Flexible Simulations of Biological Sequence Evolution


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Documentation for package ‘phylosim’ version 3.0.2

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A B C D E F G H I J K L M N O P Q R S T U V W misc

-- A --

all Undocumented object (PhyloSim package)
Alphabet The Alphabet class
Alphabet.== Check if two alaphabet objects have the same symbol set
Alphabet.as.character Get the character representation of an Alphabet object
Alphabet.checkConsistency Check object consistency
Alphabet.getSize Get the number of symbols in an Alphabet object
Alphabet.getSymbolLength Get the length of the symbols in a given alphabet object
Alphabet.getSymbols Get the symbol set from an Alphabet object
Alphabet.getType Get Alphabet obejct type
Alphabet.getWriteProtected Check if the object is write protected
Alphabet.hasSymbols Check if an Alphabet object has a given set of symbols
Alphabet.isEmpty Check if the symbol set is empty
Alphabet.setSize Forbidden action: setting the symbol set size of an Alphabet object
Alphabet.setSymbolLength Forbidden action: setting the symbol length for an Alphabet object
Alphabet.setSymbols Specify a new symbol set for an Alphabet object
Alphabet.setType Set Alphabet object type
Alphabet.setWriteProtected Set the write protection field for an object
Alphabet.summary Summarize the properties of an object
AminoAcidAlphabet The AminoAcidAlphabet class
AminoAcidSequence The AminoAcidSequence class
AminoAcidSubst The AminoAcidSubst class
AminoAcidSubst.buildFromPAML Build rate matrix from PAML file
AminoAcidSubst.checkConsistency Check object consistency
AminoAcidSubst.newAAMatrix Undocumented method
AminoAcidSubst.summary Summarize the properties of an object
AnyAlphabet The AnyAlphabet class
areSynonymous Undocumented object (PhyloSim package)
areSynonymous-method Check whether two codons are synonymous
areSynonymous.CodonAlphabet Check whether two codons are synonymous
as.character-method Get the character representation of an Alphabet object
as.character-method Get the character representation of an Event object
as.character-method Return the character representation of a GeneralSubstitution object
as.character-method Return the character representation of a PhyloSim object
as.character-method Get the character representation of a Process object
as.character-method Return the character representation of a QMatrix object
as.character-method Get the string representation of a Sequence object
as.character-method Get the character representation of a Site object
as.character-method Return the character representation of a ToleranceSubstitution object
as.character.Alphabet Get the character representation of an Alphabet object
as.character.Event Get the character representation of an Event object
as.character.GeneralSubstitution Return the character representation of a GeneralSubstitution object
as.character.PhyloSim Return the character representation of a PhyloSim object
as.character.Process Get the character representation of a Process object
as.character.QMatrix Return the character representation of a QMatrix object
as.character.Sequence Get the string representation of a Sequence object
as.character.Site Get the character representation of a Site object
as.character.ToleranceSubstitution Return the character representation of a ToleranceSubstitution object
attachHookToNode Undocumented object (PhyloSim package)
attachHookToNode-method Attach a callback function to a given node of a phylo object aggregated by a PhyloSim object
attachHookToNode.PhyloSim Attach a callback function to a given node of a phylo object aggregated by a PhyloSim object
attachProcess Undocumented object (PhyloSim package)
attachProcess-method Attach a Process object to a set of Site objects aggregated by a Sequence object
attachProcess-method Attach a Process object to a Site object
attachProcess.Sequence Attach a Process object to a set of Site objects aggregated by a Sequence object
attachProcess.Site Attach a Process object to a Site object
attachSeqToNode Undocumented object (PhyloSim package)
attachSeqToNode-method Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim object
attachSeqToNode.PhyloSim Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim object

-- B --

BinaryAlphabet The BinaryAlphabet class
BinarySequence The BinarySequence class
BinarySubst The BinarySubst class
BinarySubst.checkConsistency Check object consistency
BinarySubst.summary Summarize the properties of an object
BrownianInsertor The BrownianInsertor class
BrownianInsertor.BrownianPath Generate a Brownian path
BrownianInsertor.checkConsistency Check object consistency
BrownianInsertor.getScale Get scale parameter
BrownianInsertor.getType Get the type of the BrownianInsertor process
BrownianInsertor.setScale Set scale parameter
BrownianInsertor.setType Forbidden action: setting the type of a BrownianInsertor object
BrownianInsertor.summary Summarize the properties of an object
BrownianPath Undocumented object (PhyloSim package)
BrownianPath-method Generate a Brownian path
BrownianPath.BrownianInsertor Generate a Brownian path
buildFromPAML Undocumented object (PhyloSim package)
buildFromPAML-method Build rate matrix from PAML file
buildFromPAML-method Build rate matrix from PAML file
buildFromPAML.AminoAcidSubst Build rate matrix from PAML file
buildFromPAML.CodonSubst Build rate matrix from PAML file

-- C --

checkConsistency Undocumented object (PhyloSim package)
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency-method Check object consistency
checkConsistency.Alphabet Check object consistency
checkConsistency.AminoAcidSubst Check object consistency
checkConsistency.BinarySubst Check object consistency
checkConsistency.BrownianInsertor Check object consistency
checkConsistency.CodonAlphabet Check object consistency
checkConsistency.CodonSequence Check object consistency
checkConsistency.CodonSubst Check object consistency
checkConsistency.CodonUNREST Check object consistency
checkConsistency.ContinuousDeletor Check object consistency
checkConsistency.ContinuousInsertor Check object consistency
checkConsistency.DiscreteDeletor Check object consistency
checkConsistency.DiscreteInsertor Check object consistency
checkConsistency.Event Check object consistency
checkConsistency.F81 Check object consistency
checkConsistency.F84 Check object consistency
checkConsistency.FastFieldDeletor Check object consistency
checkConsistency.GeneralDeletor Check object consistency
checkConsistency.GeneralInDel Check object consistency
checkConsistency.GeneralInsertor Check object consistency
checkConsistency.GeneralSubstitution Check object consistency
checkConsistency.GTR Check object consistency
checkConsistency.GY94 Check object consistency
checkConsistency.HKY Check object consistency
checkConsistency.JC69 Check object consistency
checkConsistency.K80 Check object consistency
checkConsistency.K81 Check object consistency
checkConsistency.PhyloSim Check object consistency
checkConsistency.Process Check object consistency
checkConsistency.PSRoot Check object consistency
checkConsistency.PSRootSummary Check object consistency
checkConsistency.QMatrix Check object consistency
checkConsistency.Sequence Check object consistency
checkConsistency.Site Check object consistency
checkConsistency.T92 Check object consistency
checkConsistency.TN93 Check object consistency
checkConsistency.ToleranceSubstitution Check object consistency
checkConsistency.UNREST Check object consistency
clearStates Undocumented object (PhyloSim package)
clearStates-method Set the states of a collection of Site objects aggregated by a Sequence object to undefined (NA)
clearStates.Sequence Set the states of a collection of Site objects aggregated by a Sequence object to undefined (NA)
clone-method Clone a GeneralSubstitution object
clone-method Clone a process object
clone-method Clone a Sequence object
clone-method Clone a ToleranceSubstitution object
clone.GeneralSubstitution Clone a GeneralSubstitution object
clone.Process Clone a process object
clone.Sequence Clone a Sequence object
clone.ToleranceSubstitution Clone a ToleranceSubstitution object
CodonAlphabet The CodonAlphabet class
CodonAlphabet.areSynonymous Check whether two codons are synonymous
CodonAlphabet.checkConsistency Check object consistency
CodonAlphabet.getTableId Get the genetic code id
CodonAlphabet.getTransTable Get the list storing the genetic code table
CodonAlphabet.isStartCodon Check if a codon is a start codon
CodonAlphabet.isStopCodon Check if a codon is a stop codon
CodonAlphabet.setTableId Forbidden action: setting the genetic code id
CodonAlphabet.setTransTable Forbidden action: setting the genetic code table for a CodonAlphabet object
CodonAlphabet.summary Summarize the properties of an object
CodonAlphabet.translateCodon Translate a codon
CodonSequence The CodonSequence class
CodonSequence.checkConsistency Check object consistency
CodonSequence.getOmegas Get the omegas from a collection of sites
CodonSequence.omegaHist Plot a histogram of omega values from a range
CodonSequence.omegaVarM0 The M0 (one-ratio) model of variable omega ratios among sites
CodonSequence.omegaVarM1 The M1 (neutral) model of variable omega ratios among sites
CodonSequence.omegaVarM2 The M2 (selection) model of variable omega ratios among sites
CodonSequence.omegaVarM3 The M3 (discrete) model of variable omega ratios among sites
CodonSequence.omegaVarM4 The M4 (freqs) model of variable omega ratios among sites
CodonSequence.setOmegas Set the omegas for a collection of sites
CodonSequence.Translate Translate a CodonSequence object
CodonSubst The CodonSubst class
CodonSubst.buildFromPAML Build rate matrix from PAML file
CodonSubst.checkConsistency Check object consistency
CodonSubst.newMatrix New codon substitution matrix from PAML file
CodonSubst.summary Summarize the properties of an object
CodonUNREST The CodonUNREST class
CodonUNREST.checkConsistency Check object consistency
ContinuousDeletor The ContinuousDeletor class
ContinuousDeletor.checkConsistency Check object consistency
ContinuousDeletor.getDist Get the length sampling expression
ContinuousDeletor.getMaxLength Get the maximum length
ContinuousDeletor.plot Plot the density of proposed lengths
ContinuousDeletor.setDist Set the length sampling expression
ContinuousDeletor.setMaxLength Set the maximum length
ContinuousDeletor.summary Summarize the properties of an object
ContinuousInsertor The ContinuousInsertor class
ContinuousInsertor.checkConsistency Check object consistency
ContinuousInsertor.getDist Get the length sampling expression
ContinuousInsertor.getMaxLength Get the maximum length
ContinuousInsertor.plot Plot the density of proposed lengths
ContinuousInsertor.setDist Set the length sampling expression
ContinuousInsertor.setMaxLength Set the maximum length
ContinuousInsertor.summary Summarize the properties of an object
copySubSequence Undocumented object (PhyloSim package)
copySubSequence-method Copy a collection of Site objects aggregated by a Sequence object into a new Sequence object
copySubSequence.Sequence Copy a collection of Site objects aggregated by a Sequence object into a new Sequence object
cpREV The cpREV empirical amino acid substitution model

-- D --

Debug Undocumented object (PhyloSim package)
Debug-method Save a debug message in the PhyloSim log file
Debug.PhyloSim Save a debug message in the PhyloSim log file
default Undocumented object (PhyloSim package)
deleteSubSequence Undocumented object (PhyloSim package)
deleteSubSequence-method Delete a collection of sites aggregated by a Sequence object
deleteSubSequence.Sequence Delete a collection of sites aggregated by a Sequence object
detachHookFromNode Undocumented object (PhyloSim package)
detachHookFromNode-method Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object
detachHookFromNode.PhyloSim Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object
detachProcess Undocumented object (PhyloSim package)
detachProcess-method Detach a Process object from a set of Site objects aggregated by a Sequence object
detachProcess-method Site
detachProcess.Sequence Detach a Process object from a set of Site objects aggregated by a Sequence object
detachProcess.Site Site
detachSeqFromNode Undocumented object (PhyloSim package)
detachSeqFromNode-method Detach a Sequence object from a given node of a phylo object aggregated by a PhyloSim object
detachSeqFromNode.PhyloSim Detach a Sequence object from a given node of a phylo object aggregated by a PhyloSim object
DiscreteDeletor The DiscreteDeletor class
DiscreteDeletor.checkConsistency Check object consistency
DiscreteDeletor.getProbs Get the deletion length probabilities
DiscreteDeletor.getSizes Get the sizes of the proposed deletions
DiscreteDeletor.plot Plot the deletion length distribution
DiscreteDeletor.setProbs Set the deletion length probabilities
DiscreteDeletor.setSizes Set the sizes of the proposed deletions
DiscreteDeletor.summary Summarize the properties of an object
DiscreteInsertor The DiscreteInsertor class
DiscreteInsertor.checkConsistency Check object consistency
DiscreteInsertor.getProbs Get the insertion length probabilities
DiscreteInsertor.getSizes Get the sizes of the proposed insertions
DiscreteInsertor.plot Plot the insertion length distribution
DiscreteInsertor.setProbs Set the insertion length probabilities
DiscreteInsertor.setSizes Set the sizes of the proposed insertions
DiscreteInsertor.summary Summarize the properties of an object

