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phylosim (version 3.0.2)

Flexible Simulations of Biological Sequence Evolution

Description

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions.

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Install

install.packages('phylosim')

Monthly Downloads

34

Version

3.0.2

License

GPL (>= 3)

Issues

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Repository

https://github.com/bsipos/phylosim

Maintainer

Botond Sipos

Last Published

September 8th, 2016

Functions in phylosim (3.0.2)

The Alphabet class

Check whether the two supplied Process objects are identical

AminoAcidSequence

The AminoAcidSequence class

AminoAcidAlphabet

The AminoAcidAlphabet class

as.character.Event

Get the character representation of an Event object

areSynonymous.CodonAlphabet

Check whether two codons are synonymous

The AnyAlphabet class

Check if two alaphabet objects have the same symbol set

as.character.Alphabet

Get the character representation of an Alphabet object

The AminoAcidSubst class

attachProcess.Sequence

Attach a Process object to a set of Site objects aggregated by a Sequence object

as.character.Process

Get the character representation of a Process object

attachProcess.Site

Attach a Process object to a Site object

attachHookToNode.PhyloSim

Attach a callback function to a given node of a phylo object aggregated by a PhyloSim object

as.character.ToleranceSubstitution

Return the character representation of a ToleranceSubstitution object

as.character.QMatrix

Return the character representation of a QMatrix object

as.character.GeneralSubstitution

Return the character representation of a GeneralSubstitution object

as.character.Site

Get the character representation of a Site object

as.character.Sequence

Get the string representation of a Sequence object

as.character.PhyloSim

Return the character representation of a PhyloSim object

The BinaryAlphabet class

The BinarySubst class

buildFromPAML.CodonSubst

Build rate matrix from PAML file

BrownianInsertor

The BrownianInsertor class

buildFromPAML.AminoAcidSubst

Build rate matrix from PAML file

The BinarySequence class

attachSeqToNode.PhyloSim

Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim object

BrownianPath.BrownianInsertor

Generate a Brownian path

checkConsistency.AminoAcidSubst

Check object consistency

checkConsistency.Alphabet

Check object consistency

checkConsistency.ContinuousDeletor

Check object consistency

checkConsistency.DiscreteDeletor

Check object consistency

checkConsistency.DiscreteInsertor

Check object consistency

checkConsistency.ContinuousInsertor

Check object consistency

checkConsistency.CodonSubst

Check object consistency

checkConsistency.BrownianInsertor

Check object consistency

checkConsistency.BinarySubst

Check object consistency

checkConsistency.CodonAlphabet

Check object consistency

checkConsistency.CodonUNREST

Check object consistency

checkConsistency.CodonSequence

Check object consistency

checkConsistency.GeneralDeletor

Check object consistency

checkConsistency.GeneralInDel

Check object consistency

checkConsistency.GeneralSubstitution

Check object consistency

checkConsistency.GY94

Check object consistency

checkConsistency.Event

Check object consistency

checkConsistency.GTR

Check object consistency

checkConsistency.F81

Check object consistency

checkConsistency.FastFieldDeletor

Check object consistency

checkConsistency.F84

Check object consistency

checkConsistency.GeneralInsertor

Check object consistency

checkConsistency.QMatrix

Check object consistency

checkConsistency.Sequence

Check object consistency

checkConsistency.PSRootSummary

Check object consistency

checkConsistency.PSRoot

Check object consistency

checkConsistency.JC69

Check object consistency

checkConsistency.Process

Check object consistency

checkConsistency.PhyloSim

Check object consistency

checkConsistency.HKY

Check object consistency

checkConsistency.K81

Check object consistency

checkConsistency.K80

Check object consistency

checkConsistency.TN93

Check object consistency

checkConsistency.ToleranceSubstitution

Check object consistency

enableVirtual.PSRoot

Enable the use of virtual fields for a given object

ContinuousDeletor

The ContinuousDeletor class

The Event class

ContinuousInsertor

The ContinuousInsertor class

clone.ToleranceSubstitution

Clone a ToleranceSubstitution object

The CodonAlphabet class

Clone a Sequence object

The CodonSequence class

detachProcess.Site

detachSeqFromNode.PhyloSim

Detach a Sequence object from a given node of a phylo object aggregated by a PhyloSim object

