SequenceAttach a Process object to a set of Site objects aggregated...
attachProcess.SiteAttach a Process object to a Site object
attachSeqToNode.PhyloSimAssotiate a Sequence object with a given node of a phylo...
BinaryAlphabetThe BinaryAlphabet class
BinarySequenceThe BinarySequence class
BinarySubstThe BinarySubst class
BrownianInsertorThe BrownianInsertor class
BrownianPath.BrownianInsertorGenerate a Brownian path
buildFromPAML.AminoAcidSubstBuild rate matrix from PAML file
buildFromPAML.CodonSubstBuild rate matrix from PAML file
checkConsistency.AlphabetCheck object consistency
checkConsistency.AminoAcidSubstCheck object consistency
checkConsistency.BinarySubstCheck object consistency
checkConsistency.BrownianInsertorCheck object consistency
checkConsistency.CodonAlphabetCheck object consistency
checkConsistency.CodonSequenceCheck object consistency
checkConsistency.CodonSubstCheck object consistency
checkConsistency.CodonUNRESTCheck object consistency
checkConsistency.ContinuousDeletorCheck object consistency
checkConsistency.ContinuousInsertorCheck object consistency
checkConsistency.DiscreteDeletorCheck object consistency
checkConsistency.DiscreteInsertorCheck object consistency
checkConsistency.EventCheck object consistency
checkConsistency.F81Check object consistency
checkConsistency.F84Check object consistency
checkConsistency.FastFieldDeletorCheck object consistency
checkConsistency.GeneralDeletorCheck object consistency
checkConsistency.GeneralInDelCheck object consistency
checkConsistency.GeneralInsertorCheck object consistency
checkConsistency.GeneralSubstitutionCheck object consistency
checkConsistency.GTRCheck object consistency
checkConsistency.GY94Check object consistency
checkConsistency.HKYCheck object consistency
checkConsistency.JC69Check object consistency
checkConsistency.K80Check object consistency
checkConsistency.K81Check object consistency
checkConsistency.PhyloSimCheck object consistency
checkConsistency.ProcessCheck object consistency
checkConsistency.PSRootCheck object consistency
checkConsistency.PSRootSummaryCheck object consistency
checkConsistency.QMatrixCheck object consistency
checkConsistency.SequenceCheck object consistency
checkConsistency.SiteCheck object consistency
checkConsistency.T92Check object consistency
checkConsistency.TN93Check object consistency
checkConsistency.ToleranceSubstitutionCheck object consistency
checkConsistency.UNRESTCheck object consistency
clearStates.SequenceSet the states of a collection of Site objects aggregated by...
clone.GeneralSubstitutionClone a GeneralSubstitution object
clone.ProcessClone a process object
clone.SequenceClone a Sequence object
clone.ToleranceSubstitutionClone a ToleranceSubstitution object
CodonAlphabetThe CodonAlphabet class
CodonSequenceThe CodonSequence class
CodonSubstThe CodonSubst class
CodonUNRESTThe CodonUNREST class
ContinuousDeletorThe ContinuousDeletor class
ContinuousInsertorThe ContinuousInsertor class
copySubSequence.SequenceCopy a collection of Site objects aggregated by a Sequence...
cpREVThe cpREV empirical amino acid substitution model
Debug.PhyloSimSave a debug message in the PhyloSim log file
deleteSubSequence.SequenceDelete a collection of sites aggregated by a Sequence object
detachHookFromNode.PhyloSimDetach a node hook function from a given node of a phylo...
detachProcess.SequenceDetach a Process object from a set of Site objects aggregated...
detachProcess.SiteSite
detachSeqFromNode.PhyloSimDetach a Sequence object from a given node of a phylo object...