-- E --

ECMrest The ECMrest empirical codon substitution model
ECMunrest The ECMunrest empirical codon substitution model
enableVirtual Undocumented object (PhyloSim package)
enableVirtual-method Enable the use of virtual fields for a given object
enableVirtual.PSRoot Enable the use of virtual fields for a given object
equal Undocumented object (PhyloSim package)
Event The Event class
Event.as.character Get the character representation of an Event object
Event.checkConsistency Check object consistency
Event.getHandler Get the handler function of an Event object
Event.getName Get the name of an Event object
Event.getPosition Get the position of the Site object associated to an Event object in the enclosing Sequence object
Event.getProcess Get the Process object which generated an Event object
Event.getRate Get the rate of an Event object
Event.getSite Get the Site object associated with an Event object
Event.getWriteProtected Check if the object is write protected
Event.Perform Perform an event
Event.setHandler Forbidden action: setting the handler function of an Event object
Event.setName Set the name of an Event object
Event.setPosition Set the position of the Site object associated to an Event object
Event.setProcess Set the generator process for an Event object
Event.setRate Set the rate of an Event object
Event.setSite Assotiate an Event object with a Site object
Event.setWriteProtected Set the write protection field for an object
Event.summary Summarize the properties of an object
exportStatTree Undocumented object (PhyloSim package)
exportStatTree-method Export the per-branch counts of an event as a phylo object
exportStatTree.PhyloSim Export the per-branch counts of an event as a phylo object

-- F --

F81 The F81 class
F81.checkConsistency Check object consistency
F81.getBaseFreqs Get the base frequency parameters
F81.getRateParam Forbidden action: the value of a rate parameters
F81.getRateParamList Forbidden action: getting the list of rate parameters
F81.setBaseFreqs Set the base frequency parameters
F81.setRateParam Forbidden action: getting the list of rate parameters
F81.setRateParamList Forbidden action: getting the list of rate parameters
F81.summary Summarize the properties of an object
F84 The F84 class
F84.checkConsistency Check object consistency
F84.getBaseFreqs Get the base frequency parameters
F84.getKappa Get the transition transversion rate ratio
F84.getRateParam Get the value of a rate parameter
F84.getRateParamList Get the rate parameters
F84.setBaseFreqs Set the base frequency parameters
F84.setKappa Get the transition transversion rate ratio
F84.setRateParam Set the value of a rate parameter
F84.setRateParamList Set the rate parameters
F84.summary Summarize the properties of an object
FastFieldDeletor The FastFieldDeletor class
FastFieldDeletor.checkConsistency Check object consistency
FastFieldDeletor.getEventsAtSite Generate a deletion event object given the state of the target site
FastFieldDeletor.getLengthParam1 Get the first length parameter
FastFieldDeletor.getLengthParam2 Get the second length parameter
FastFieldDeletor.getToleranceMargin Get the tolerance margin
FastFieldDeletor.getType Get the type of a FastFieldDeletor object
FastFieldDeletor.setLengthParam1 Set the first length parameter
FastFieldDeletor.setLengthParam2 Set the second length parameter
FastFieldDeletor.setToleranceMargin Set the tolerance margin
FastFieldDeletor.setType Forbidden action: setting the type of a FastFieldDeletor object
FastFieldDeletor.summary Summarize the properties of an object
flagTotalRate Undocumented object (PhyloSim package)
flagTotalRate-method Flag the total event rate
flagTotalRate.Site Flag the total event rate