getAlignment.PhyloSim

Get the alignment stored in a PhyloSim object

flagTotalRate.Site

Flag the total event rate

The GeneralDeletor class

checkConsistency.UNREST

Check object consistency

getAlignmentLength.PhyloSim

Get the alignment length from a PhyloSim object

clearStates.Sequence

Set the states of a collection of Site objects aggregated by a Sequence object to undefined (NA)

copySubSequence.Sequence

Copy a collection of Site objects aggregated by a Sequence object into a new Sequence object

The cpREV empirical amino acid substitution model

The ECMrest empirical codon substitution model

The ECMunrest empirical codon substitution model

getAlphabet.Site

Get the Alphabet object attached to a Site object

getAlphabet.QMatrix

Get the Alphabet object associated with a QMatrix object

exportStatTree.PhyloSim

Export the per-branch counts of an event as a phylo object

getAlphabets.Sequence

Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object

getAlphabet.ToleranceSubstitution

Get the Alphabet object aggregated by a ToleranceSubstitution object

getAncestral.Sequence

Get the ancestral object of a Sequence object

getAncestral.Site

Get the ancestral object of a Site object

getBranchEvents.PhyloSim

Get the list of events having per-branch statistics recorded

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

getCodonFreqs.GY94

Get codon frequencies

Save a debug message in the PhyloSim log file

getLengthParam1.FastFieldDeletor

Get the first length parameter

getLength.Sequence

Get the number of Site objects aggregated in a Sequence object

deleteSubSequence.Sequence

Delete a collection of sites aggregated by a Sequence object

detachProcess.Sequence

Detach a Process object from a set of Site objects aggregated by a Sequence object