DiscreteDeletorThe DiscreteDeletor class
DiscreteInsertorThe DiscreteInsertor class
ECMrestThe ECMrest empirical codon substitution model
ECMunrestThe ECMunrest empirical codon substitution model
enableVirtual.PSRootEnable the use of virtual fields for a given object
EventThe Event class
exportStatTree.PhyloSimExport the per-branch counts of an event as a phylo object
F81The F81 class
F84The F84 class
FastFieldDeletorThe FastFieldDeletor class
flagTotalRate.SiteFlag the total event rate
GeneralDeletorThe GeneralDeletor class
GeneralInDelThe GeneralInDel class
GeneralInsertorThe GeneralInsertor class
GeneralSubstitutionThe GeneralSubstitution class
generateInsert.GeneralInsertorGenerate an insert
getAcceptBy.GeneralInDelGet the function used for accepting/rejecting indel events
getAcceptWin.GeneralInsertorGet the size of the acceptance window
getAlignmentLength.PhyloSimGet the alignment length from a PhyloSim object
getAlignment.PhyloSimGet the alignment stored in a PhyloSim object
getAlphabet.GeneralSubstitutionGet the Alphabet object aggregated by a GeneralSubstitution...
getAlphabet.ProcessGet the Alphabet object associated with a given Process...
getAlphabet.QMatrixGet the Alphabet object associated with a QMatrix object
getAlphabet.SiteGet the Alphabet object attached to a Site object
getAlphabets.SequenceGet the list of the Alphabet objects attached to the Site...
getAlphabet.ToleranceSubstitutionGet the Alphabet object aggregated by a ToleranceSubstitution...
getAncestral.SequenceGet the ancestral object of a Sequence object
getAncestral.SiteGet the ancestral object of a Site object
getBaseFreqs.F81Get the base frequency parameters
getBaseFreqs.F84Get the base frequency parameters
getBaseFreqs.GTRGet the base frequency parameters
getBaseFreqs.HKYGet the base frequency parameters
getBaseFreqs.K80Get the base frequency parameters
getBaseFreqs.K81Get the base frequency parameters
getBaseFreqs.TN93Get the base frequency parameters
getBigRate.SequenceGet the sum of all active event rates from a Sequence object
getBranchEvents.PhyloSimGet the list of events having per-branch statistics recorded
getCodonFreqs.GY94Get codon frequencies
getComments.PSRootGet the comments associated with an object
getCumulativeRatesFromRange.SequenceGet the cumulative site rates for a collection of Site...
getCumulativeRates.SequenceGet the total site rates from a Sequence object
getDeletionTolerance.SequenceGet the deletion tolerance site-process specific parameter...
getDist.ContinuousDeletorGet the length sampling expression
getDist.ContinuousInsertorGet the length sampling expression
getEdge.PhyloSimGet and edge from the edge matrix
getEdges.PhyloSimGet the edge matrix from a phylo object aggregated by a...
getEquDist.GeneralSubstitutionGet the equilibrium distribution from a GeneralSubstitution...
getEquDist.ToleranceSubstitutionGet the equilibrium distribution from a ToleranceSubstitution...
getEventRateAtSite.GeneralSubstitutionGet the site spcific rate of an event from a...
getEventRateAtSite.ToleranceSubstitutionGet the site spcific rate of an event from a...
getEventRate.GeneralSubstitutionGet the scaled rate of an event from a GeneralSubstitution...
getEventRate.QMatrixGet the unscaled rate of an event from a QMatrix object
getEventRate.ToleranceSubstitutionGet the scaled rate of an event from a ToleranceSubstitution...
getEventsAtSite.FastFieldDeletorGenerate a deletion event object given the state of the...
getEventsAtSite.GeneralDeletorTitle
getEventsAtSite.GeneralInsertorGenerate insertion event object given the state of the target...
getEventsAtSite.GeneralSubstitutionGenerate the list of active Event objects for a given...
getEventsAtSite.GY94Generate the list of active Event objects for a given...
getEventsAtSite.ProcessGenerate the list of active Event objects given a Site object
getEventsAtSite.ToleranceSubstitutionGenerate the list of active Event objects for a given...
getEvents.SequenceGet the list of active Event objects for a set of Site...
getEvents.SiteGet the list of active event objects given the current state...