-- G --

GeneralDeletor The GeneralDeletor class
GeneralDeletor.checkConsistency Check object consistency
GeneralDeletor.getEventsAtSite Title
GeneralDeletor.summary Summarize the properties of an object
GeneralInDel The GeneralInDel class
GeneralInDel.checkConsistency Check object consistency
GeneralInDel.getAcceptBy Get the function used for accepting/rejecting indel events
GeneralInDel.getProposeBy Get the function used for proposing indel lengths
GeneralInDel.getRate Get the general rate
GeneralInDel.hasUndefinedRate Check whether the general rate of a GeneralInDel object is undefined
GeneralInDel.proposeLength Propose indel length
GeneralInDel.setAcceptBy Set the function used for accepting/rejecting indel events
GeneralInDel.setProposeBy Set the function used for proposing indel lengths
GeneralInDel.setRate Set the general rate
GeneralInDel.summary Summarize the properties of an object
GeneralInsertor The GeneralInsertor class
GeneralInsertor.checkConsistency Check object consistency
GeneralInsertor.generateInsert Generate an insert
GeneralInsertor.getAcceptWin Get the size of the acceptance window
GeneralInsertor.getEventsAtSite Generate insertion event object given the state of the target site
GeneralInsertor.getGenerateBy Get the function object used for generating inserts
GeneralInsertor.getInsertHook Get the insert hook function
GeneralInsertor.getTemplateSeq Get the template sequence object
GeneralInsertor.setAcceptWin Set the size of the acceptance window
GeneralInsertor.setGenerateBy Set the function object used for generating inserts
GeneralInsertor.setInsertHook Set the insert hook function
GeneralInsertor.setTemplateSeq Set the template sequence object
GeneralInsertor.summary Summarize the properties of an object
GeneralSubstitution The GeneralSubstitution class
GeneralSubstitution.as.character Return the character representation of a GeneralSubstitution object
GeneralSubstitution.checkConsistency Check object consistency
GeneralSubstitution.clone Clone a GeneralSubstitution object
GeneralSubstitution.getAlphabet Get the Alphabet object aggregated by a GeneralSubstitution object
GeneralSubstitution.getEquDist Get the equilibrium distribution from a GeneralSubstitution object
GeneralSubstitution.getEventRate Get the scaled rate of an event from a GeneralSubstitution object
GeneralSubstitution.getEventRateAtSite Get the site spcific rate of an event from a GeneralSubstitution object
GeneralSubstitution.getEventsAtSite Generate the list of active Event objects for a given attached Site object
GeneralSubstitution.getQMatrix Get the QMatrix object aggregated by a GeneralSubstitution object
GeneralSubstitution.getRate Get an unscaled rate of an event from a GeneralSubstitution object
GeneralSubstitution.getRateList Get a list of events and their unscaled rates from a GeneralSubstitution object
GeneralSubstitution.hasUndefinedRate Check if a GeneralSubstitution object has undefined rates
GeneralSubstitution.plot Create a bubble plot of the substitution process
GeneralSubstitution.rescaleQMatrix Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object
GeneralSubstitution.sampleState Sample a state from the equlibrium distribution of a GeneralSubstitution object
GeneralSubstitution.setAlphabet Set the Alphabet object aggregated by a GeneralSubstitution object
GeneralSubstitution.setEquDist Set the equilibrium distribution for a GeneralSubstitution object
GeneralSubstitution.setQMatrix Set the QMatrix object aggregated by a GeneralSubstitution object
GeneralSubstitution.setRate Set an unscaled rate for an event from a GeneralSubstitution object
GeneralSubstitution.setRateList Setting the rates for a GeneralSubstitution object
GeneralSubstitution.summary Summarize the properties of an object
generateInsert Undocumented object (PhyloSim package)
generateInsert-method Generate an insert
generateInsert.GeneralInsertor Generate an insert
getAcceptBy Undocumented object (PhyloSim package)
getAcceptBy-method Get the function used for accepting/rejecting indel events
getAcceptBy.GeneralInDel Get the function used for accepting/rejecting indel events
getAcceptBy.GeneralInsertor Get the function used for accepting/rejecting indel events
getAcceptWin Undocumented object (PhyloSim package)
getAcceptWin-method Get the size of the acceptance window
getAcceptWin.GeneralInsertor Get the size of the acceptance window
getAlignment Undocumented object (PhyloSim package)
getAlignment-method Get the alignment stored in a PhyloSim object
getAlignment.PhyloSim Get the alignment stored in a PhyloSim object
getAlignmentLength Undocumented object (PhyloSim package)
getAlignmentLength-method Get the alignment length from a PhyloSim object
getAlignmentLength.PhyloSim Get the alignment length from a PhyloSim object
getAlphabet Undocumented object (PhyloSim package)
getAlphabet-method Get the Alphabet object aggregated by a GeneralSubstitution object
getAlphabet-method Get the Alphabet object associated with a given Process object
getAlphabet-method Get the Alphabet object associated with a QMatrix object
getAlphabet-method Get the Alphabet object attached to a Site object
getAlphabet-method Get the Alphabet object aggregated by a ToleranceSubstitution object
getAlphabet.GeneralSubstitution Get the Alphabet object aggregated by a GeneralSubstitution object
getAlphabet.Process Get the Alphabet object associated with a given Process object
getAlphabet.QMatrix Get the Alphabet object associated with a QMatrix object
getAlphabet.Site Get the Alphabet object attached to a Site object
getAlphabet.ToleranceSubstitution Get the Alphabet object aggregated by a ToleranceSubstitution object
getAlphabets Undocumented object (PhyloSim package)
getAlphabets-method Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object
getAlphabets.Sequence Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object
getAncestral Undocumented object (PhyloSim package)
getAncestral-method Get the ancestral object of a Sequence object
getAncestral-method Get the ancestral object of a Site object
getAncestral.Sequence Get the ancestral object of a Sequence object
getAncestral.Site Get the ancestral object of a Site object
getBaseFreqs Undocumented object (PhyloSim package)
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs-method Get the base frequency parameters
getBaseFreqs.F81 Get the base frequency parameters
getBaseFreqs.F84 Get the base frequency parameters
getBaseFreqs.GTR Get the base frequency parameters
getBaseFreqs.HKY Get the base frequency parameters
getBaseFreqs.K80 Get the base frequency parameters
getBaseFreqs.K81 Get the base frequency parameters
getBaseFreqs.TN93 Get the base frequency parameters
getBigRate Undocumented object (PhyloSim package)
getBigRate-method Get the sum of all active event rates from a Sequence object
getBigRate.Sequence Get the sum of all active event rates from a Sequence object
getBranchEvents Undocumented object (PhyloSim package)
getBranchEvents-method Get the list of events having per-branch statistics recorded
getBranchEvents.PhyloSim Get the list of events having per-branch statistics recorded
getCodonFreqs Undocumented object (PhyloSim package)
getCodonFreqs-method Get codon frequencies
getCodonFreqs.GY94 Get codon frequencies
getComments Undocumented object (PhyloSim package)
getComments-method Get the comments associated with an object
getComments.PSRoot Get the comments associated with an object
getCumulativeRates Undocumented object (PhyloSim package)
getCumulativeRates-method Get the total site rates from a Sequence object
getCumulativeRates.Sequence Get the total site rates from a Sequence object
getCumulativeRatesFromRange Undocumented object (PhyloSim package)
getCumulativeRatesFromRange-method Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object
getCumulativeRatesFromRange.Sequence Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object
getDeletionTolerance Undocumented object (PhyloSim package)
getDeletionTolerance-method Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
getDeletionTolerance.Sequence Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
getDist Undocumented object (PhyloSim package)
getDist-method Get the length sampling expression
getDist-method Get the length sampling expression
getDist.ContinuousDeletor Get the length sampling expression
getDist.ContinuousInsertor Get the length sampling expression
getEdge Undocumented object (PhyloSim package)
getEdge-method Get and edge from the edge matrix
getEdge.PhyloSim Get and edge from the edge matrix
getEdges Undocumented object (PhyloSim package)
getEdges-method Get the edge matrix from a phylo object aggregated by a PhyloSim object
getEdges.PhyloSim Get the edge matrix from a phylo object aggregated by a PhyloSim object
getEquDist Undocumented object (PhyloSim package)
getEquDist-method Get the equilibrium distribution from a GeneralSubstitution object
getEquDist-method Get the equilibrium distribution from a ToleranceSubstitution object
getEquDist.GeneralSubstitution Get the equilibrium distribution from a GeneralSubstitution object
getEquDist.ToleranceSubstitution Get the equilibrium distribution from a ToleranceSubstitution object
getEventRate Undocumented object (PhyloSim package)
getEventRate-method Get the scaled rate of an event from a GeneralSubstitution object
getEventRate-method Get the unscaled rate of an event from a QMatrix object
getEventRate-method Get the scaled rate of an event from a ToleranceSubstitution object
getEventRate.GeneralSubstitution Get the scaled rate of an event from a GeneralSubstitution object
getEventRate.QMatrix Get the unscaled rate of an event from a QMatrix object
getEventRate.ToleranceSubstitution Get the scaled rate of an event from a ToleranceSubstitution object
getEventRateAtSite Undocumented object (PhyloSim package)
getEventRateAtSite-method Get the site spcific rate of an event from a GeneralSubstitution object
getEventRateAtSite-method Get the site spcific rate of an event from a ToleranceSubstitution object
getEventRateAtSite.GeneralSubstitution Get the site spcific rate of an event from a GeneralSubstitution object
getEventRateAtSite.ToleranceSubstitution Get the site spcific rate of an event from a ToleranceSubstitution object
getEvents Undocumented object (PhyloSim package)
getEvents-method Get the list of active Event objects for a set of Site objects aggregated by a Sequence object
getEvents-method Get the list of active event objects given the current state of the Site object
getEvents.Sequence Get the list of active Event objects for a set of Site objects aggregated by a Sequence object
getEvents.Site Get the list of active event objects given the current state of the Site object
getEventsAtSite Undocumented object (PhyloSim package)
getEventsAtSite-method Generate a deletion event object given the state of the target site
getEventsAtSite-method Generate the list of active Event objects for a given attached Site object
getEventsAtSite-method Title
getEventsAtSite-method Generate insertion event object given the state of the target site
getEventsAtSite-method Generate the list of active Event objects for a given attached Site object
getEventsAtSite-method Generate the list of active Event objects given a Site object
getEventsAtSite-method Generate the list of active Event objects for a given attached Site object
getEventsAtSite.FastFieldDeletor Generate a deletion event object given the state of the target site
getEventsAtSite.GeneralDeletor Title
getEventsAtSite.GeneralInsertor Generate insertion event object given the state of the target site
getEventsAtSite.GeneralSubstitution Generate the list of active Event objects for a given attached Site object
getEventsAtSite.GY94 Generate the list of active Event objects for a given attached Site object
getEventsAtSite.Process Generate the list of active Event objects given a Site object
getEventsAtSite.ToleranceSubstitution Generate the list of active Event objects for a given attached Site object
getGenerateBy Undocumented object (PhyloSim package)
getGenerateBy-method Get the function object used for generating inserts
getGenerateBy.GeneralInsertor Get the function object used for generating inserts
getHandler Undocumented object (PhyloSim package)
getHandler-method Get the handler function of an Event object
getHandler.Event Get the handler function of an Event object
getId Undocumented object (PhyloSim package)
getId-method Get the unique identifier of a PhyloSim object
getId-method Get the unique identifier of a Process object
getId-method Get the unique identifier of a QMatrix object
getId-method Get the unique identifier of a Sequence object
getId.PhyloSim Get the unique identifier of a PhyloSim object
getId.Process Get the unique identifier of a Process object
getId.QMatrix Get the unique identifier of a QMatrix object
getId.Sequence Get the unique identifier of a Sequence object
getInsertHook Undocumented object (PhyloSim package)
getInsertHook-method Get the insert hook function
getInsertHook.GeneralInsertor Get the insert hook function
getInsertionTolerance Undocumented object (PhyloSim package)
getInsertionTolerance-method Get the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
getInsertionTolerance.Sequence Get the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
getKappa Undocumented object (PhyloSim package)
getKappa-method Get the transition transversion rate ratio
getKappa-method Get the transition/transversion rate ratio
getKappa.F84 Get the transition transversion rate ratio
getKappa.GY94 Get the transition/transversion rate ratio
getLength Undocumented object (PhyloSim package)
getLength-method Get the number of Site objects aggregated in a Sequence object
getLength.Sequence Get the number of Site objects aggregated in a Sequence object
getLengthParam1 Undocumented object (PhyloSim package)
getLengthParam1-method Get the first length parameter
getLengthParam1.FastFieldDeletor Get the first length parameter
getLengthParam2 Undocumented object (PhyloSim package)
getLengthParam2-method Get the second length parameter
getLengthParam2.FastFieldDeletor Get the second length parameter
getLogFile Undocumented object (PhyloSim package)
getLogFile-method Get the name of the file used for logging
getLogFile.PhyloSim Get the name of the file used for logging
getLogLevel Undocumented object (PhyloSim package)
getLogLevel-method Get the log level from a PhyloSim object
getLogLevel.PhyloSim Get the log level from a PhyloSim object
getMatrix Undocumented object (PhyloSim package)
getMatrix-method Get the unscaled rate matrix form a QMatrix object
getMatrix.QMatrix Get the unscaled rate matrix form a QMatrix object
getMaxLength Undocumented object (PhyloSim package)
getMaxLength-method Get the maximum length
getMaxLength-method Get the maximum length
getMaxLength.ContinuousDeletor Get the maximum length
getMaxLength.ContinuousInsertor Get the maximum length
getMethodsList Undocumented object (PhyloSim package)
getMethodsList-method Get the list of applicable methods for an object
getMethodsList.PSRoot Get the list of applicable methods for an object
getName-method Get the name of an Event object
getName-method Get the name of a PhyloSim object
getName-method Get the name of a Process object
getName-method Get the name of a QMatrix object
getName-method Get the name of a Sequence object
getName.Event Get the name of an Event object
getName.PhyloSim Get the name of a PhyloSim object
getName.Process Get the name of a Process object
getName.QMatrix Get the name of a QMatrix object
getName.Sequence Get the name of a Sequence object
getNedges Undocumented object (PhyloSim package)
getNedges-method Get the number of edges from phylo object aggregated by a PhyloSim object
getNedges.PhyloSim Get the number of edges from phylo object aggregated by a PhyloSim object
getNodes Undocumented object (PhyloSim package)
getNodes-method Get the node identifiers from a PhyloSim object
getNodes.PhyloSim Get the node identifiers from a PhyloSim object
getNtips Undocumented object (PhyloSim package)
getNtips-method Get the number of the tips form a phylo object aggregated by a PhyloSim object
getNtips.PhyloSim Get the number of the tips form a phylo object aggregated by a PhyloSim object
getOmegas Undocumented object (PhyloSim package)
getOmegas-method Get the omegas from a collection of sites
getOmegas.CodonSequence Get the omegas from a collection of sites
getOmegas.Sequence Get the omegas from a collection of sites
getOmegaScalingFactor Undocumented object (PhyloSim package)
getOmegaScalingFactor-method Get the omega scaling factor
getOmegaScalingFactor.GY94 Get the omega scaling factor
getParameterAtSite Undocumented object (PhyloSim package)
getParameterAtSite-method Get the value of a site-process specific paramter from a Site object attached to a Process object
getParameterAtSite.Process Get the value of a site-process specific paramter from a Site object attached to a Process object
getParameterAtSites Undocumented object (PhyloSim package)
getParameterAtSites-method Get the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
getParameterAtSites.Sequence Get the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
getPhylo Undocumented object (PhyloSim package)
getPhylo-method Get the phylo object aggregated in a PhyloSim object
getPhylo.PhyloSim Get the phylo object aggregated in a PhyloSim object
getPosition-method Get the position of the Site object associated to an Event object in the enclosing Sequence object
getPosition.Event Get the position of the Site object associated to an Event object in the enclosing Sequence object
getProbs Undocumented object (PhyloSim package)
getProbs-method Get the deletion length probabilities
getProbs-method Get the insertion length probabilities
getProbs.DiscreteDeletor Get the deletion length probabilities
getProbs.DiscreteInsertor Get the insertion length probabilities
getProcess Undocumented object (PhyloSim package)
getProcess-method Get the Process object which generated an Event object
getProcess-method Get the process object associated with a QMatrix object
getProcess.Event Get the Process object which generated an Event object
getProcess.QMatrix Get the process object associated with a QMatrix object
getProcesses Undocumented object (PhyloSim package)
getProcesses-method Get the Process objects attached to the Site objects aggregated by a Sequence object
getProcesses-method Get the list of Process objects attached to a Site object
getProcesses.Sequence Get the Process objects attached to the Site objects aggregated by a Sequence object
getProcesses.Site Get the list of Process objects attached to a Site object
getProposeBy Undocumented object (PhyloSim package)
getProposeBy-method Get the function used for proposing indel lengths
getProposeBy.GeneralInDel Get the function used for proposing indel lengths
getProposeBy.GeneralInsertor Get the function used for proposing indel lengths
getQMatrix Undocumented object (PhyloSim package)
getQMatrix-method Get the QMatrix object aggregated by a GeneralSubstitution object
getQMatrix-method Get the QMatrix object aggregated by a ToleranceSubstitution object
getQMatrix.GeneralSubstitution Get the QMatrix object aggregated by a GeneralSubstitution object
getQMatrix.ToleranceSubstitution Get the QMatrix object aggregated by a ToleranceSubstitution object
getRate Undocumented object (PhyloSim package)
getRate-method Get the rate of an Event object
getRate-method Get the general rate
getRate-method Get an unscaled rate of an event from a GeneralSubstitution object
getRate-method Get an unscaled rate of an event from a QMatrix object
getRate-method Get an unscaled rate of an event from a ToleranceSubstitution object
getRate.Event Get the rate of an Event object
getRate.GeneralInDel Get the general rate
getRate.GeneralSubstitution Get an unscaled rate of an event from a GeneralSubstitution object
getRate.QMatrix Get an unscaled rate of an event from a QMatrix object
getRate.ToleranceSubstitution Get an unscaled rate of an event from a ToleranceSubstitution object
getRateList Undocumented object (PhyloSim package)
getRateList-method Get a list of events and their unscaled rates from a GeneralSubstitution object
getRateList-method Get a list of events and their unscaled rates from a QMatrix object
getRateList-method Get a list of events and their unscaled rates from a ToleranceSubstitution object
getRateList.GeneralSubstitution Get a list of events and their unscaled rates from a GeneralSubstitution object
getRateList.QMatrix Get a list of events and their unscaled rates from a QMatrix object
getRateList.ToleranceSubstitution Get a list of events and their unscaled rates from a ToleranceSubstitution object
getRateMultipliers Undocumented object (PhyloSim package)
getRateMultipliers-method Get the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
getRateMultipliers.Sequence Get the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
getRateParam Undocumented object (PhyloSim package)
getRateParam-method Forbidden action: the value of a rate parameters
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam-method Get the value of a rate parameter
getRateParam.F81 Forbidden action: the value of a rate parameters
getRateParam.F84 Get the value of a rate parameter
getRateParam.GTR Get the value of a rate parameter
getRateParam.HKY Get the value of a rate parameter
getRateParam.K80 Get the value of a rate parameter
getRateParam.K81 Get the value of a rate parameter
getRateParam.T92 Get the value of a rate parameter
getRateParam.TN93 Get the value of a rate parameter
getRateParamList Undocumented object (PhyloSim package)
getRateParamList-method Forbidden action: getting the list of rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList-method Get the rate parameters
getRateParamList.F81 Forbidden action: getting the list of rate parameters
getRateParamList.F84 Get the rate parameters
getRateParamList.GTR Get the rate parameters
getRateParamList.HKY Get the rate parameters
getRateParamList.K80 Get the rate parameters
getRateParamList.K81 Get the rate parameters
getRateParamList.T92 Get the rate parameters
getRateParamList.TN93 Get the rate parameters
getRootNode Undocumented object (PhyloSim package)
getRootNode-method Get the identifier of the root node from a PhyloSim object
getRootNode.PhyloSim Get the identifier of the root node from a PhyloSim object
getRootSeq Undocumented object (PhyloSim package)
getRootSeq-method Get the root sequence aggregated by a PhyloSim object
getRootSeq.PhyloSim Get the root sequence aggregated by a PhyloSim object
getScale Undocumented object (PhyloSim package)
getScale-method Get scale parameter
getScale.BrownianInsertor Get scale parameter
getScaledMatrix Undocumented object (PhyloSim package)
getScaledMatrix-method Get the scaled rate matrix form a QMatrix object
getScaledMatrix.QMatrix Get the scaled rate matrix form a QMatrix object
getSeqFromNode Undocumented object (PhyloSim package)
getSeqFromNode-method Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object
getSeqFromNode.PhyloSim Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object
getSequence Undocumented object (PhyloSim package)
getSequence-method Get the Sequence object associated with a given Site object
getSequence.Site Get the Sequence object associated with a given Site object
getSequences Undocumented object (PhyloSim package)
getSequences-method Gets all the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
getSequences.PhyloSim Gets all the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
getSite Undocumented object (PhyloSim package)
getSite-method Get the Site object associated with an Event object
getSite.Event Get the Site object associated with an Event object
getSites Undocumented object (PhyloSim package)
getSites-method Get the list of the Site object aggregated in a Sequence object
getSites.Sequence Get the list of the Site object aggregated in a Sequence object
getSiteSpecificParamIds Undocumented object (PhyloSim package)
getSiteSpecificParamIds-method Get the site specific paramter identifiers from a Process object
getSiteSpecificParamIds.Process Get the site specific paramter identifiers from a Process object
getSiteSpecificParamList Undocumented object (PhyloSim package)
getSiteSpecificParamList-method Get the list of site specific parameters of a Process object
getSiteSpecificParamList.Process Get the list of site specific parameters of a Process object
getSize Undocumented object (PhyloSim package)
getSize-method Get the number of symbols in an Alphabet object
getSize.Alphabet Get the number of symbols in an Alphabet object
getSizes Undocumented object (PhyloSim package)
getSizes-method Get the sizes of the proposed deletions
getSizes-method Get the sizes of the proposed insertions
getSizes.DiscreteDeletor Get the sizes of the proposed deletions
getSizes.DiscreteInsertor Get the sizes of the proposed insertions
getState Undocumented object (PhyloSim package)
getState-method Get the current state of a Site object
getState.Site Get the current state of a Site object
getStates Undocumented object (PhyloSim package)
getStates-method Get the states of a set of Site objects aggregated by a Sequence object
getStates.Sequence Get the states of a set of Site objects aggregated by a Sequence object
getString Undocumented object (PhyloSim package)
getString-method Get the string representation of a Sequence object
getString.Sequence Get the string representation of a Sequence object
getSymbolFreqs Undocumented object (PhyloSim package)
getSymbolFreqs-method Get a table with the frequencies of the states of a collection of Site objects aggregated by a Sequence object
getSymbolFreqs.Sequence Get a table with the frequencies of the states of a collection of Site objects aggregated by a Sequence object
getSymbolLength Undocumented object (PhyloSim package)
getSymbolLength-method Get the length of the symbols in a given alphabet object
getSymbolLength.Alphabet Get the length of the symbols in a given alphabet object
getSymbols Undocumented object (PhyloSim package)
getSymbols-method Get the symbol set from an Alphabet object
getSymbols.Alphabet Get the symbol set from an Alphabet object
getTableId Undocumented object (PhyloSim package)
getTableId-method Get the genetic code id
getTableId.CodonAlphabet Get the genetic code id
getTargetState Undocumented object (PhyloSim package)
getTemplateSeq Undocumented object (PhyloSim package)
getTemplateSeq-method Get the template sequence object
getTemplateSeq.GeneralInsertor Get the template sequence object
getTheta Undocumented object (PhyloSim package)
getTheta-method Get the GC content
getTheta.T92 Get the GC content
getTipLabels Undocumented object (PhyloSim package)
getTipLabels-method Get the tip labels from a phylo object aggregated by a PhyloSim object
getTipLabels.PhyloSim Get the tip labels from a phylo object aggregated by a PhyloSim object
getTips Undocumented object (PhyloSim package)
getTips-method Get the node identifiers of the tip nodes from a PhyloSim object
getTips.PhyloSim Get the node identifiers of the tip nodes from a PhyloSim object
getToleranceMargin Undocumented object (PhyloSim package)
getToleranceMargin-method Get the tolerance margin
getToleranceMargin.FastFieldDeletor Get the tolerance margin
getTotalRate Undocumented object (PhyloSim package)
getTotalRate-method Get the total active event rate
getTotalRate.Site Get the total active event rate
getTotalRates Undocumented object (PhyloSim package)
getTotalRates-method Get the total site rates from a Sequence object
getTotalRates.Sequence Get the total site rates from a Sequence object
getTotalRatesFromRange Undocumented object (PhyloSim package)
getTotalRatesFromRange-method Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object
getTotalRatesFromRange.Sequence Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object
getTransTable Undocumented object (PhyloSim package)
getTransTable-method Get the list storing the genetic code table
getTransTable.CodonAlphabet Get the list storing the genetic code table
getTreeLength Undocumented object (PhyloSim package)
getTreeLength-method Get the tree length from a PhyloSim object
getTreeLength.PhyloSim Get the tree length from a PhyloSim object
getType Undocumented object (PhyloSim package)
getType-method Get Alphabet obejct type
getType-method Get the type of the BrownianInsertor process
getType-method Get the type of a FastFieldDeletor object
getType.Alphabet Get Alphabet obejct type
getType.BrownianInsertor Get the type of the BrownianInsertor process
getType.FastFieldDeletor Get the type of a FastFieldDeletor object
getUniqueAlphabets Undocumented object (PhyloSim package)
getUniqueAlphabets-method Get the list of unique Alphabet objects associated to Site objects aggaregated by a Sequence object
getUniqueAlphabets.Sequence Get the list of unique Alphabet objects associated to Site objects aggaregated by a Sequence object
getUniqueProcesses Undocumented object (PhyloSim package)
getUniqueProcesses-method Get the list of unique Process instances attached to the Site objects aggregated by a Sequence object
getUniqueProcesses.Sequence Get the list of unique Process instances attached to the Site objects aggregated by a Sequence object
getWriteProtected Undocumented object (PhyloSim package)
getWriteProtected-method Check if the object is write protected
getWriteProtected-method Check if the object is write protected
getWriteProtected-method Check if the object is write protected
getWriteProtected-method Check if the object is write protected
getWriteProtected-method Check if the object is write protected
getWriteProtected.Alphabet Check if the object is write protected
getWriteProtected.Event Check if the object is write protected
getWriteProtected.Process Check if the object is write protected
getWriteProtected.QMatrix Check if the object is write protected
getWriteProtected.Sequence Check if the object is write protected
globalConsistencyCheck Undocumented object (PhyloSim package)
globalConsistencyCheck-method Check the consistency of all objects inheriting form PSRoot in the current environment
globalConsistencyCheck.PSRoot Check the consistency of all objects inheriting form PSRoot in the current environment
GTR The GTR class
GTR.checkConsistency Check object consistency
GTR.getBaseFreqs Get the base frequency parameters
GTR.getRateParam Get the value of a rate parameter
GTR.getRateParamList Get the rate parameters
GTR.setBaseFreqs Set the base frequency parameters
GTR.setRateParam Set the value of a rate parameter
GTR.setRateParamList Set the rate parameters
GTR.summary Summarize the properties of an object
GY94 The GY94 class
GY94.checkConsistency Check object consistency
GY94.getCodonFreqs Get codon frequencies
GY94.getEventsAtSite Generate the list of active Event objects for a given attached Site object
GY94.getKappa Get the transition/transversion rate ratio
GY94.getOmegaScalingFactor Get the omega scaling factor
GY94.setCodonFreqs Get codon frequencies
GY94.setKappa Set the transition/transversion rate ratio
GY94.setRate Set an unscaled rate for an event from a GY94 object
GY94.summary Summarize the properties of an object

