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 |