getGenerateBy.GeneralInsertorGet the function object used for generating inserts
getHandler.EventGet the handler function of an Event object
getId.PhyloSimGet the unique identifier of a PhyloSim object
getId.ProcessGet the unique identifier of a Process object
getId.QMatrixGet the unique identifier of a QMatrix object
getId.SequenceGet the unique identifier of a Sequence object
getInsertHook.GeneralInsertorGet the insert hook function
getInsertionTolerance.SequenceGet the insertion tolerance site-process specific parameter...
getKappa.F84Get the transition transversion rate ratio
getKappa.GY94Get the transition/transversion rate ratio
getLengthParam1.FastFieldDeletorGet the first length parameter
getLengthParam2.FastFieldDeletorGet the second length parameter
getLength.SequenceGet the number of Site objects aggregated in a Sequence...
getLogFile.PhyloSimGet the name of the file used for logging
getLogLevel.PhyloSimGet the log level from a PhyloSim object
getMatrix.QMatrixGet the unscaled rate matrix form a QMatrix object
getMaxLength.ContinuousDeletorGet the maximum length
getMaxLength.ContinuousInsertorGet the maximum length
getMethodsList.PSRootGet the list of applicable methods for an object
getName.EventGet the name of an Event object
getName.PhyloSimGet the name of a PhyloSim object
getName.ProcessGet the name of a Process object
getName.QMatrixGet the name of a QMatrix object
getName.SequenceGet the name of a Sequence object
getNedges.PhyloSimGet the number of edges from phylo object aggregated by a...
getNodes.PhyloSimGet the node identifiers from a PhyloSim object
getNtips.PhyloSimGet the number of the tips form a phylo object aggregated by...
getOmegaScalingFactor.GY94Get the omega scaling factor
getOmegas.CodonSequenceGet the omegas from a collection of sites
getParameterAtSite.ProcessGet the value of a site-process specific paramter from a Site...
getParameterAtSites.SequenceGet the values of a site-process specific paramater for a...
getPhylo.PhyloSimGet the phylo object aggregated in a PhyloSim object
getPosition.EventGet the position of the Site object associated to an Event...
getProbs.DiscreteDeletorGet the deletion length probabilities
getProbs.DiscreteInsertorGet the insertion length probabilities
getProcesses.SequenceGet the Process objects attached to the Site objects...
getProcesses.SiteGet the list of Process objects attached to a Site object
getProcess.EventGet the Process object which generated an Event object
getProcess.QMatrixGet the process object associated with a QMatrix object
getProposeBy.GeneralInDelGet the function used for proposing indel lengths
getQMatrix.GeneralSubstitutionGet the QMatrix object aggregated by a GeneralSubstitution...
getQMatrix.ToleranceSubstitutionGet the QMatrix object aggregated by a ToleranceSubstitution...
getRate.EventGet the rate of an Event object
getRate.GeneralInDelGet the general rate
getRate.GeneralSubstitutionGet an unscaled rate of an event from a GeneralSubstitution...
getRateList.GeneralSubstitutionGet a list of events and their unscaled rates from a...
getRateList.QMatrixGet a list of events and their unscaled rates from a QMatrix...
getRateList.ToleranceSubstitutionGet a list of events and their unscaled rates from a...
getRateMultipliers.SequenceGet the values of the rate multiplier parameters for a given...
getRateParam.F81Forbidden action: the value of a rate parameters
getRateParam.F84Get the value of a rate parameter
getRateParam.GTRGet the value of a rate parameter
getRateParam.HKYGet the value of a rate parameter
getRateParam.K80Get the value of a rate parameter
getRateParam.K81Get the value of a rate parameter
getRateParamList.F81Forbidden action: getting the list of rate parameters
getRateParamList.F84Get the rate parameters
getRateParamList.GTRGet the rate parameters
getRateParamList.HKYGet the rate parameters
getRateParamList.K80Get the rate parameters
getRateParamList.K81Get the rate parameters
getRateParamList.T92Get the rate parameters
getRateParamList.TN93Get the rate parameters
getRateParam.T92Get the value of a rate parameter
getRateParam.TN93Get the value of a rate parameter
getRate.QMatrixGet an unscaled rate of an event from a QMatrix object
getRate.ToleranceSubstitutionGet an unscaled rate of an event from a ToleranceSubstitution...
