# Flexible Simulations of Biological Sequence Evolution

## Documentation for package ‘phylosim’ version 3.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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