-- H --

hasSiteSpecificParameter Undocumented object (PhyloSim package)
hasSiteSpecificParameter-method Check if a Process object has the site-process specific parameter with the given id
hasSiteSpecificParameter.Process Check if a Process object has the site-process specific parameter with the given id
hasSymbols Undocumented object (PhyloSim package)
hasSymbols-method Check if an Alphabet object has a given set of symbols
hasSymbols.Alphabet Check if an Alphabet object has a given set of symbols
hasUndefinedRate Undocumented object (PhyloSim package)
hasUndefinedRate-method Check whether the general rate of a GeneralInDel object is undefined
hasUndefinedRate-method Check if a GeneralSubstitution object has undefined rates
hasUndefinedRate-method Check if the Process object has undefined rate parameters
hasUndefinedRate-method Check if a ToleranceSubstitution object has undefined rates
hasUndefinedRate.GeneralInDel Check whether the general rate of a GeneralInDel object is undefined
hasUndefinedRate.GeneralSubstitution Check if a GeneralSubstitution object has undefined rates
hasUndefinedRate.Process Check if the Process object has undefined rate parameters
hasUndefinedRate.ToleranceSubstitution Check if a ToleranceSubstitution object has undefined rates
HKY The HKY class
HKY.checkConsistency Check object consistency
HKY.getBaseFreqs Get the base frequency parameters
HKY.getRateParam Get the value of a rate parameter
HKY.getRateParamList Get the rate parameters
HKY.setBaseFreqs Set the base frequency parameters
HKY.setRateParam Set the value of a rate parameter
HKY.setRateParamList Set the rate parameters
HKY.summary Summarize the properties of an object

-- I --

insertSequence Undocumented object (PhyloSim package)
insertSequence-method Insert a Sequence object into another Sequence object after a specified position
insertSequence.Sequence Insert a Sequence object into another Sequence object after a specified position
intersect Undocumented object (PhyloSim package)
intersect.list Undocumented object (PhyloSim package)
intersect.list-method Utility method returning the intersection of two lists
intersect.list.PSRoot Utility method returning the intersection of two lists
is Undocumented object (PhyloSim package)
is.Alphabet Check if an object is an instance of the Alphabet class
is.Alphabet.default Check if an object is an instance of the Alphabet class
is.CodonAlphabet Check if an object inherits from CodonAlphabet
is.CodonAlphabet.default Check if an object inherits from CodonAlphabet
is.CodonUNREST Check whether an object inherits from CodonUNREST
is.CodonUNREST.default Check whether an object inherits from CodonUNREST
is.Event Check whether an object inherits from the class Event
is.Event.default Check whether an object inherits from the class Event
is.GeneralDeletor Check whether an object inherits from GeneralDeletor
is.GeneralDeletor.default Check whether an object inherits from GeneralDeletor
is.GeneralInDel Check if an object inherits from the GeneralInDel class
is.GeneralInDel.default Check if an object inherits from the GeneralInDel class
is.GeneralInsertor Check whether an object inherits from GeneralInsertor
is.GeneralInsertor.default Check whether an object inherits from GeneralInsertor
is.GeneralSubstitution Check if an object is an instance of the GeneralSubstitution class
is.GeneralSubstitution.default Check if an object is an instance of the GeneralSubstitution class
is.GY94 Check whether an object inherits from GY94
is.GY94.default Check whether an object inherits from GY94
is.na-method Check if a PSRoot object is NA
is.na.PSRoot Check if a PSRoot object is NA
is.phylo Check if an object is an instance of the phylo class
is.phylo.default Check if an object is an instance of the phylo class
is.Process Check if an object is an instance of the Process class
is.Process.default Check if an object is an instance of the Process class
is.PSRoot Check if an object inherits from PSRoot
is.PSRoot.default Check if an object inherits from PSRoot
is.QMatrix Check if an object is an instance of the QMatrix class
is.QMatrix.default Check if an object is an instance of the QMatrix class
is.Sequence Check whether an object inherits from the Sequence class
is.Sequence.default Check whether an object inherits from the Sequence class
is.Site Check if an object is an instance of the Site class
is.Site.default Check if an object is an instance of the Site class
is.tip Undocumented object (PhyloSim package)
is.tip-method Check if a node is a tip
is.tip.PhyloSim Check if a node is a tip
is.ToleranceSubstitution Check if an object is an instance of the ToleranceSubstitution class
is.ToleranceSubstitution.default Check if an object is an instance of the ToleranceSubstitution class
isAttached Undocumented object (PhyloSim package)
isAttached-method Check whether a Process object is attached to a Site object
isAttached.Site Check whether a Process object is attached to a Site object
isEmpty Undocumented object (PhyloSim package)
isEmpty-method Check if the symbol set is empty
isEmpty.Alphabet Check if the symbol set is empty
isStartCodon Undocumented object (PhyloSim package)
isStartCodon-method Check if a codon is a start codon
isStartCodon.CodonAlphabet Check if a codon is a start codon
isStopCodon Undocumented object (PhyloSim package)
isStopCodon-method Check if a codon is a stop codon
isStopCodon.CodonAlphabet Check if a codon is a stop codon