getRootNode.PhyloSimGet the identifier of the root node from a PhyloSim object
getRootSeq.PhyloSimGet the root sequence aggregated by a PhyloSim object
getScale.BrownianInsertorGet scale parameter
getScaledMatrix.QMatrixGet the scaled rate matrix form a QMatrix object
getSeqFromNode.PhyloSimGet the Sequence object associated with a given node of a...
getSequence.SiteGet the Sequence object associated with a given Site object
getSequences.PhyloSimGets all the Sequence objects associated with the nodes of a...
getSite.EventGet the Site object associated with an Event object
getSiteSpecificParamIds.ProcessGet the site specific paramter identifiers from a Process...
getSiteSpecificParamList.ProcessGet the list of site specific parameters of a Process object
getSites.SequenceGet the list of the Site object aggregated in a Sequence...
getSize.AlphabetGet the number of symbols in an Alphabet object
getSizes.DiscreteDeletorGet the sizes of the proposed deletions
getSizes.DiscreteInsertorGet the sizes of the proposed insertions
getState.SiteGet the current state of a Site object
getStates.SequenceGet the states of a set of Site objects aggregated by a...
getString.SequenceGet the string representation of a Sequence object
getSymbolFreqs.SequenceGet a table with the frequencies of the states of a...
getSymbolLength.AlphabetGet the length of the symbols in a given alphabet object
getSymbols.AlphabetGet the symbol set from an Alphabet object
getTableId.CodonAlphabetGet the genetic code id
getTemplateSeq.GeneralInsertorGet the template sequence object
getTheta.T92Get the GC content
getTipLabels.PhyloSimGet the tip labels from a phylo object aggregated by a...
getTips.PhyloSimGet the node identifiers of the tip nodes from a PhyloSim...
getToleranceMargin.FastFieldDeletorGet the tolerance margin
getTotalRatesFromRange.SequenceGet the vector of total site rates for a collection of Site...
getTotalRate.SiteGet the total active event rate
getTotalRates.SequenceGet the total site rates from a Sequence object
getTransTable.CodonAlphabetGet the list storing the genetic code table
getTreeLength.PhyloSimGet the tree length from a PhyloSim object
getType.AlphabetGet Alphabet obejct type
getType.BrownianInsertorGet the type of the BrownianInsertor process
getType.FastFieldDeletorGet the type of a FastFieldDeletor object
getUniqueAlphabets.SequenceGet the list of unique Alphabet objects associated to Site...
getUniqueProcesses.SequenceGet the list of unique Process instances attached to the Site...
getWriteProtected.AlphabetCheck if the object is write protected
getWriteProtected.EventCheck if the object is write protected
getWriteProtected.ProcessCheck if the object is write protected
getWriteProtected.QMatrixCheck if the object is write protected
getWriteProtected.SequenceCheck if the object is write protected
globalConsistencyCheck.PSRootCheck the consistency of all objects inheriting form PSRoot...
GTRThe GTR class
GY94The GY94 class
hasSiteSpecificParameter.ProcessCheck if a Process object has the site-process specific...
hasSymbols.AlphabetCheck if an Alphabet object has a given set of symbols
hasUndefinedRate.GeneralInDelCheck whether the general rate of a GeneralInDel object is...
hasUndefinedRate.GeneralSubstitutionCheck if a GeneralSubstitution object has undefined rates
hasUndefinedRate.ProcessCheck if the Process object has undefined rate parameters
hasUndefinedRate.ToleranceSubstitutionCheck if a ToleranceSubstitution object has undefined rates
HKYThe HKY class
insertSequence.SequenceInsert a Sequence object into another Sequence object after a...
intersect.list.PSRootUtility method returning the intersection of two lists
is.AlphabetCheck if an object is an instance of the Alphabet class
isAttached.SiteCheck whether a Process object is attached to a Site object
is.CodonAlphabetCheck if an object inherits from CodonAlphabet
is.CodonUNRESTCheck whether an object inherits from CodonUNREST
isEmpty.AlphabetCheck if the symbol set is empty
is.EventCheck whether an object inherits from the class Event
is.GeneralDeletorCheck whether an object inherits from GeneralDeletor
is.GeneralInDelCheck if an object inherits from the GeneralInDel class
is.GeneralInsertorCheck whether an object inherits from GeneralInsertor
is.GeneralSubstitutionCheck if an object is an instance of the GeneralSubstitution...