getAlphabet.Process

Get the Alphabet object associated with a given Process object

FastFieldDeletor

The FastFieldDeletor class

Clone a process object

getAlphabet.GeneralSubstitution

Get the Alphabet object aggregated by a GeneralSubstitution object

clone.GeneralSubstitution

Clone a GeneralSubstitution object

The CodonSubst class

DiscreteDeletor

The DiscreteDeletor class

The CodonUNREST class

getBigRate.Sequence

Get the sum of all active event rates from a Sequence object

DiscreteInsertor

The DiscreteInsertor class

The GeneralInDel class

getComments.PSRoot

Get the comments associated with an object

getCumulativeRates.Sequence

Get the total site rates from a Sequence object

GeneralInsertor

The GeneralInsertor class

getBaseFreqs.GTR

Get the base frequency parameters

Get the list of active event objects given the current state of the Site object

getEdges.PhyloSim

Get the edge matrix from a phylo object aggregated by a PhyloSim object

getEdge.PhyloSim

Get and edge from the edge matrix

getBaseFreqs.HKY

Get the base frequency parameters

getEventsAtSite.FastFieldDeletor

Generate a deletion event object given the state of the target site

getInsertHook.GeneralInsertor

Get the insert hook function

detachHookFromNode.PhyloSim

Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object

getMatrix.QMatrix

Get the unscaled rate matrix form a QMatrix object

getInsertionTolerance.Sequence

Get the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

getLogLevel.PhyloSim

Get the log level from a PhyloSim object

checkConsistency.Site

Check object consistency

checkConsistency.T92

Check object consistency

generateInsert.GeneralInsertor

Generate an insert

GeneralSubstitution

The GeneralSubstitution class

getAcceptBy.GeneralInDel

Get the function used for accepting/rejecting indel events

getAcceptWin.GeneralInsertor

Get the size of the acceptance window

getBaseFreqs.F84

Get the base frequency parameters

getBaseFreqs.F81

Get the base frequency parameters

getBaseFreqs.TN93

Get the base frequency parameters

getEventRate.QMatrix

Get the unscaled rate of an event from a QMatrix object

getEventRate.GeneralSubstitution

Get the scaled rate of an event from a GeneralSubstitution object

getEventRate.ToleranceSubstitution

Get the scaled rate of an event from a ToleranceSubstitution object

getEventsAtSite.GeneralDeletor

getEventRateAtSite.GeneralSubstitution

Get the site spcific rate of an event from a GeneralSubstitution object

getEventsAtSite.GeneralInsertor

Generate insertion event object given the state of the target site

Get the transition transversion rate ratio

Get the transition/transversion rate ratio

getProcesses.Site

Get the list of Process objects attached to a Site object

getName.Sequence

Get the name of a Sequence object

getName.QMatrix

Get the name of a QMatrix object

getProposeBy.GeneralInDel

Get the function used for proposing indel lengths

getEventsAtSite.GeneralSubstitution

Generate the list of active Event objects for a given attached Site object

getName.PhyloSim

Get the name of a PhyloSim object

getEventsAtSite.GY94

Generate the list of active Event objects for a given attached Site object

getName.Process

Get the name of a Process object

getPosition.Event

Get the position of the Site object associated to an Event object in the enclosing Sequence object

getProbs.DiscreteDeletor

Get the deletion length probabilities

getProbs.DiscreteInsertor

Get the insertion length probabilities

getRate.QMatrix

Get an unscaled rate of an event from a QMatrix object

getProcess.Event

Get the Process object which generated an Event object

getRate.GeneralSubstitution

Get an unscaled rate of an event from a GeneralSubstitution object

getParameterAtSite.Process

Get the value of a site-process specific paramter from a Site object attached to a Process object

getOmegaScalingFactor.GY94

Get the omega scaling factor

getRate.GeneralInDel

Get the general rate

Get the rate of an Event object

getRateParam.TN93

Get the value of a rate parameter

getRate.ToleranceSubstitution

Get an unscaled rate of an event from a ToleranceSubstitution object

getRateList.GeneralSubstitution

Get a list of events and their unscaled rates from a GeneralSubstitution object

getTotalRate.Site

Get the total active event rate

getToleranceMargin.FastFieldDeletor

Get the tolerance margin

getRateParamList.F81

Forbidden action: getting the list of rate parameters

getRateParamList.K81

Get the rate parameters

getRateParam.F81

Forbidden action: the value of a rate parameters

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

getRateParamList.T92

Get the rate parameters

getSymbols.Alphabet

Get the symbol set from an Alphabet object

getUniqueProcesses.Sequence

Get the list of unique Process instances attached to the Site objects aggregated by a Sequence object

getSize.Alphabet

Get the number of symbols in an Alphabet object

getTableId.CodonAlphabet

Get the genetic code id

hasSiteSpecificParameter.Process

Check if a Process object has the site-process specific parameter with the given id

getType.Alphabet

Get Alphabet obejct type

getWriteProtected.Alphabet

Check if the object is write protected

hasUndefinedRate.ToleranceSubstitution

Check if a ToleranceSubstitution object has undefined rates

isStopCodon.CodonAlphabet

Check if a codon is a stop codon

isStartCodon.CodonAlphabet

Check if a codon is a start codon

Check whether an object inherits from CodonUNREST

The JTT empirical amino acid substitution model

Check whether an object inherits from the class Event

globalConsistencyCheck.PSRoot

Check the consistency of all objects inheriting form PSRoot in the current environment

is.GeneralInDel

Check if an object inherits from the GeneralInDel class

is.GeneralDeletor

Check whether an object inherits from GeneralDeletor

Check whether an object inherits from the Sequence class

Check if an object is an instance of the Site class

getBaseFreqs.K81

Get the base frequency parameters

Display detailed information about the virtual fields and methods defined for a given object

getCumulativeRatesFromRange.Sequence

Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object

Save a message in the PhyloSim log file

getBaseFreqs.K80

Get the base frequency parameters

getEventRateAtSite.ToleranceSubstitution

Get the site spcific rate of an event from a ToleranceSubstitution object

getDeletionTolerance.Sequence

Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

getEvents.Sequence

Get the list of active Event objects for a set of Site objects aggregated by a Sequence object