-- J --

JC69 The JC69 class
JC69.checkConsistency Check object consistency
JC69.summary Summarize the properties of an object
JTT The JTT empirical amino acid substitution model
JTT.dcmut The JTT.dcmut empirical amino acid substitution model

-- K --

K80 The K80 class
K80.checkConsistency Check object consistency
K80.getBaseFreqs Get the base frequency parameters
K80.getRateParam Get the value of a rate parameter
K80.getRateParamList Get the rate parameters
K80.setBaseFreqs Forbidden action: setting the base frequency parameters for a K80 object
K80.setRateParam Set the value of a rate parameter
K80.setRateParamList Set the rate parameters
K80.summary Summarize the properties of an object
K81 The K81 class
K81.checkConsistency Check object consistency
K81.getBaseFreqs Get the base frequency parameters
K81.getRateParam Get the value of a rate parameter
K81.getRateParamList Get the rate parameters
K81.setBaseFreqs Forbidden action: setting the base frequency parameters for a K81 model
K81.setRateParam Set the value of a rate parameter
K81.setRateParamList Set the rate parameters
K81.summary Summarize the properties of an object

-- L --

LG The LG empirical amino acid substitution model
list Undocumented object (PhyloSim package)
ll-method Display detailed information about the virtual fields and methods defined for a given object
ll.PSRoot Display detailed information about the virtual fields and methods defined for a given object
Log Undocumented object (PhyloSim package)
Log-method Save a message in the PhyloSim log file
Log.PhyloSim Save a message in the PhyloSim log file

-- M --

mtArt The mtArt empirical amino acid substitution model
mtMam The mtMam empirical amino acid substitution model
mtREV24 The mtREV24 empirical amino acid substitution model
MtZoa The MtZoa empirical amino acid substitution model
my Undocumented object (PhyloSim package)
my.all.equal Undocumented object (PhyloSim package)
my.all.equal-method Test if two objects are nearly equal
my.all.equal.PSRoot Test if two objects are nearly equal

-- N --

newAAMatrix Undocumented object (PhyloSim package)
newAAMatrix-method Undocumented method
newAAMatrix.AminoAcidSubst Undocumented method
newMatrix Undocumented object (PhyloSim package)
newMatrix-method New codon substitution matrix from PAML file
newMatrix.CodonSubst New codon substitution matrix from PAML file
NucleotideAlphabet The NucleotideAlphabet class
NucleotideSequence The NucleotideSequence class
NucleotideSequence.revComp Reverse complmenet a NucleotideSequence object

-- O --

omegaHist Undocumented object (PhyloSim package)
omegaHist-method Plot a histogram of omega values from a range
omegaHist.CodonSequence Plot a histogram of omega values from a range
omegaVarM0 Undocumented object (PhyloSim package)
omegaVarM0-method The M0 (one-ratio) model of variable omega ratios among sites
omegaVarM0.CodonSequence The M0 (one-ratio) model of variable omega ratios among sites
omegaVarM1 Undocumented object (PhyloSim package)
omegaVarM1-method The M1 (neutral) model of variable omega ratios among sites
omegaVarM1.CodonSequence The M1 (neutral) model of variable omega ratios among sites
omegaVarM10Cont Undocumented object (PhyloSim package)
omegaVarM2 Undocumented object (PhyloSim package)
omegaVarM2-method The M2 (selection) model of variable omega ratios among sites
omegaVarM2.CodonSequence The M2 (selection) model of variable omega ratios among sites
omegaVarM3 Undocumented object (PhyloSim package)
omegaVarM3-method The M3 (discrete) model of variable omega ratios among sites
omegaVarM3.CodonSequence The M3 (discrete) model of variable omega ratios among sites
omegaVarM4 Undocumented object (PhyloSim package)
omegaVarM4-method The M4 (freqs) model of variable omega ratios among sites
omegaVarM4.CodonSequence The M4 (freqs) model of variable omega ratios among sites

-- P --

PAM The PAM empirical amino acid substitution model
PAM.dcmut The PAM.dcmut empirical amino acid substitution model
Perform Undocumented object (PhyloSim package)
Perform-method Perform an event
Perform.Event Perform an event
PhyloSim The PhyloSim class
phylosim The PhyloSim class
PhyloSim.as.character Return the character representation of a PhyloSim object
PhyloSim.attachHookToNode Attach a callback function to a given node of a phylo object aggregated by a PhyloSim object
PhyloSim.attachSeqToNode Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim object
PhyloSim.checkConsistency Check object consistency
PhyloSim.Debug Save a debug message in the PhyloSim log file
PhyloSim.detachHookFromNode Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object
PhyloSim.detachSeqFromNode Detach a Sequence object from a given node of a phylo object aggregated by a PhyloSim object
PhyloSim.exportStatTree Export the per-branch counts of an event as a phylo object
PhyloSim.getAlignment Get the alignment stored in a PhyloSim object
PhyloSim.getAlignmentLength Get the alignment length from a PhyloSim object
PhyloSim.getBranchEvents Get the list of events having per-branch statistics recorded
PhyloSim.getEdge Get and edge from the edge matrix
PhyloSim.getEdges Get the edge matrix from a phylo object aggregated by a PhyloSim object
PhyloSim.getId Get the unique identifier of a PhyloSim object
PhyloSim.getLogFile Get the name of the file used for logging
PhyloSim.getLogLevel Get the log level from a PhyloSim object
PhyloSim.getName Get the name of a PhyloSim object
PhyloSim.getNedges Get the number of edges from phylo object aggregated by a PhyloSim object
PhyloSim.getNodes Get the node identifiers from a PhyloSim object
PhyloSim.getNtips Get the number of the tips form a phylo object aggregated by a PhyloSim object
PhyloSim.getPhylo Get the phylo object aggregated in a PhyloSim object
PhyloSim.getRootNode Get the identifier of the root node from a PhyloSim object
PhyloSim.getRootSeq Get the root sequence aggregated by a PhyloSim object
PhyloSim.getSeqFromNode Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object
PhyloSim.getSequences Gets all the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
PhyloSim.getTipLabels Get the tip labels from a phylo object aggregated by a PhyloSim object
PhyloSim.getTips Get the node identifiers of the tip nodes from a PhyloSim object
PhyloSim.getTreeLength Get the tree length from a PhyloSim object
PhyloSim.is.tip Check if a node is a tip
PhyloSim.Log Save a message in the PhyloSim log file
PhyloSim.plot Plot a PhyloSim object
PhyloSim.readAlignment Read alignment from file
PhyloSim.readTree Read tree from file
PhyloSim.saveAlignment Save the alignment stored in a PhyloSim object in a Fasta file
PhyloSim.scaleTree Scale the branch lengths of a phylo object aggragted by a PhyloSim object
PhyloSim.setAlignment Forbidden action: setting the alignment stored in a PhyloSim object
PhyloSim.setBranchEvents Forbidden action: setting the list of events having per-branch statistics recorded
PhyloSim.setEdges Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object
PhyloSim.setId Forbidden action: setting the unique identifier of a PhyloSim object
PhyloSim.setLogFile Set the name of the file used for logging
PhyloSim.setLogLevel Set the log level for a given PhyloSim object
PhyloSim.setName Set the name of a PhyloSim object
PhyloSim.setNedges Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object
PhyloSim.setNodes Forbidden action: setting the node identifiers for a PhyloSim object
PhyloSim.setNtips Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object
PhyloSim.setPhylo Set the phylo object for a PhyloSim object
PhyloSim.setRootNode Forbidden action: setting the identifier of the root node for a PhyloSim object
PhyloSim.setRootSeq Set the root sequence for a PhyloSim object
PhyloSim.setSequences Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
PhyloSim.setTipLabels Forbidden action: setting the tip labels for a phylo object aggregated by a PhyloSim object
PhyloSim.setTips Forbidden action: setting the node identifiers of the tip nodes for a PhyloSim object
PhyloSim.setTreeLength Forbidden action: setting the tree length for a PhyloSim object
PhyloSim.Simulate Run a simulation according to a PhyloSim object
PhyloSim.summary Summarize the properties of an object
PhyloSim.Undocumented Undocumented object (PhyloSim package)
plot Undocumented object (PhyloSim package)
plot-method Plot the density of proposed lengths
plot-method Plot the density of proposed lengths
plot-method Plot the deletion length distribution
plot-method Plot the insertion length distribution
plot-method Create a bubble plot of the substitution process
plot-method Plot a PhyloSim object
plot-method Plot the total site rates for a collection of Site objects aggregated by a Sequence object
plot-method Create a bubble plot of the substitution process
plot.ContinuousDeletor Plot the density of proposed lengths
plot.ContinuousInsertor Plot the density of proposed lengths
plot.DiscreteDeletor Plot the deletion length distribution
plot.DiscreteInsertor Plot the insertion length distribution
plot.GeneralSubstitution Create a bubble plot of the substitution process
plot.PhyloSim Plot a PhyloSim object
plot.PSRoot Undocumented object (PhyloSim package)
plot.Sequence Plot the total site rates for a collection of Site objects aggregated by a Sequence object
plot.ToleranceSubstitution Create a bubble plot of the substitution process
plotParametersAtSites Undocumented object (PhyloSim package)
plotParametersAtSites-method Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object
plotParametersAtSites.Sequence Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object
plusGamma Undocumented object (PhyloSim package)
plusGamma-method Sample the rate multiplier parameters of a Process from a Gamma distribution for a collection of Site objects aggregated by a Sequence object
plusGamma.Sequence Sample the rate multiplier parameters of a Process from a Gamma distribution for a collection of Site objects aggregated by a Sequence object
plusInvGamma Undocumented object (PhyloSim package)
plusInvGamma-method Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object
plusInvGamma.Sequence Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object
print-method Print out a PSRootSummary object
print-method Print the character representation of a QMatrix object
print.PSRootSummary Print out a PSRootSummary object
print.QMatrix Print the character representation of a QMatrix object
Process The Process class
Process.== Check whether the two supplied Process objects are identical
Process.as.character Get the character representation of a Process object
Process.checkConsistency Check object consistency
Process.clone Clone a process object
Process.getAlphabet Get the Alphabet object associated with a given Process object
Process.getEventsAtSite Generate the list of active Event objects given a Site object
Process.getId Get the unique identifier of a Process object
Process.getName Get the name of a Process object
Process.getParameterAtSite Get the value of a site-process specific paramter from a Site object attached to a Process object
Process.getSiteSpecificParamIds Get the site specific paramter identifiers from a Process object
Process.getSiteSpecificParamList Get the list of site specific parameters of a Process object
Process.getWriteProtected Check if the object is write protected
Process.hasSiteSpecificParameter Check if a Process object has the site-process specific parameter with the given id
Process.hasUndefinedRate Check if the Process object has undefined rate parameters
Process.setAlphabet Assotiate an Alphabet object with a Process object
Process.setId Forbidden action: setting the unique Process object identifier
Process.setName Set the name of a Process object
Process.setParameterAtSite Set the value of a site-process specific paramter in a Site object attached to a Process object
Process.setSiteSpecificParamIds Forbidden action: setting the paramter identifiers of the site specific paramters from a Process object
Process.setSiteSpecificParamList Forbidden action: setting the site specific paramter list for a Process object
Process.setWriteProtected Set the write protection field for an object
Process.summary Summarize the properties of an object
proposeLength Undocumented object (PhyloSim package)
proposeLength-method Propose indel length
proposeLength.GeneralInDel Propose indel length
PSRoot The root class for all phylosim objects
PSRoot.checkConsistency Check object consistency
PSRoot.enableVirtual Enable the use of virtual fields for a given object
PSRoot.getComments Get the comments associated with an object
PSRoot.getMethodsList Get the list of applicable methods for an object
PSRoot.globalConsistencyCheck Check the consistency of all objects inheriting form PSRoot in the current environment
PSRoot.intersect.list Utility method returning the intersection of two lists
PSRoot.is.na Check if a PSRoot object is NA
PSRoot.ll Display detailed information about the virtual fields and methods defined for a given object
PSRoot.my.all.equal Test if two objects are nearly equal
PSRoot.setComments Set the comments associated with an object
PSRoot.setMethodsList Forbidden action: setting the list of applicable methods for an object
PSRoot.summary Summarize the properties of an object
PSRoot.virtualAssignmentForbidden Throws an error message informing the user about forbidden action on virtual a field
PSRootSummary The PSRootSummary class
PSRootSummary.checkConsistency Check object consistency
PSRootSummary.print Print out a PSRootSummary object