is.GY94Check whether an object inherits from GY94
is.na.PSRootCheck if a PSRoot object is NA
is.phyloCheck if an object is an instance of the phylo class
is.ProcessCheck if an object is an instance of the Process class
is.PSRootCheck if an object inherits from PSRoot
is.QMatrixCheck if an object is an instance of the QMatrix class
is.SequenceCheck whether an object inherits from the Sequence class
is.SiteCheck if an object is an instance of the Site class
isStartCodon.CodonAlphabetCheck if a codon is a start codon
isStopCodon.CodonAlphabetCheck if a codon is a stop codon
is.tip.PhyloSimCheck if a node is a tip
is.ToleranceSubstitutionCheck if an object is an instance of the...
JC69The JC69 class
JTTThe JTT empirical amino acid substitution model
JTT.dcmutThe JTT.dcmut empirical amino acid substitution model
K80The K80 class
K81The K81 class
LGThe LG empirical amino acid substitution model
ll.PSRootDisplay detailed information about the virtual fields and...
Log.PhyloSimSave a message in the PhyloSim log file
mtArtThe mtArt empirical amino acid substitution model
mtMamThe mtMam empirical amino acid substitution model
mtREV24The mtREV24 empirical amino acid substitution model
MtZoaThe MtZoa empirical amino acid substitution model
my.all.equal.PSRootTest if two objects are nearly equal
newAAMatrix.AminoAcidSubstUndocumented method
newMatrix.CodonSubstNew codon substitution matrix from PAML file
NucleotideAlphabetThe NucleotideAlphabet class
NucleotideSequenceThe NucleotideSequence class
omegaHist.CodonSequencePlot a histogram of omega values from a range
omegaVarM0.CodonSequenceThe M0 (one-ratio) model of variable omega ratios among sites
omegaVarM1.CodonSequenceThe M1 (neutral) model of variable omega ratios among sites
omegaVarM2.CodonSequenceThe M2 (selection) model of variable omega ratios among sites
omegaVarM3.CodonSequenceThe M3 (discrete) model of variable omega ratios among sites
omegaVarM4.CodonSequenceThe M4 (freqs) model of variable omega ratios among sites
PAMThe PAM empirical amino acid substitution model
PAM.dcmutThe PAM.dcmut empirical amino acid substitution model
Perform.EventPerform an event
PhyloSimThe PhyloSim class
plot.ContinuousDeletorPlot the density of proposed lengths
plot.ContinuousInsertorPlot the density of proposed lengths
plot.DiscreteDeletorPlot the deletion length distribution
plot.DiscreteInsertorPlot the insertion length distribution
plot.GeneralSubstitutionCreate a bubble plot of the substitution process
plotParametersAtSites.SequencePlot the value of a site-process specifc paramter for a...
plot.PhyloSimPlot a PhyloSim object
plot.SequencePlot the total site rates for a collection of Site objects...
plot.ToleranceSubstitutionCreate a bubble plot of the substitution process
plusGamma.SequenceSample the rate multiplier parameters of a Process from a...
plusInvGamma.SequenceSample the rate multiplier parameters of a Process from an...
print.PSRootSummaryPrint out a PSRootSummary object
print.QMatrixPrint the character representation of a QMatrix object
ProcessThe Process class
proposeLength.GeneralInDelPropose indel length
PSRootThe root class for all phylosim objects
PSRootSummaryThe PSRootSummary class
QMatrixThe QMatrix class
readAlignment.PhyloSimRead alignment from file
readTree.PhyloSimRead tree from file
rescaleQMatrix.GeneralSubstitutionRescale the scaled rate matrix of a QMatrix object aggregated...
rescaleQMatrix.ToleranceSubstitutionRescale the scaled rate matrix of a QMatrix object aggregated...
revComp.NucleotideSequenceReverse complmenet a NucleotideSequence object
sampleState.GeneralSubstitutionSample a state from the equlibrium distribution of a...
sampleStates.SequenceSample the states for a collection of Site objects aggregated...
sampleState.ToleranceSubstitutionSample a state from the equlibrium distribution of a...
saveAlignment.PhyloSimSave the alignment stored in a PhyloSim object in a Fasta...