Get the unique identifier of a PhyloSim object

Get the unique identifier of a Sequence object

Get the unique identifier of a QMatrix object

Get the unique identifier of a Process object

getType.BrownianInsertor

Get the type of the BrownianInsertor process

omegaVarM3.CodonSequence

The M3 (discrete) model of variable omega ratios among sites

omegaVarM2.CodonSequence

The M2 (selection) model of variable omega ratios among sites

The PhyloSim class

plot.ContinuousDeletor

Plot the density of proposed lengths

print.PSRootSummary

Print out a PSRootSummary object

Print the character representation of a QMatrix object

setBaseFreqs.GTR

Set the base frequency parameters

readAlignment.PhyloSim

Read alignment from file

The QMatrix class

setComments.PSRoot

Set the comments associated with an object

setCumulativeRates.Sequence

Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object

setBaseFreqs.HKY

Set the base frequency parameters

Forbidden action: setting the list of active events for a Site object

Forbidden action: setting the unique identifier of a Sequence object

setGenerateBy.GeneralInsertor

Set the function object used for generating inserts

setInsertHook.GeneralInsertor

Set the insert hook function

setName.Sequence

Set the name of a Sequence object

setNedges.PhyloSim

Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object

setProbs.DiscreteDeletor

Set the deletion length probabilities

getRateParam.K81

Get the value of a rate parameter

setPosition.Event

Set the position of the Site object associated to an Event object

getRootNode.PhyloSim

Get the identifier of the root node from a PhyloSim object

getRateParamList.TN93

Get the rate parameters

getRateParam.T92

Get the value of a rate parameter

getSizes.DiscreteInsertor

Get the sizes of the proposed insertions

Get the current state of a Site object

Check if a PSRoot object is NA

Check whether an object inherits from GY94

getTips.PhyloSim

Get the node identifiers of the tip nodes from a PhyloSim object

getTipLabels.PhyloSim

Get the tip labels from a phylo object aggregated by a PhyloSim object

getRateParam.GTR

Get the value of a rate parameter

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

getRateParam.F84

Get the value of a rate parameter

getPhylo.PhyloSim

Get the phylo object aggregated in a PhyloSim object

getSizes.DiscreteDeletor

Get the sizes of the proposed deletions

getRateParamList.F84

Get the rate parameters

getRateParamList.GTR

Get the rate parameters

getSequence.Site

Get the Sequence object associated with a given Site object

The MtZoa empirical amino acid substitution model

The mtREV24 empirical amino acid substitution model

getSiteSpecificParamList.Process

Get the list of site specific parameters of a Process object

getSiteSpecificParamIds.Process

Get the site specific paramter identifiers from a Process object

getSequences.PhyloSim

Gets all the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object

NucleotideAlphabet

The NucleotideAlphabet class

newMatrix.CodonSubst

New codon substitution matrix from PAML file

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

plot.DiscreteInsertor

Plot the insertion length distribution

plot.GeneralSubstitution

Create a bubble plot of the substitution process

The PSRootSummary class

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

The root class for all phylosim objects

setAcceptBy.GeneralInDel

Set the function used for accepting/rejecting indel events

sampleState.ToleranceSubstitution

Sample a state from the equlibrium distribution of a ToleranceSubstitution object