-- Q --

QMatrix The QMatrix class
QMatrix.as.character Return the character representation of a QMatrix object
QMatrix.checkConsistency Check object consistency
QMatrix.getAlphabet Get the Alphabet object associated with a QMatrix object
QMatrix.getEventRate Get the unscaled rate of an event from a QMatrix object
QMatrix.getId Get the unique identifier of a QMatrix object
QMatrix.getMatrix Get the unscaled rate matrix form a QMatrix object
QMatrix.getName Get the name of a QMatrix object
QMatrix.getProcess Get the process object associated with a QMatrix object
QMatrix.getRate Get an unscaled rate of an event from a QMatrix object
QMatrix.getRateList Get a list of events and their unscaled rates from a QMatrix object
QMatrix.getScaledMatrix Get the scaled rate matrix form a QMatrix object
QMatrix.getWriteProtected Check if the object is write protected
QMatrix.print Print the character representation of a QMatrix object
QMatrix.Scale Scale the scaled rate matrix stored in a QMatrix object by the provided factor
QMatrix.setAlphabet Set the Alphabet object for a QMatrix object
QMatrix.setId Forbidden action: setting the unique identifier for a QMatrix object
QMatrix.setMatrix Forbidden action: setting the unscaled rate matrix for a QMatrix object
QMatrix.setName Set the name of a QMatrix object
QMatrix.setProcess Assotiate a process object with a QMatrix object
QMatrix.setRate Set an unscaled rate in a QMatrix object
QMatrix.setRateList Setting the unscaled rates stored in a QMatrix object
QMatrix.setScaledMatrix Forbidden action: setting the scaled rate matrix for a QMatrix object
QMatrix.setWriteProtected Set the write protection field for a QMatrix object
QMatrix.summary Summarize the properties of an object

-- R --

readAlignment Undocumented object (PhyloSim package)
readAlignment-method Read alignment from file
readAlignment.PhyloSim Read alignment from file
readTree Undocumented object (PhyloSim package)
readTree-method Read tree from file
readTree.PhyloSim Read tree from file
rescaleQMatrix Undocumented object (PhyloSim package)
rescaleQMatrix-method Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object
rescaleQMatrix-method Rescale the scaled rate matrix of a QMatrix object aggregated by a ToleranceSubstitution object
rescaleQMatrix.GeneralSubstitution Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object
rescaleQMatrix.ToleranceSubstitution Rescale the scaled rate matrix of a QMatrix object aggregated by a ToleranceSubstitution object
revComp Undocumented object (PhyloSim package)
revComp-method Reverse complmenet a NucleotideSequence object
revComp.NucleotideSequence Reverse complmenet a NucleotideSequence object