Scale.QMatrixScale the scaled rate matrix stored in a QMatrix object by...
scaleTree.PhyloSimScale the branch lengths of a phylo object aggragted by a...
SequenceThe Sequence class
setAcceptBy.GeneralInDelSet the function used for accepting/rejecting indel events
setAcceptWin.GeneralInsertorSet the size of the acceptance window
setAlignment.PhyloSimForbidden action: setting the alignment stored in a PhyloSim...
setAlphabet.GeneralSubstitutionSet the Alphabet object aggregated by a GeneralSubstitution...
setAlphabet.ProcessAssotiate an Alphabet object with a Process object
setAlphabet.QMatrixSet the Alphabet object for a QMatrix object
setAlphabet.SiteAttach an Alphabet object to a Site object
setAlphabets.SequenceAssotiate Alphabet objects to a set of Site objects...
setAlphabet.ToleranceSubstitutionSet the Alphabet object aggregated by a ToleranceSubstitution...
setAncestral.SequenceSet the ancestral object of a Sequence object
setAncestral.SiteForbidden action: setting the ancestral object for a Site...
setBaseFreqs.F81Set the base frequency parameters
setBaseFreqs.F84Set the base frequency parameters
setBaseFreqs.GTRSet the base frequency parameters
setBaseFreqs.HKYSet the base frequency parameters
setBaseFreqs.K80Forbidden action: setting the base frequency parameters for a...
setBaseFreqs.K81Forbidden action: setting the base frequency parameters for a...
setBaseFreqs.TN93Set the base frequency parameters
setBigRate.SequenceForbidden action: setting the sum of total active event rates...
setBranchEvents.PhyloSimForbidden action: setting the list of events having...
setCodonFreqs.GY94Get codon frequencies
setComments.PSRootSet the comments associated with an object
setCumulativeRates.SequenceForbidden action: setting the cumulative rates for the sites...
setDeletionTolerance.SequenceSet the deletion tolerance site-process specific parameter...
setDist.ContinuousDeletorSet the length sampling expression
setDist.ContinuousInsertorSet the length sampling expression
setEdges.PhyloSimForbidden action: setting the edge matrix for a phylo object...
setEquDist.GeneralSubstitutionSet the equilibrium distribution for a GeneralSubstitution...
setEquDist.ToleranceSubstitutionSet the equilibrium distribution for a ToleranceSubstitution...
setEvents.SiteForbidden action: setting the list of active events for a...
setGenerateBy.GeneralInsertorSet the function object used for generating inserts
setHandler.EventForbidden action: setting the handler function of an Event...
setId.PhyloSimForbidden action: setting the unique identifier of a PhyloSim...
setId.ProcessForbidden action: setting the unique Process object...
setId.QMatrixForbidden action: setting the unique identifier for a QMatrix...
setId.SequenceForbidden action: setting the unique identifier of a Sequence...
setInsertHook.GeneralInsertorSet the insert hook function
setInsertionTolerance.SequenceSet the insertion tolerance site-process specific parameter...
setKappa.F84Get the transition transversion rate ratio
setKappa.GY94Set the transition/transversion rate ratio
setLengthParam1.FastFieldDeletorSet the first length parameter
setLengthParam2.FastFieldDeletorSet the second length parameter
setLength.SequenceForbidden action: setting the length of a Sequence object
setLogFile.PhyloSimSet the name of the file used for logging
setLogLevel.PhyloSimSet the log level for a given PhyloSim object
setMatrix.QMatrixForbidden action: setting the unscaled rate matrix for a...
setMaxLength.ContinuousDeletorSet the maximum length
setMaxLength.ContinuousInsertorSet the maximum length
setMethodsList.PSRootForbidden action: setting the list of applicable methods for...