sampleState.GeneralSubstitution

Sample a state from the equlibrium distribution of a GeneralSubstitution object

The Sequence class

setBaseFreqs.F81

Set the base frequency parameters

setBaseFreqs.F84

Set the base frequency parameters

setEquDist.GeneralSubstitution

Set the equilibrium distribution for a GeneralSubstitution object

setDist.ContinuousDeletor

Set the length sampling expression

setDeletionTolerance.Sequence

Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

getWriteProtected.Event

Check if the object is write protected

setEquDist.ToleranceSubstitution

Set the equilibrium distribution for a ToleranceSubstitution object

getWriteProtected.Process

Check if the object is write protected

getTotalRatesFromRange.Sequence

Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object

Check if an object is an instance of the Alphabet class

is.CodonAlphabet

Check if an object inherits from CodonAlphabet

is.GeneralInsertor

Check whether an object inherits from GeneralInsertor

is.GeneralSubstitution

Check if an object is an instance of the GeneralSubstitution class

The mtMam empirical amino acid substitution model

is.ToleranceSubstitution

Check if an object is an instance of the ToleranceSubstitution class

The mtArt empirical amino acid substitution model

is.tip.PhyloSim

Check if a node is a tip

newAAMatrix.AminoAcidSubst

Undocumented method

my.all.equal.PSRoot

Test if two objects are nearly equal

plot.ContinuousInsertor

Plot the density of proposed lengths

plot.DiscreteDeletor

Plot the deletion length distribution

Plot a PhyloSim object

setRateList.ToleranceSubstitution

Setting the rates for a ToleranceSubstitution object

setRate.GeneralSubstitution

Set an unscaled rate for an event from a GeneralSubstitution object

Set an unscaled rate for an event from a GY94 object

readTree.PhyloSim

Read tree from file

Plot the total site rates for a collection of Site objects aggregated by a Sequence object

setSize.Alphabet

Forbidden action: setting the symbol set size of an Alphabet object

setSiteSpecificParamList.Process

Forbidden action: setting the site specific paramter list for a Process 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

setTotalRates.Sequence

Forbidden action: setting the list of total site rates for a Sequence object

setWriteProtected.Alphabet

Set the write protection field for an object

setWriteProtected.Event

Set the write protection field for an object

setTransTable.CodonAlphabet

Forbidden action: setting the genetic code table for a CodonAlphabet object

setAncestral.Sequence

Set the ancestral object of a Sequence object

Scale the scaled rate matrix stored in a QMatrix object by the provided factor

setBranchEvents.PhyloSim

Forbidden action: setting the list of events having per-branch statistics recorded

setCodonFreqs.GY94

Get codon frequencies

getTotalRates.Sequence

Get the total site rates from a Sequence object

scaleTree.PhyloSim

Scale the branch lengths of a phylo object aggragted by a PhyloSim object

setHandler.Event

Forbidden action: setting the handler function of an Event object

Forbidden action: setting the unique identifier of a PhyloSim object

setLength.Sequence

Forbidden action: setting the length of a Sequence object

Set the transition/transversion rate ratio

setMethodsList.PSRoot

Forbidden action: setting the list of applicable methods for an object

setMaxLength.ContinuousInsertor

Set the maximum length

setQMatrix.GeneralSubstitution

Set the QMatrix object aggregated by a GeneralSubstitution 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.PhyloSim

