A B C D E F G H I J K L M N O P Q R S T U V W misc
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| WAG | The WAG empirical amino acid substitution model |
| !=.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 |