setName.EventSet the name of an Event object
setName.PhyloSimSet the name of a PhyloSim object
setName.ProcessSet the name of a Process object
setName.QMatrixSet the name of a QMatrix object
setName.SequenceSet the name of a Sequence object
setNedges.PhyloSimForbidden action: setting the number of edges for phylo...
setNodes.PhyloSimForbidden action: setting the node identifiers for a PhyloSim...
setNtips.PhyloSimForbidden action: setting the number of the tips for a phylo...
setOmegas.CodonSequenceSet the omegas for a collection of sites
setParameterAtSite.ProcessSet the value of a site-process specific paramter in a Site...
setParameterAtSites.SequenceSet the values of a site-process specific paramater for a...
setPhylo.PhyloSimSet the phylo object for a PhyloSim object
setPosition.EventSet the position of the Site object associated to an Event...
setProbs.DiscreteDeletorSet the deletion length probabilities
setProbs.DiscreteInsertorSet the insertion length probabilities
setProcesses.SequenceSpecify a set of Process objects to be attached to a set of...
setProcesses.SiteSpecify the list of Process objects attached to a Site object
setProcess.EventSet the generator process for an Event object
setProcess.QMatrixAssotiate a process object with a QMatrix object
setProposeBy.GeneralInDelSet the function used for proposing indel lengths
setQMatrix.GeneralSubstitutionSet the QMatrix object aggregated by a GeneralSubstitution...
setQMatrix.ToleranceSubstitutionSet the QMatrix object aggregated by a ToleranceSubstitution...
setRate.EventSet the rate of an Event object
setRate.GeneralInDelSet the general rate
setRate.GeneralSubstitutionSet an unscaled rate for an event from a GeneralSubstitution...
setRate.GY94Set an unscaled rate for an event from a GY94 object
setRateList.GeneralSubstitutionSetting the rates for a GeneralSubstitution object
setRateList.QMatrixSetting the unscaled rates stored in a QMatrix object
setRateList.ToleranceSubstitutionSetting the rates for a ToleranceSubstitution object
setRateMultipliers.SequenceSet the values of the rate multiplier parameters for a given...
setRateParam.F81Forbidden action: getting the list of rate parameters
setRateParam.F84Set the value of a rate parameter
setRateParam.GTRSet the value of a rate parameter
setRateParam.HKYSet the value of a rate parameter
setRateParam.K80Set the value of a rate parameter
setRateParam.K81Set the value of a rate parameter
setRateParamList.F81Forbidden action: getting the list of rate parameters
setRateParamList.F84Set the rate parameters
setRateParamList.GTRSet the rate parameters
setRateParamList.HKYSet the rate parameters
setRateParamList.K80Set the rate parameters
setRateParamList.K81Set the rate parameters
setRateParamList.T92Set the rate parameters
setRateParamList.TN93Set the rate parameters
setRateParam.T92Set the value of a rate parameter
setRateParam.TN93Set the value of a rate parameter
setRate.QMatrixSet an unscaled rate in a QMatrix object
setRate.ToleranceSubstitutionSet an unscaled rate for an event from a...
setRootNode.PhyloSimForbidden action: setting the identifier of the root node for...
setRootSeq.PhyloSimSet the root sequence for a PhyloSim object
setScale.BrownianInsertorSet scale parameter
setScaledMatrix.QMatrixForbidden action: setting the scaled rate matrix for a...
setSequence.SiteAssotiate a Sequence object with a Site object
setSequences.PhyloSimForbidden action: setting the Sequence objects associated...
setSite.EventAssotiate an Event object with a Site object
setSiteSpecificParamIds.ProcessForbidden action: setting the paramter identifiers of the...
setSiteSpecificParamList.ProcessForbidden action: setting the site specific paramter list for...
setSize.AlphabetForbidden action: setting the symbol set size of an Alphabet...
setSizes.DiscreteDeletorSet the sizes of the proposed deletions
setSizes.DiscreteInsertorSet the sizes of the proposed insertions
setState.SiteSet the state of a Site object
setStates.SequenceSet the states for a set of Site objects aggregated by a...