-- S --

sampleState Undocumented object (PhyloSim package)
sampleState-method Sample a state from the equlibrium distribution of a GeneralSubstitution object
sampleState-method Sample a state from the equlibrium distribution of a ToleranceSubstitution object
sampleState.GeneralSubstitution Sample a state from the equlibrium distribution of a GeneralSubstitution object
sampleState.ToleranceSubstitution Sample a state from the equlibrium distribution of a ToleranceSubstitution object
sampleStates Undocumented object (PhyloSim package)
sampleStates-method Sample the states for a collection of Site objects aggregated by a Sequence object
sampleStates.Sequence Sample the states for a collection of Site objects aggregated by a Sequence object
saveAlignment Undocumented object (PhyloSim package)
saveAlignment-method Save the alignment stored in a PhyloSim object in a Fasta file
saveAlignment.PhyloSim Save the alignment stored in a PhyloSim object in a Fasta file
saveLoadReference Undocumented object (PhyloSim package)
Scale Undocumented object (PhyloSim package)
Scale-method Scale the scaled rate matrix stored in a QMatrix object by the provided factor
Scale.QMatrix Scale the scaled rate matrix stored in a QMatrix object by the provided factor
scaleTree Undocumented object (PhyloSim package)
scaleTree-method Scale the branch lengths of a phylo object aggragted by a PhyloSim object
scaleTree.PhyloSim Scale the branch lengths of a phylo object aggragted by a PhyloSim object
Sequence The Sequence class
Sequence.as.character Get the string representation of a Sequence object
Sequence.attachProcess Attach a Process object to a set of Site objects aggregated by a Sequence object
Sequence.checkConsistency Check object consistency
Sequence.clearStates Set the states of a collection of Site objects aggregated by a Sequence object to undefined (NA)
Sequence.clone Clone a Sequence object
Sequence.copySubSequence Copy a collection of Site objects aggregated by a Sequence object into a new Sequence object
Sequence.deleteSubSequence Delete a collection of sites aggregated by a Sequence object
Sequence.detachProcess Detach a Process object from a set of Site objects aggregated by a Sequence object
Sequence.getAlphabets Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object
Sequence.getAncestral Get the ancestral object of a Sequence object
Sequence.getBigRate Get the sum of all active event rates from a Sequence object
Sequence.getCumulativeRates Get the total site rates from a Sequence object
Sequence.getCumulativeRatesFromRange Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object
Sequence.getDeletionTolerance Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Sequence.getEvents Get the list of active Event objects for a set of Site objects aggregated by a Sequence object
Sequence.getId Get the unique identifier of a Sequence object
Sequence.getInsertionTolerance Get the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Sequence.getLength Get the number of Site objects aggregated in a Sequence object
Sequence.getName Get the name of a Sequence object
Sequence.getParameterAtSites Get the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
Sequence.getProcesses Get the Process objects attached to the Site objects aggregated by a Sequence object
Sequence.getRateMultipliers Get the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
Sequence.getSites Get the list of the Site object aggregated in a Sequence object
Sequence.getStates Get the states of a set of Site objects aggregated by a Sequence object
Sequence.getString Get the string representation of a Sequence object
Sequence.getSymbolFreqs Get a table with the frequencies of the states of a collection of Site objects aggregated by a Sequence object
Sequence.getTotalRates Get the total site rates from a Sequence object
Sequence.getTotalRatesFromRange Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object
Sequence.getUniqueAlphabets Get the list of unique Alphabet objects associated to Site objects aggaregated by a Sequence object
Sequence.getUniqueProcesses Get the list of unique Process instances attached to the Site objects aggregated by a Sequence object
Sequence.getWriteProtected Check if the object is write protected
Sequence.insertSequence Insert a Sequence object into another Sequence object after a specified position
Sequence.plot Plot the total site rates for a collection of Site objects aggregated by a Sequence object
Sequence.plotParametersAtSites Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object
Sequence.plusGamma Sample the rate multiplier parameters of a Process from a Gamma distribution for a collection of Site objects aggregated by a Sequence object
Sequence.plusInvGamma Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object
Sequence.sampleStates Sample the states for a collection of Site objects aggregated by a Sequence object
Sequence.setAlphabets Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object
Sequence.setAncestral Set the ancestral object of a Sequence object
Sequence.setBigRate Forbidden action: setting the sum of total active event rates for a Sequence object
Sequence.setCumulativeRates Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object
Sequence.setDeletionTolerance Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Sequence.setId Forbidden action: setting the unique identifier of a Sequence object
Sequence.setInsertionTolerance Set the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Sequence.setLength Forbidden action: setting the length of a Sequence object
Sequence.setName Set the name of a Sequence object
Sequence.setParameterAtSites Set the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
Sequence.setProcesses Specify a set of Process objects to be attached to a set of Site objects aggregated by a Sequence object
Sequence.setRateMultipliers Set the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
Sequence.setStates Set the states for a set of Site objects aggregated by a Sequence object
Sequence.setString Forbidden action: setting the string representation of a Sequence object
Sequence.setTotalRates Forbidden action: setting the list of total site rates for a Sequence object
Sequence.setUniqueAlphabets Forbidden action: setting the list of unique Alphabet objects attached to the Site object aggregated by a Sequence object
Sequence.setUniqueProcesses Forbidden action: setting the list of unique Process instances attached to the sites of a Sequence object
Sequence.setWriteProtected Set the write protection field for an object
Sequence.summary Summarize the properties of an object
setAcceptBy Undocumented object (PhyloSim package)
setAcceptBy-method Set the function used for accepting/rejecting indel events
setAcceptBy.GeneralInDel Set the function used for accepting/rejecting indel events
setAcceptBy.GeneralInsertor Set the function used for accepting/rejecting indel events
setAcceptWin Undocumented object (PhyloSim package)
setAcceptWin-method Set the size of the acceptance window
setAcceptWin.GeneralInsertor Set the size of the acceptance window
setAlignment Undocumented object (PhyloSim package)
setAlignment-method Forbidden action: setting the alignment stored in a PhyloSim object
setAlignment.PhyloSim Forbidden action: setting the alignment stored in a PhyloSim object
setAlphabet Undocumented object (PhyloSim package)
setAlphabet-method Set the Alphabet object aggregated by a GeneralSubstitution object
setAlphabet-method Assotiate an Alphabet object with a Process object
setAlphabet-method Set the Alphabet object for a QMatrix object
setAlphabet-method Attach an Alphabet object to a Site object
setAlphabet-method Set the Alphabet object aggregated by a ToleranceSubstitution object
setAlphabet.GeneralSubstitution Set the Alphabet object aggregated by a GeneralSubstitution object
setAlphabet.Process Assotiate an Alphabet object with a Process object
setAlphabet.QMatrix Set the Alphabet object for a QMatrix object
setAlphabet.Site Attach an Alphabet object to a Site object
setAlphabet.ToleranceSubstitution Set the Alphabet object aggregated by a ToleranceSubstitution object
setAlphabets Undocumented object (PhyloSim package)
setAlphabets-method Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object
setAlphabets.Sequence Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object
setAncestral Undocumented object (PhyloSim package)
setAncestral-method Set the ancestral object of a Sequence object
setAncestral-method Forbidden action: setting the ancestral object for a Site object
setAncestral.Sequence Set the ancestral object of a Sequence object
setAncestral.Site Forbidden action: setting the ancestral object for a Site object
setBaseFreqs Undocumented object (PhyloSim package)
setBaseFreqs-method Set the base frequency parameters
setBaseFreqs-method Set the base frequency parameters
setBaseFreqs-method Set the base frequency parameters
setBaseFreqs-method Set the base frequency parameters
setBaseFreqs-method Forbidden action: setting the base frequency parameters for a K80 object
setBaseFreqs-method Forbidden action: setting the base frequency parameters for a K81 model
setBaseFreqs-method Set the base frequency parameters
setBaseFreqs.F81 Set the base frequency parameters
setBaseFreqs.F84 Set the base frequency parameters
setBaseFreqs.GTR Set the base frequency parameters
setBaseFreqs.HKY Set the base frequency parameters
setBaseFreqs.K80 Forbidden action: setting the base frequency parameters for a K80 object
setBaseFreqs.K81 Forbidden action: setting the base frequency parameters for a K81 model
setBaseFreqs.TN93 Set the base frequency parameters
setBigRate Undocumented object (PhyloSim package)
setBigRate-method Forbidden action: setting the sum of total active event rates for a Sequence object
setBigRate.Sequence Forbidden action: setting the sum of total active event rates for a Sequence object
setBranchEvents Undocumented object (PhyloSim package)
setBranchEvents-method Forbidden action: setting the list of events having per-branch statistics recorded
setBranchEvents.PhyloSim Forbidden action: setting the list of events having per-branch statistics recorded
setCodonFreqs Undocumented object (PhyloSim package)
setCodonFreqs-method Get codon frequencies
setCodonFreqs.GY94 Get codon frequencies
setComments Undocumented object (PhyloSim package)
setComments-method Set the comments associated with an object
setComments.PSRoot Set the comments associated with an object
setCumulativeRates Undocumented object (PhyloSim package)
setCumulativeRates-method Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object
setCumulativeRates.Sequence Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object
setDeletionTolerance Undocumented object (PhyloSim package)
setDeletionTolerance-method Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
setDeletionTolerance.Sequence Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
setDist Undocumented object (PhyloSim package)
setDist-method Set the length sampling expression
setDist-method Set the length sampling expression
setDist.ContinuousDeletor Set the length sampling expression
setDist.ContinuousInsertor Set the length sampling expression
setEdges Undocumented object (PhyloSim package)
setEdges-method Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object
setEdges.PhyloSim Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object
setEquDist Undocumented object (PhyloSim package)
setEquDist-method Set the equilibrium distribution for a GeneralSubstitution object
setEquDist-method Set the equilibrium distribution for a ToleranceSubstitution object
setEquDist.AminoAcidSubst Set the equilibrium distribution for a GeneralSubstitution object
setEquDist.CodonSubst Undocumented object (PhyloSim package)
setEquDist.GeneralSubstitution Set the equilibrium distribution for a GeneralSubstitution object
setEquDist.ToleranceSubstitution Set the equilibrium distribution for a ToleranceSubstitution object
setEvents Undocumented object (PhyloSim package)
setEvents-method Forbidden action: setting the list of active events for a Site object
setEvents.Site Forbidden action: setting the list of active events for a Site object
setGenerateBy Undocumented object (PhyloSim package)
setGenerateBy-method Set the function object used for generating inserts
setGenerateBy.GeneralInsertor Set the function object used for generating inserts
setHandler Undocumented object (PhyloSim package)
setHandler-method Forbidden action: setting the handler function of an Event object
setHandler.Event Forbidden action: setting the handler function of an Event object
setId Undocumented object (PhyloSim package)
setId-method Forbidden action: setting the unique identifier of a PhyloSim object
setId-method Forbidden action: setting the unique Process object identifier
setId-method Forbidden action: setting the unique identifier for a QMatrix object
setId-method Forbidden action: setting the unique identifier of a Sequence object
setId.PhyloSim Forbidden action: setting the unique identifier of a PhyloSim object
setId.Process Forbidden action: setting the unique Process object identifier
setId.QMatrix Forbidden action: setting the unique identifier for a QMatrix object
setId.Sequence Forbidden action: setting the unique identifier of a Sequence object
setInsertHook Undocumented object (PhyloSim package)
setInsertHook-method Set the insert hook function
setInsertHook.GeneralInsertor Set the insert hook function
setInsertionTolerance Undocumented object (PhyloSim package)
setInsertionTolerance-method Set the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
setInsertionTolerance.Sequence Set the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
setKappa Undocumented object (PhyloSim package)
setKappa-method Get the transition transversion rate ratio
setKappa-method Set the transition/transversion rate ratio
setKappa.F84 Get the transition transversion rate ratio
setKappa.GY94 Set the transition/transversion rate ratio
setLength Undocumented object (PhyloSim package)
setLength-method Forbidden action: setting the length of a Sequence object
setLength.Sequence Forbidden action: setting the length of a Sequence object
setLengthParam1 Undocumented object (PhyloSim package)
setLengthParam1-method Set the first length parameter
setLengthParam1.FastFieldDeletor Set the first length parameter
setLengthParam2 Undocumented object (PhyloSim package)
setLengthParam2-method Set the second length parameter
setLengthParam2.FastFieldDeletor Set the second length parameter
setLogFile Undocumented object (PhyloSim package)
setLogFile-method Set the name of the file used for logging
setLogFile.PhyloSim Set the name of the file used for logging
setLogLevel Undocumented object (PhyloSim package)
setLogLevel-method Set the log level for a given PhyloSim object
setLogLevel.PhyloSim Set the log level for a given PhyloSim object
setMatrix Undocumented object (PhyloSim package)
setMatrix-method Forbidden action: setting the unscaled rate matrix for a QMatrix object
setMatrix.QMatrix Forbidden action: setting the unscaled rate matrix for a QMatrix object
setMaxLength Undocumented object (PhyloSim package)
setMaxLength-method Set the maximum length
setMaxLength-method Set the maximum length
setMaxLength.ContinuousDeletor Set the maximum length
setMaxLength.ContinuousInsertor Set the maximum length
setMethodsList Undocumented object (PhyloSim package)
setMethodsList-method Forbidden action: setting the list of applicable methods for an object
setMethodsList.PSRoot Forbidden action: setting the list of applicable methods for an object
setName Undocumented object (PhyloSim package)
setName-method Set the name of an Event object
setName-method Set the name of a PhyloSim object
setName-method Set the name of a Process object
setName-method Set the name of a QMatrix object
setName-method Set the name of a Sequence object
setName.Event Set the name of an Event object
setName.PhyloSim Set the name of a PhyloSim object
setName.Process Set the name of a Process object
setName.QMatrix Set the name of a QMatrix object
setName.Sequence Set the name of a Sequence object
setNedges Undocumented object (PhyloSim package)
setNedges-method Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object
setNedges.PhyloSim Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object
setNodes Undocumented object (PhyloSim package)
setNodes-method Forbidden action: setting the node identifiers for a PhyloSim object
setNodes.PhyloSim Forbidden action: setting the node identifiers for a PhyloSim object
setNtips Undocumented object (PhyloSim package)
setNtips-method Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object
setNtips.PhyloSim Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object
setOmegas Undocumented object (PhyloSim package)
setOmegas-method Set the omegas for a collection of sites
setOmegas.CodonSequence Set the omegas for a collection of sites
setOmegas.Sequence Set the omegas for a collection of sites
setParameterAtSite Undocumented object (PhyloSim package)
setParameterAtSite-method Set the value of a site-process specific paramter in a Site object attached to a Process object
setParameterAtSite.FastFieldDeletor Set the value of a site-process specific paramter in a Site object attached to a Process object
setParameterAtSite.Process Set the value of a site-process specific paramter in a Site object attached to a Process object
setParameterAtSites Undocumented object (PhyloSim package)
setParameterAtSites-method Set the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
setParameterAtSites.Sequence Set the values of a site-process specific paramater for a process and a collection of Site objects aggregated by a Sequence object
setPhylo Undocumented object (PhyloSim package)
setPhylo-method Set the phylo object for a PhyloSim object
setPhylo.PhyloSim Set the phylo object for a PhyloSim object
setPosition Undocumented object (PhyloSim package)
setPosition-method Set the position of the Site object associated to an Event object
setPosition.Event Set the position of the Site object associated to an Event object
setProbs Undocumented object (PhyloSim package)
setProbs-method Set the deletion length probabilities
setProbs-method Set the insertion length probabilities
setProbs.DiscreteDeletor Set the deletion length probabilities
setProbs.DiscreteInsertor Set the insertion length probabilities
setProcess Undocumented object (PhyloSim package)
setProcess-method Set the generator process for an Event object
setProcess-method Assotiate a process object with a QMatrix object
setProcess.Event Set the generator process for an Event object
setProcess.QMatrix Assotiate a process object with a QMatrix object
setProcesses Undocumented object (PhyloSim package)
setProcesses-method Specify a set of Process objects to be attached to a set of Site objects aggregated by a Sequence object
setProcesses-method Specify the list of Process objects attached to a Site object
setProcesses.Sequence Specify a set of Process objects to be attached to a set of Site objects aggregated by a Sequence object
setProcesses.Site Specify the list of Process objects attached to a Site object
setProposeBy Undocumented object (PhyloSim package)
setProposeBy-method Set the function used for proposing indel lengths
setProposeBy.GeneralInDel Set the function used for proposing indel lengths
setProposeBy.GeneralInsertor Set the function used for proposing indel lengths
setQMatrix Undocumented object (PhyloSim package)
setQMatrix-method Set the QMatrix object aggregated by a GeneralSubstitution object
setQMatrix-method Set the QMatrix object aggregated by a ToleranceSubstitution object
setQMatrix.GeneralSubstitution Set the QMatrix object aggregated by a GeneralSubstitution object
setQMatrix.ToleranceSubstitution Set the QMatrix object aggregated by a ToleranceSubstitution object
setRate Undocumented object (PhyloSim package)
setRate-method Set the rate of an Event object
setRate-method Set an unscaled rate for an event from a GY94 object
setRate-method Set the general rate
setRate-method Set an unscaled rate for an event from a GeneralSubstitution object
setRate-method Set an unscaled rate in a QMatrix object
setRate-method Set an unscaled rate for an event from a ToleranceSubstitution object
setRate.Event Set the rate of an Event object
setRate.GeneralInDel Set the general rate
setRate.GeneralSubstitution Set an unscaled rate for an event from a GeneralSubstitution object
setRate.GY94 Set an unscaled rate for an event from a GY94 object
setRate.QMatrix Set an unscaled rate in a QMatrix object
setRate.ToleranceSubstitution Set an unscaled rate for an event from a ToleranceSubstitution object
setRateList Undocumented object (PhyloSim package)
setRateList-method Setting the rates for a GeneralSubstitution object
setRateList-method Setting the unscaled rates stored in a QMatrix object
setRateList-method Setting the rates for a ToleranceSubstitution object
setRateList.GeneralSubstitution Setting the rates for a GeneralSubstitution object
setRateList.QMatrix Setting the unscaled rates stored in a QMatrix object
setRateList.ToleranceSubstitution Setting the rates for a ToleranceSubstitution object
setRateMultipliers Undocumented object (PhyloSim package)
setRateMultipliers-method Set the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
setRateMultipliers.Sequence Set the values of the rate multiplier parameters for a given Process object and a collection of Site object aggregated by a Sequence object
setRateParam Undocumented object (PhyloSim package)
setRateParam-method Forbidden action: getting the list of rate parameters
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam-method Set the value of a rate parameter
setRateParam.F81 Forbidden action: getting the list of rate parameters
setRateParam.F84 Set the value of a rate parameter
setRateParam.GTR Set the value of a rate parameter
setRateParam.HKY Set the value of a rate parameter
setRateParam.K80 Set the value of a rate parameter
setRateParam.K81 Set the value of a rate parameter
setRateParam.T92 Set the value of a rate parameter
setRateParam.TN93 Set the value of a rate parameter
setRateParamList Undocumented object (PhyloSim package)
setRateParamList-method Forbidden action: getting the list of rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList-method Set the rate parameters
setRateParamList.F81 Forbidden action: getting the list of rate parameters
setRateParamList.F84 Set the rate parameters
setRateParamList.GTR Set the rate parameters
setRateParamList.HKY Set the rate parameters
setRateParamList.K80 Set the rate parameters
setRateParamList.K81 Set the rate parameters
setRateParamList.T92 Set the rate parameters
setRateParamList.TN93 Set the rate parameters
setRootNode Undocumented object (PhyloSim package)
setRootNode-method Forbidden action: setting the identifier of the root node for a PhyloSim object
setRootNode.PhyloSim Forbidden action: setting the identifier of the root node for a PhyloSim object
setRootSeq Undocumented object (PhyloSim package)
setRootSeq-method Set the root sequence for a PhyloSim object
setRootSeq.PhyloSim Set the root sequence for a PhyloSim object
setScale Undocumented object (PhyloSim package)
setScale-method Set scale parameter
setScale.BrownianInsertor Set scale parameter
setScaledMatrix Undocumented object (PhyloSim package)
setScaledMatrix-method Forbidden action: setting the scaled rate matrix for a QMatrix object
setScaledMatrix.QMatrix Forbidden action: setting the scaled rate matrix for a QMatrix object
setSequence Undocumented object (PhyloSim package)
setSequence-method Assotiate a Sequence object with a Site object
setSequence.Site Assotiate a Sequence object with a Site object
setSequences Undocumented object (PhyloSim package)
setSequences-method Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
setSequences.PhyloSim Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
setSite Undocumented object (PhyloSim package)
setSite-method Assotiate an Event object with a Site object
setSite.Event Assotiate an Event object with a Site object
setSiteSpecificParamIds Undocumented object (PhyloSim package)
setSiteSpecificParamIds-method Forbidden action: setting the paramter identifiers of the site specific paramters from a Process object
setSiteSpecificParamIds.Process Forbidden action: setting the paramter identifiers of the site specific paramters from a Process object
setSiteSpecificParamList Undocumented object (PhyloSim package)
setSiteSpecificParamList-method Forbidden action: setting the site specific paramter list for a Process object
setSiteSpecificParamList.Process Forbidden action: setting the site specific paramter list for a Process object
setSize Undocumented object (PhyloSim package)
setSize-method Forbidden action: setting the symbol set size of an Alphabet object
setSize.Alphabet Forbidden action: setting the symbol set size of an Alphabet object
setSizes Undocumented object (PhyloSim package)
setSizes-method Set the sizes of the proposed deletions
setSizes-method Set the sizes of the proposed insertions
setSizes.DiscreteDeletor Set the sizes of the proposed deletions
setSizes.DiscreteInsertor Set the sizes of the proposed insertions
setState Undocumented object (PhyloSim package)
setState-method Set the state of a Site object
setState.Site Set the state of a Site object
setStates Undocumented object (PhyloSim package)
setStates-method Set the states for a set of Site objects aggregated by a Sequence object
setStates.Sequence Set the states for a set of Site objects aggregated by a Sequence object
setString Undocumented object (PhyloSim package)
setString-method Forbidden action: setting the string representation of a Sequence object
setString.Sequence Forbidden action: setting the string representation of a Sequence object
setSymbolLength Undocumented object (PhyloSim package)
setSymbolLength-method Forbidden action: setting the symbol length for an Alphabet object
setSymbolLength.Alphabet Forbidden action: setting the symbol length for an Alphabet object
setSymbols Undocumented object (PhyloSim package)
setSymbols-method Specify a new symbol set for an Alphabet object
setSymbols.Alphabet Specify a new symbol set for an Alphabet object
setTableId Undocumented object (PhyloSim package)
setTableId-method Forbidden action: setting the genetic code id
setTableId.CodonAlphabet Forbidden action: setting the genetic code id
setTargetState Undocumented object (PhyloSim package)
setTemplateSeq Undocumented object (PhyloSim package)
setTemplateSeq-method Set the template sequence object
setTemplateSeq.GeneralInsertor Set the template sequence object
setTheta Undocumented object (PhyloSim package)
setTheta-method Set the GC content
setTheta.T92 Set the GC content
setTipLabels Undocumented object (PhyloSim package)
setTipLabels-method Forbidden action: setting the tip labels for a phylo object aggregated by a PhyloSim object
setTipLabels.PhyloSim Forbidden action: setting the tip labels for a phylo object aggregated by a PhyloSim object
setTips Undocumented object (PhyloSim package)
setTips-method Forbidden action: setting the node identifiers of the tip nodes for a PhyloSim object
setTips.PhyloSim Forbidden action: setting the node identifiers of the tip nodes for a PhyloSim object
setToleranceMargin Undocumented object (PhyloSim package)
setToleranceMargin-method Set the tolerance margin
setToleranceMargin.FastFieldDeletor Set the tolerance margin
setTotalRate Undocumented object (PhyloSim package)
setTotalRate-method Forbidden action: setting the total active event rate for a Site object
setTotalRate.Site Forbidden action: setting the total active event rate for a Site object
setTotalRates Undocumented object (PhyloSim package)
setTotalRates-method Forbidden action: setting the list of total site rates for a Sequence object
setTotalRates.Sequence Forbidden action: setting the list of total site rates for a Sequence object
setTransTable Undocumented object (PhyloSim package)
setTransTable-method Forbidden action: setting the genetic code table for a CodonAlphabet object
setTransTable.CodonAlphabet Forbidden action: setting the genetic code table for a CodonAlphabet object
setTreeLength Undocumented object (PhyloSim package)
setTreeLength-method Forbidden action: setting the tree length for a PhyloSim object
setTreeLength.PhyloSim Forbidden action: setting the tree length for a PhyloSim object
setType Undocumented object (PhyloSim package)
setType-method Set Alphabet object type
setType-method Forbidden action: setting the type of a BrownianInsertor object
setType-method Forbidden action: setting the type of a FastFieldDeletor object
setType.Alphabet Set Alphabet object type
setType.BrownianInsertor Forbidden action: setting the type of a BrownianInsertor object
setType.FastFieldDeletor Forbidden action: setting the type of a FastFieldDeletor object
setUniqueAlphabets Undocumented object (PhyloSim package)
setUniqueAlphabets-method Forbidden action: setting the list of unique Alphabet objects attached to the Site object aggregated by a Sequence object
setUniqueAlphabets.Sequence Forbidden action: setting the list of unique Alphabet objects attached to the Site object aggregated by a Sequence object
setUniqueProcesses Undocumented object (PhyloSim package)
setUniqueProcesses-method Forbidden action: setting the list of unique Process instances attached to the sites of a Sequence object
setUniqueProcesses.Sequence Forbidden action: setting the list of unique Process instances attached to the sites of a Sequence object
setWriteProtected Undocumented object (PhyloSim package)
setWriteProtected-method Set the write protection field for an object
setWriteProtected-method Set the write protection field for an object
setWriteProtected-method Set the write protection field for an object
setWriteProtected-method Set the write protection field for a QMatrix object
setWriteProtected-method Set the write protection field for an object
setWriteProtected.Alphabet Set the write protection field for an object
setWriteProtected.Event Set the write protection field for an object
setWriteProtected.Process Set the write protection field for an object
setWriteProtected.QMatrix Set the write protection field for a QMatrix object
setWriteProtected.Sequence Set the write protection field for an object
Simulate Undocumented object (PhyloSim package)
Simulate-method Run a simulation according to a PhyloSim object
Simulate.PhyloSim Run a simulation according to a PhyloSim object
Site The Site class
Site.as.character Get the character representation of a Site object
Site.attachProcess Attach a Process object to a Site object
Site.checkConsistency Check object consistency
Site.detachProcess Site
Site.flagTotalRate Flag the total event rate
Site.getAlphabet Get the Alphabet object attached to a Site object
Site.getAncestral Get the ancestral object of a Site object
Site.getEvents Get the list of active event objects given the current state of the Site object
Site.getProcesses Get the list of Process objects attached to a Site object
Site.getSequence Get the Sequence object associated with a given Site object
Site.getState Get the current state of a Site object
Site.getTotalRate Get the total active event rate
Site.isAttached Check whether a Process object is attached to a Site object
Site.setAlphabet Attach an Alphabet object to a Site object
Site.setAncestral Forbidden action: setting the ancestral object for a Site object
Site.setEvents Forbidden action: setting the list of active events for a Site object
Site.setProcesses Specify the list of Process objects attached to a Site object
Site.setSequence Assotiate a Sequence object with a Site object
Site.setState Set the state of a Site object
Site.setTotalRate Forbidden action: setting the total active event rate for a Site object
Site.summary Summarize the properties of an object
stringLength Returns the string length of the character representation of an object
stringLength.default Returns the string length of the character representation of an object
stringLengthVector Returns the string lengths of the character represenations of a collection of objects
stringLengthVector.default Returns the string lengths of the character represenations of a collection of objects
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary-method Summarize the properties of an object
summary.Alphabet Summarize the properties of an object
summary.AminoAcidSubst Summarize the properties of an object
summary.BinarySubst Summarize the properties of an object
summary.BrownianInsertor Summarize the properties of an object
summary.CodonAlphabet Summarize the properties of an object
summary.CodonSubst Summarize the properties of an object
summary.ContinuousDeletor Summarize the properties of an object
summary.ContinuousInsertor Summarize the properties of an object
summary.DiscreteDeletor Summarize the properties of an object
summary.DiscreteInsertor Summarize the properties of an object
summary.Event Summarize the properties of an object
summary.F81 Summarize the properties of an object
summary.F84 Summarize the properties of an object
summary.FastFieldDeletor Summarize the properties of an object
summary.GeneralDeletor Summarize the properties of an object
summary.GeneralInDel Summarize the properties of an object
summary.GeneralInsertor Summarize the properties of an object
summary.GeneralSubstitution Summarize the properties of an object
summary.GTR Summarize the properties of an object
summary.GY94 Summarize the properties of an object
summary.HKY Summarize the properties of an object
summary.JC69 Summarize the properties of an object
summary.K80 Summarize the properties of an object
summary.K81 Summarize the properties of an object
summary.PhyloSim Summarize the properties of an object
summary.Process Summarize the properties of an object
summary.PSRoot Summarize the properties of an object
summary.QMatrix Summarize the properties of an object
summary.Sequence Summarize the properties of an object
summary.Site Summarize the properties of an object
summary.T92 Summarize the properties of an object
summary.TN93 Summarize the properties of an object
summary.ToleranceSubstitution Summarize the properties of an object
summary.UNREST Summarize the properties of an object