Set the phylo object for a PhyloSim object

setQMatrix.ToleranceSubstitution

Set the QMatrix object aggregated by a ToleranceSubstitution object

setRate.QMatrix

Set an unscaled rate in a QMatrix object

Get the transition transversion rate ratio

setInsertionTolerance.Sequence

Set the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object

setRate.ToleranceSubstitution

Set an unscaled rate for an event from a ToleranceSubstitution object

setRateParamList.F81

Forbidden action: getting the list of rate parameters

setName.Process

Set the name of a Process object

setNtips.PhyloSim

Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object

setNodes.PhyloSim

Forbidden action: setting the node identifiers for a PhyloSim object

setName.QMatrix

Set the name of a QMatrix object

Set the rate of an Event object

setRate.GeneralInDel

Set the general rate

setRateList.GeneralSubstitution

Setting the rates for a GeneralSubstitution object

setRateParamList.GTR

Set the rate parameters

setAncestral.Site

Forbidden action: setting the ancestral object for a Site object

rescaleQMatrix.GeneralSubstitution

Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object

setRateList.QMatrix

Setting the unscaled rates stored in a QMatrix object

setRateParamList.T92

Set the rate parameters

setRateParamList.HKY

Set the rate parameters

setString.Sequence

Forbidden action: setting the string representation of a Sequence object

setRateParamList.TN93

Set the rate parameters

setSymbolLength.Alphabet

Forbidden action: setting the symbol length for an Alphabet object

Simulate.PhyloSim

Run a simulation according to a PhyloSim object

summary.CodonSubst

Summarize the properties of an object

setWriteProtected.Sequence

Set the write protection field for an object

setRateParamList.F84

Set the rate parameters

setRootNode.PhyloSim

Forbidden action: setting the identifier of the root node for a PhyloSim object

summary.ContinuousDeletor

Summarize the properties of an object

setType.BrownianInsertor

Forbidden action: setting the type of a BrownianInsertor object

setRootSeq.PhyloSim

Set the root sequence for a PhyloSim object

setType.Alphabet

Set Alphabet object type

setType.FastFieldDeletor

Forbidden action: setting the type of a FastFieldDeletor object

stringLengthVector

Returns the string lengths of the character represenations of a collection of objects

Summarize the properties of an object

summary.DiscreteDeletor

Summarize the properties of an object

summary.GeneralInDel

Summarize the properties of an object

summary.ContinuousInsertor

Summarize the properties of an object

summary.Alphabet

Summarize the properties of an object

Summarize the properties of an object

summary.Sequence

Summarize the properties of an object

summary.QMatrix

Summarize the properties of an object

Translate.CodonSequence

Translate a CodonSequence object

translateCodon.CodonAlphabet

Translate a codon

setBaseFreqs.TN93

Set the base frequency parameters

setAlphabets.Sequence

Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object

setAlphabet.ToleranceSubstitution

Set the Alphabet object aggregated by a ToleranceSubstitution object

saveAlignment.PhyloSim

Save the alignment stored in a PhyloSim object in a Fasta file

sampleStates.Sequence

Sample the states for a collection of Site objects aggregated by a Sequence object

setBigRate.Sequence

Forbidden action: setting the sum of total active event rates for a Sequence object

setLengthParam1.FastFieldDeletor

Set the first length parameter

setLengthParam2.FastFieldDeletor

Set the second length parameter

setProcesses.Site

Specify the list of Process objects attached to a Site object

setProposeBy.GeneralInDel

Set the function used for proposing indel lengths

Summarize the properties of an object

summary.GeneralInsertor

Summarize the properties of an object

setTreeLength.PhyloSim

Forbidden action: setting the tree length for a PhyloSim object

summary.PhyloSim

Summarize the properties of an object

ToleranceSubstitution

The ToleranceSubstitution class

getDist.ContinuousDeletor

Get the length sampling expression

getDist.ContinuousInsertor

Get the length sampling expression

getEquDist.GeneralSubstitution

Get the equilibrium distribution from a GeneralSubstitution object

getEquDist.ToleranceSubstitution

Get the equilibrium distribution from a ToleranceSubstitution object

getMaxLength.ContinuousDeletor

Get the maximum length

getLogFile.PhyloSim

Get the name of the file used for logging

getLengthParam2.FastFieldDeletor

Get the second length parameter

getHandler.Event

Get the handler function of an Event object

getGenerateBy.GeneralInsertor

Get the function object used for generating inserts

getNedges.PhyloSim

Get the number of edges from phylo object aggregated by a PhyloSim object

getMaxLength.ContinuousInsertor

Get the maximum length

getNodes.PhyloSim

Get the node identifiers from a PhyloSim object

getQMatrix.ToleranceSubstitution

Get the QMatrix object aggregated by a ToleranceSubstitution object

getRateParam.HKY

Get the value of a rate parameter

Get the Site object associated with an Event object

getScaledMatrix.QMatrix

Get the scaled rate matrix form a QMatrix object

getSeqFromNode.PhyloSim

Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object

getRateParam.K80

Get the value of a rate parameter

Get the name of an Event object

getMethodsList.PSRoot

Get the list of applicable methods for an object

getNtips.PhyloSim

Get the number of the tips form a phylo object aggregated by a PhyloSim object

getOmegas.CodonSequence

Get the omegas from a collection of sites

getProcess.QMatrix

Get the process object associated with a QMatrix object

getProcesses.Sequence

Get the Process objects attached to the Site objects aggregated by a Sequence object