setString.SequenceForbidden action: setting the string representation of a...
setSymbolLength.AlphabetForbidden action: setting the symbol length for an Alphabet...
setSymbols.AlphabetSpecify a new symbol set for an Alphabet object
setTableId.CodonAlphabetForbidden action: setting the genetic code id
setTemplateSeq.GeneralInsertorSet the template sequence object
setTheta.T92Set the GC content
setTipLabels.PhyloSimForbidden action: setting the tip labels for a phylo object...
setTips.PhyloSimForbidden action: setting the node identifiers of the tip...
setToleranceMargin.FastFieldDeletorSet the tolerance margin
setTotalRate.SiteForbidden action: setting the total active event rate for a...
setTotalRates.SequenceForbidden action: setting the list of total site rates for a...
setTransTable.CodonAlphabetForbidden action: setting the genetic code table for a...
setTreeLength.PhyloSimForbidden action: setting the tree length for a PhyloSim...
setType.AlphabetSet Alphabet object type
setType.BrownianInsertorForbidden action: setting the type of a BrownianInsertor...
setType.FastFieldDeletorForbidden action: setting the type of a FastFieldDeletor...
setUniqueAlphabets.SequenceForbidden action: setting the list of unique Alphabet objects...
setUniqueProcesses.SequenceForbidden action: setting the list of unique Process...
setWriteProtected.AlphabetSet the write protection field for an object
setWriteProtected.EventSet the write protection field for an object
setWriteProtected.ProcessSet the write protection field for an object
setWriteProtected.QMatrixSet the write protection field for a QMatrix object
setWriteProtected.SequenceSet the write protection field for an object
Simulate.PhyloSimRun a simulation according to a PhyloSim object
SiteThe Site class
stringLengthReturns the string length of the character representation of...
stringLengthVectorReturns the string lengths of the character represenations of...
summary.AlphabetSummarize the properties of an object
summary.AminoAcidSubstSummarize the properties of an object
summary.BinarySubstSummarize the properties of an object
summary.BrownianInsertorSummarize the properties of an object
summary.CodonAlphabetSummarize the properties of an object
summary.CodonSubstSummarize the properties of an object
summary.ContinuousDeletorSummarize the properties of an object
summary.ContinuousInsertorSummarize the properties of an object
summary.DiscreteDeletorSummarize the properties of an object
summary.DiscreteInsertorSummarize the properties of an object
summary.EventSummarize the properties of an object
summary.F81Summarize the properties of an object
summary.F84Summarize the properties of an object
summary.FastFieldDeletorSummarize the properties of an object
summary.GeneralDeletorSummarize the properties of an object
summary.GeneralInDelSummarize the properties of an object
summary.GeneralInsertorSummarize the properties of an object
summary.GeneralSubstitutionSummarize the properties of an object
summary.GTRSummarize the properties of an object
summary.GY94Summarize the properties of an object
summary.HKYSummarize the properties of an object
summary.JC69Summarize the properties of an object
summary.K80Summarize the properties of an object
summary.K81Summarize the properties of an object
summary.PhyloSimSummarize the properties of an object
summary.ProcessSummarize the properties of an object
summary.PSRootSummarize the properties of an object
summary.QMatrixSummarize the properties of an object
summary.SequenceSummarize the properties of an object
summary.SiteSummarize the properties of an object
summary.T92Summarize the properties of an object
summary.TN93Summarize the properties of an object
summary.ToleranceSubstitutionSummarize the properties of an object
summary.UNRESTSummarize the properties of an object
T92The T92 class
TN93The TN93 class
ToleranceSubstitutionThe ToleranceSubstitution class
translateCodon.CodonAlphabetTranslate a codon
Translate.CodonSequenceTranslate a CodonSequence object
Undocumented.PhyloSimUndocumented object (PhyloSim package)
UNRESTThe UNREST class
virtualAssignmentForbidden.PSRootThrows an error message informing the user about forbidden...
WAGThe WAG empirical amino acid substitution model
phylosim documentation built on May 29, 2017, 3:21 p.m.