-- T --

T92 The T92 class
T92.checkConsistency Check object consistency
T92.getRateParam Get the value of a rate parameter
T92.getRateParamList Get the rate parameters
T92.getTheta Get the GC content
T92.setRateParam Set the value of a rate parameter
T92.setRateParamList Set the rate parameters
T92.setTheta Set the GC content
T92.summary Summarize the properties of an object
tip Undocumented object (PhyloSim package)
TN93 The TN93 class
TN93.checkConsistency Check object consistency
TN93.getBaseFreqs Get the base frequency parameters
TN93.getRateParam Get the value of a rate parameter
TN93.getRateParamList Get the rate parameters
TN93.setBaseFreqs Set the base frequency parameters
TN93.setRateParam Set the value of a rate parameter
TN93.setRateParamList Set the rate parameters
TN93.summary Summarize the properties of an object
ToleranceSubstitution The ToleranceSubstitution class
ToleranceSubstitution.as.character Return the character representation of a ToleranceSubstitution object
ToleranceSubstitution.checkConsistency Check object consistency
ToleranceSubstitution.clone Clone a ToleranceSubstitution object
ToleranceSubstitution.getAlphabet Get the Alphabet object aggregated by a ToleranceSubstitution object
ToleranceSubstitution.getEquDist Get the equilibrium distribution from a ToleranceSubstitution object
ToleranceSubstitution.getEventRate Get the scaled rate of an event from a ToleranceSubstitution object
ToleranceSubstitution.getEventRateAtSite Get the site spcific rate of an event from a ToleranceSubstitution object
ToleranceSubstitution.getEventsAtSite Generate the list of active Event objects for a given attached Site object
ToleranceSubstitution.getQMatrix Get the QMatrix object aggregated by a ToleranceSubstitution object
ToleranceSubstitution.getRate Get an unscaled rate of an event from a ToleranceSubstitution object
ToleranceSubstitution.getRateList Get a list of events and their unscaled rates from a ToleranceSubstitution object
ToleranceSubstitution.hasUndefinedRate Check if a ToleranceSubstitution object has undefined rates
ToleranceSubstitution.plot Create a bubble plot of the substitution process
ToleranceSubstitution.rescaleQMatrix Rescale the scaled rate matrix of a QMatrix object aggregated by a ToleranceSubstitution object
ToleranceSubstitution.sampleState Sample a state from the equlibrium distribution of a ToleranceSubstitution object
ToleranceSubstitution.setAlphabet Set the Alphabet object aggregated by a ToleranceSubstitution object
ToleranceSubstitution.setEquDist Set the equilibrium distribution for a ToleranceSubstitution object
ToleranceSubstitution.setQMatrix Set the QMatrix object aggregated by a ToleranceSubstitution object
ToleranceSubstitution.setRate Set an unscaled rate for an event from a ToleranceSubstitution object
ToleranceSubstitution.setRateList Setting the rates for a ToleranceSubstitution object
ToleranceSubstitution.summary Summarize the properties of an object
Translate Undocumented object (PhyloSim package)
Translate-method Translate a CodonSequence object
Translate.CodonSequence Translate a CodonSequence object
translateCodon Undocumented object (PhyloSim package)
translateCodon-method Translate a codon
translateCodon.CodonAlphabet Translate a codon

-- U --

Undocumented Undocumented object (PhyloSim package)
Undocumented-method Undocumented object (PhyloSim package)
Undocumented.PhyloSim Undocumented object (PhyloSim package)
UNREST The UNREST class
UNREST.checkConsistency Check object consistency
UNREST.summary Summarize the properties of an object

-- V --

virtualAssignmentForbidden Undocumented object (PhyloSim package)
virtualAssignmentForbidden-method Throws an error message informing the user about forbidden action on virtual a field
virtualAssignmentForbidden.PSRoot Throws an error message informing the user about forbidden action on virtual a field

-- W --

WAG The WAG empirical amino acid substitution model

-- misc --

!=.Alphabet Check if two alaphabet objects have the same symbol set
!=.Process Check whether the two supplied Process objects are identical
==-method Check if two alaphabet objects have the same symbol set
==-method Check whether the two supplied Process objects are identical
==.Alphabet Check if two alaphabet objects have the same symbol set
==.Process Check whether the two supplied Process objects are identical