getRateList.ToleranceSubstitution

Get a list of events and their unscaled rates from a ToleranceSubstitution object

getRateList.QMatrix

Get a list of events and their unscaled rates from a QMatrix object

getRateParamList.HKY

Get the rate parameters

getRateParamList.K80

Get the rate parameters

setRateParam.F81

Forbidden action: getting the list of rate parameters

setRateParam.T92

Set the value of a rate parameter

setRateParam.F84

Set the value of a rate parameter

setRateParam.TN93

Set the value of a rate parameter

setSequences.PhyloSim

Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object

setSequence.Site

Assotiate a Sequence object with a Site object

setWriteProtected.Process

Set the write protection field for an object

Set the GC content

setTemplateSeq.GeneralInsertor

Set the template sequence object

setStates.Sequence

Set the states for a set of Site objects aggregated by a Sequence object

Set the state of a Site object

summary.AminoAcidSubst

Summarize the properties of an object

setWriteProtected.QMatrix

Set the write protection field for a QMatrix object

summary.BinarySubst

Summarize the properties of an object

summary.GeneralDeletor

Summarize the properties of an object

summary.FastFieldDeletor

Summarize the properties of an object

Summarize the properties of an object

Summarize the properties of an object

The WAG empirical amino acid substitution model

virtualAssignmentForbidden.PSRoot

Throws an error message informing the user about forbidden action on virtual a field

getQMatrix.GeneralSubstitution

Get the QMatrix object aggregated by a GeneralSubstitution object

Summarize the properties of an object

Summarize the properties of an object

getRootSeq.PhyloSim

Get the root sequence aggregated by a PhyloSim object

getScale.BrownianInsertor

Get scale parameter

getStates.Sequence

Get the states of a set 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

getString.Sequence

Get the string representation of a Sequence object

getSymbolLength.Alphabet

Get the length of the symbols in a given alphabet object

getTreeLength.PhyloSim

Get the tree length from a PhyloSim object

getTransTable.CodonAlphabet

Get the list storing the genetic code table

getWriteProtected.QMatrix

Check if the object is write protected

getWriteProtected.Sequence

Check if the object is write protected

getSites.Sequence

Get the list of the Site object aggregated in a Sequence object

Get the GC content

getTemplateSeq.GeneralInsertor

Get the template sequence object

hasSymbols.Alphabet

Check if an Alphabet object has a given set of symbols

getUniqueAlphabets.Sequence

Get the list of unique Alphabet objects associated to Site objects aggaregated by a Sequence object

getType.FastFieldDeletor

Get the type of a FastFieldDeletor object

hasUndefinedRate.Process

Check if the Process object has undefined rate parameters

hasUndefinedRate.GeneralSubstitution

Check if a GeneralSubstitution object has undefined rates

hasUndefinedRate.GeneralInDel

Check whether the general rate of a GeneralInDel object is undefined

intersect.list.PSRoot

Utility method returning the intersection of two lists

insertSequence.Sequence

Insert a Sequence object into another Sequence object after a specified position

Check if an object is an instance of the QMatrix class

Check if an object inherits from PSRoot

The PAM empirical amino acid substitution model

omegaVarM1.CodonSequence

The M1 (neutral) model of variable omega ratios among sites

omegaVarM0.CodonSequence

The M0 (one-ratio) model of variable omega ratios among sites

The JTT.dcmut empirical amino acid substitution model

plot.ToleranceSubstitution

Create a bubble plot of the substitution process

Perform an event

plotParametersAtSites.Sequence

Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object

rescaleQMatrix.ToleranceSubstitution

Rescale the scaled rate matrix of a QMatrix object aggregated by a ToleranceSubstitution object

revComp.NucleotideSequence

Reverse complmenet a NucleotideSequence object

setAcceptWin.GeneralInsertor

Set the size of the acceptance window

setAlphabet.Site

Attach an Alphabet object to a Site object

setAlphabet.QMatrix

Set the Alphabet object for a QMatrix object

setAlignment.PhyloSim

Forbidden action: setting the alignment stored in a PhyloSim object

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

Check if an object is an instance of the phylo class

Check if an object is an instance of the Process class

isAttached.Site

Check whether a Process object is attached to a Site object

isEmpty.Alphabet

Check if the symbol set is empty

NucleotideSequence

The NucleotideSequence class

The LG empirical amino acid substitution model

omegaHist.CodonSequence

Plot a histogram of omega values from a range

omegaVarM4.CodonSequence

The M4 (freqs) model of variable omega ratios among sites

The PAM.dcmut empirical amino acid substitution model

The Process class

proposeLength.GeneralInDel

Propose indel length

setAlphabet.GeneralSubstitution

Set the Alphabet object aggregated by a GeneralSubstitution object

setAlphabet.Process

Assotiate an Alphabet object with a Process object

Forbidden action: setting the unique Process object identifier

Forbidden action: setting the unique identifier for a QMatrix object

setMatrix.QMatrix

Forbidden action: setting the unscaled rate matrix for a QMatrix object

setLogLevel.PhyloSim

Set the log level for a given PhyloSim object

setLogFile.PhyloSim

Set the name of the file used for logging

setMaxLength.ContinuousDeletor

Set the maximum length

setProbs.DiscreteInsertor

Set the insertion length probabilities

setProcess.Event

Set the generator process for an Event object

setRateParam.K80

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

setScale.BrownianInsertor

Set scale parameter

setTableId.CodonAlphabet

Forbidden action: setting the genetic code id

setSymbols.Alphabet

Specify a new symbol set for an Alphabet object

setScaledMatrix.QMatrix

Forbidden action: setting the scaled rate matrix for a QMatrix object

setRateParam.K81

Set the value of a rate parameter

setDist.ContinuousInsertor

Set the length sampling expression

setEdges.PhyloSim

Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object

Set the name of an Event object

setName.PhyloSim

Set the name of a PhyloSim object

setParameterAtSite.Process

Set the value of a site-process specific paramter in a Site object attached to a Process object

setRateParamList.K81

Set the rate parameters

setRateParamList.K80

Set the rate parameters

setProcess.QMatrix

Assotiate a process object with a QMatrix object

setProcesses.Sequence

Specify a set of Process objects to be attached to a set of Site objects aggregated by a Sequence object

setOmegas.CodonSequence

Set the omegas for a collection of sites

setSiteSpecificParamIds.Process

Forbidden action: setting the paramter identifiers of the site specific paramters from a Process object

Assotiate an Event object with a Site object

setSizes.DiscreteInsertor

Set the sizes of the proposed insertions

setSizes.DiscreteDeletor

Set the sizes of the proposed deletions

setTipLabels.PhyloSim

Forbidden action: setting the tip labels for a phylo object aggregated by a PhyloSim object

Summarize the properties of an object

Returns the string length of the character representation of an object

setTips.PhyloSim

Forbidden action: setting the node identifiers of the tip nodes for a PhyloSim object

summary.ToleranceSubstitution

Summarize the properties of an object

Summarize the properties of an object

Summarize the properties of an object

summary.BrownianInsertor

Summarize the properties of an object

summary.CodonAlphabet

Summarize the properties of an object

summary.GeneralSubstitution

Summarize the properties of an object

summary.DiscreteInsertor

Summarize the properties of an object

Summarize the properties of an object

Undocumented.PhyloSim

Undocumented object (PhyloSim package)

Summarize the properties of an object

setToleranceMargin.FastFieldDeletor

Set the tolerance margin

The UNREST class

setTotalRate.Site

Forbidden action: setting the total active event rate for a Site object

setUniqueAlphabets.Sequence

Forbidden action: setting the list of unique Alphabet objects attached to the Site object aggregated by a Sequence object

setUniqueProcesses.Sequence

Forbidden action: setting the list of unique Process instances attached to the sites of a Sequence object

Summarize the properties of an object

Summarize the properties of an object

summary.Process

Summarize the properties of an object