The following is a list of generic types that elements represent in a beast file.
Attribute
Elements of this type include:
<attr>
Description:
This element represents a name/value pair.
<compoundParameter>
Description:
A multidimensional parameter constructed from its component parameters.
<correlation>
Description:
This element returns a precision that is the element-wise reciprocal of the child precision.
<date>
Description:
Specifies a date on a given timescale
<designMatrix>
Description:
A matrix parameter constructed from its component parameters.
<diagonalMatrix>
Description:
A diagonal matrix parameter constructed from its diagonals.
<differenceStatistic>
Description:
This element returns a statistic that is the difference of the 2 child statistics.
<exponentialStatistic>
Description:
This element returns a statistic that is the element-wise exponentiation of the child statistic.
<expressionStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<externalLengthStatistic>
Description:
A statistic that has as its value(s) the length of the external branch length(s) of a set of one or more taxa in a given tree
<gmrfHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<logarithmStatistic>
Description:
This element returns a statistic that is the element-wise natural logarithm of the child statistic.
<matrixInverse>
Description:
This element returns a statistic that is the matrix inverse of the child statistic.
<matrixParameter>
Description:
A matrix parameter constructed from its component parameters.
<meanStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<monophylyStatistic>
Description:
A statistic that returns true if a given set of taxa are monophyletic for a given tree
<mrcaTraitStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<negativeStatistic>
Description:
This element returns a statistic that is the element-wise negation of the child statistic.
<nodeHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<notStatistic>
Description:
This element returns a statistic that is the element-wise inverse of the child statistic.
<parameter>
Description:
A real-valued parameter of one or more dimensions.
<parsimonyStateStatistic>
Description:
A statistic that has as its value the parsimony state reconstruction of a binary state defined by a set of taxa at a given MRCA of a tree
<parsimonyStatistic>
Description:
A statistic that has as its value the parsimony tree length of a set of a binary state defined by a set of taxa for a given tree
<popGraph>
Description:
This element returns a statistic that is the population size at evenly spaced intervals over tree.
<productStatistic>
Description:
This element returns a statistic that is the product of the child statistics.
<rateStatistic>
Description:
A statistic that returns the average of the branch rates
<ratioStatistic>
Description:
This element returns a statistic that is the ratio of the 2 child statistics.
<reciprocalStatistic>
Description:
This element returns a statistic that is the element-wise reciprocal of the child statistic.
<RPNcalculator>
Description:
This element returns a statistic evaluated from arbitrary expression.
<speciesTreeStatistic>
Description:
A statistic that returns true if the given population tree is compatible with the species tree. Compatibility is defined as the compatibility of the timings of the events, so that incompatibility arises if two individuals in the population tree coalescent before their species do in the species tree.
<statistic>
Description:
A statistic of a given name from the specified object.
<subStatistic>
Description:
Allows you to choose specific dimensions of a given statistic
<sumStatistic>
Description:
This element returns a statistic that is the element-wise sum of the child statistics.
<test>
Description:
This element represents a boolean statistic that returns 1 if the conditions are met and 0 otherwise.
<tmrcaStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<transmissionStatistic>
Description:
A statistic that returns true if the given parasite tree is compatible with the host tree.
<treeMetricStatistic>
Description:
A statistic that returns the distance between two trees. with method="topology", return a 0 for identity and a 1 for difference. With other methods return the distance metric associated with that method.
<treeShapeStatistics>
Description:
A statistic that reports a handful of tree shape statistics on the given target tree.
<varianceStatistic>
Description:
This element returns a statistic that is the variance of the child statistics.
<vectorSlice>
Description:
A vector parameter constructed from a slice of component parameters.
Identifiable
Elements of this type include:
<ACLikelihood>
Description:
This element returns an object that can calculate the likelihood of rate changes in a tree under the assumption of distributed rate changes among lineages. Specifically, each branch is assumed to draw a rate from a distribution with mean of the rate in the parent branch and the given standard deviation (the variance can be optionally proportional to branch length).
<advancedTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<alignment>
Description:
This element represents an alignment of molecular sequences.
<alloppspecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<alsTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ancestralTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<antigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space.
<anyTipObservationProcess>
Description:
This element represents an instance of the AnyTipObservationProcess for ALSTreeLikelihood calculations
<apsp>
Description:
A diploid or allopolyploid species made of individuals
<apspCoalescent>
Description:
Likelihood of a set of gene trees embedded in a allopolyploid species network.
<arbitraryBranchRates>
Description:
This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.
<argDiscretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<argTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<argTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ascertainedPatterns>
Description:
A weighted list of the unique site patterns (unique columns) in an alignment.
<ASYMQUADModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<avgPosteriorIBDReporter>
Description:
This element represents a reporter for average expected number of tips ibd conditional on observed patterns.
<siteModel>
Description:
A SiteModel that has a gamma distributed rates across sites
<benchmarker>
Description:
This element runs a benchmark on a series of likelihood calculators.
<betaPrior>
Description:
Calculates the prior probability of some data under a given beta distribution.
<betaSplittingModel>
Description:
The beta-splitting family of tree branching models (Aldous, 1996;2001).
<binaryCovarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<binomialLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<birthDeathModel>
Description:
Gernhard (2008) model of speciation (equation at bottom of page 19 of draft).
<booleanLikelihood>
Description:
A function that log likelihood of a set of boolean statistics. If all the statistics are true then it returns 0.0 otherwise -infinity.
<branchingLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<cachedPrior>
Description:
Calculates a cached likelihood of some data given some parametric or empirical distribution.
<cataclysm>
Description:
A demographic model of exponential growth.
<coalescentLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<compoundBranchRateModel>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<compoundLikelihood>
Description:
A likelihood function which is simply the product of its component likelihood functions.
<compoundParameter>
Description:
A multidimensional parameter constructed from its component parameters.
<constantExponential>
Description:
A demographic model of constant population size followed by exponential growth.
<constantLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<constantPatterns>
Description:
Creates a set of patterns for constant sites with weights as provided.
<constantSize>
Description:
A demographic model representing a constant population size through time.
<constExpConst>
Description:
A demographic model of constant population size followed by exponential growth.
<continuousTraitRateModel>
Description:
This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.
<convert>
Description:
Converts an alignment to the given data type.
<correlation>
Description:
This element returns a precision that is the element-wise reciprocal of the child precision.
<coulombPrior>
Description:
Calculates a prior density based on the force due to electrostatic charge between particles the given distance x.
<covarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<ctmcScalePrior>
Description:
This element represents the prior for CTMC scale parameter.
<decayingRateModel>
Description:
This element provides a clock model in which the rate of molecular evolution decays to a substitution rate in the past.
<designMatrix>
Description:
A matrix parameter constructed from its component parameters.
<diagonalMatrix>
Description:
A diagonal matrix parameter constructed from its diagonals.
<differenceStatistic>
Description:
This element returns a statistic that is the difference of the 2 child statistics.
<dirichletPrior>
Description:
Calculates the likelihood of some data under a Dirichlet distribution.
<dirichletProcessLikelihood>
Description:
Calculates the likelihood of some items distributed into a number of classes under a Dirichlet drocess.
<discreteAntigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space. This is a discrete classifier form of the modelwhich assigns viruses to discrete antigenic classes.
<discreteTraitRateModel>
Description:
This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and gives the rate for each branch of the tree based on the child trait of that branch. The rates for each trait value are specified in a multidimensional parameter.
<discretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<DiscretizedLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<distanceMatrix>
Description:
Constructs a distance matrix from a pattern list or alignment
<distributionLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<dummyLikelihood>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<dummyModel>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<exponentialStatistic>
Description:
This element returns a statistic that is the element-wise exponentiation of the child statistic.
<expansion>
Description:
A demographic model of constant population size followed by exponential growth.
<expConstExp>
Description:
A demographic model of exponential growth.
<exponentialLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<exponentialMarkovLikelihood>
Description:
A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.
<exponentialPrior>
Description:
Calculates the prior probability of some data under a given exponential distribution.
<exponentialSawtooth>
Description:
A demographic model of succesive exponential growth and periodic population crashes.
<expressionStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<externalLengthStatistic>
Description:
A statistic that has as its value(s) the length of the external branch length(s) of a set of one or more taxa in a given tree
<flatGeoSpatialPrior>
Description:
Calculates the likelihood of some data under a 2D geospatial distribution.
<gammaPrior>
Description:
Calculates the prior probability of some data under a given gamma distribution.
<gammaSiteBMA>
Description:
A SiteModel that does BMA for a gamma distributed rates across sites
<glmModel>
Description:
Calculates the generalized linear model likelihood of the dependent parameters given one or more blocks of independent parameters and their design matrix.
<glmSubstitutionModel>
Description:
A general model of sequence substitution for any data type where the rates come from the generalized linear model.
<gmrfDensityComponent>
Description:
This element represents a single component (coalescent or field) of the GMRF Skyride.
<gmrfHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<gmrfSkyrideLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gmrfTestLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gpSkytrackLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gtrCovarionModel>
Description:
A covarion substitution model of langauge evolution with binary data and a hidden rate state with two rates.
<gtrModel>
Description:
A general reversible model of nucleotide sequence substitution.
<HiddenLinkageModel>
Description:
A model to describe missing information about linkage among several reads from a metagenome
<HKYModel>
Description:
This element represents an instance of the HKY85 (Hasegawa, Kishino & Yano, 1985) model of nucleotide evolution.
<hypermutantAlignment>
Description:
Converts an alignment so that 'A's at specific APOBEC targeted contexts are set to an A/G ambiguity code.
<ibdReporter>
Description:
This element represents a reporter for expected number of tips ibd.
<individual>
Description:
Individual specimen from a species, possibly containing multiple genomes.
<inhibitionLikelihood>
Description:
Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.
<invgammaPrior>
Description:
Calculates the prior probability of some data under a given inverse gamma distribution.
<inverseGaussianDistributionModel>
Description:
Describes a inverse gaussian distribution with a given mean and shape (or standard deviation) that can be used in a distributionLikelihood element
<oneOnXPrior>
Description:
Calculates the (improper) prior proportional to Prod_i (1/x_i) for the given statistic x.
<laplacePrior>
Description:
Calculates the prior probability of some data under a given laplace distribution.
<lewisMk>
Description:
A parser for Lewis' Mk model
<LINEARBIASModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<LinkageConstraints>
Description:
Data representing metagenome reads that are linked by mate-pair, strobe, or other information
<LinkedGroup>
Description:
A group of metagenome reads linked with some probability
<localClockModel>
Description:
This element returns a branch rate model that adds a delta to each terminal branch length.
<location>
Description:
Specifies a location with an optional longitude and latitude
<logarithmStatistic>
Description:
This element returns a statistic that is the element-wise natural logarithm of the child statistic.
<logNormalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<logNormalPrior>
Description:
Calculates the prior probability of some data under a given lognormal distribution.
<matrixInverse>
Description:
This element returns a statistic that is the matrix inverse of the child statistic.
<matrixParameter>
Description:
A matrix parameter constructed from its component parameters.
<mcmc>
Description:
This element returns an MCMC chain and runs the chain as a side effect.
<meanStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<mergePatterns>
Description:
A weighted list of the unique site patterns (unique columns) in an alignment.
<microsatelliteSimulator>
Description:
This parser facilliates simulation of microsatellites given a tree and infinitesimal rate model
<mixtureModel>
Description:
This element represents a finite mixture of likelihood models.
<mixtureModelBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<mkSubstitutionModel>
Description:
An Mk model of substitution. This model can also accomodate arbitrary orderings of changes.
<monophylyStatistic>
Description:
A statistic that returns true if a given set of taxa are monophyletic for a given tree
<mrcaTraitStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<msatBMA>
Description:
This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.
<mulMSCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<mulSpecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<mulSpeciesTree>
Description:
Multiply-labelled species tree which includes demographic function per branch.
<multidimensionalScalingLikelihood>
Description:
Provides the likelihood of pairwise distance given vectors of coordinatesfor points according to the multidimensional scaling scheme of XXX & Rafferty (xxxx).
<multivariateGammaPrior>
Description:
Calculates the likelihood of some data under a given multivariate-gamma distribution.
<multivariateNormalPrior>
Description:
Calculates the likelihood of some data under a given multivariate-normal distribution.
<MutationDeathModel>
Description:
This element represents an instance of the MutationDeath model of CTMC evolution with deletions.
<negativeStatistic>
Description:
This element returns a statistic that is the element-wise negation of the child statistic.
<neighborJoiningTree>
Description:
This element returns a neighbour-joining tree generated from the given distances.
<newick>
Description:
Constructs a tree from a NEWICK format tree description
<nodeHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<nodePosteriorLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<normalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<normalPrior>
Description:
Calculates the prior probability of some data under a given normal distribution.
<notStatistic>
Description:
This element returns a statistic that is the element-wise inverse of the child statistic.
<ntdBMA>
Description:
A model that allows model averaging over nucleotide substitution models.
<optimizer>
Description:
This element returns a maximum likelihood heuristic optimizer and runs the optimization as a side effect.
<parameter>
Description:
A real-valued parameter of one or more dimensions.
<parsimonyStateStatistic>
Description:
A statistic that has as its value the parsimony state reconstruction of a binary state defined by a set of taxa at a given MRCA of a tree
<parsimonyStatistic>
Description:
A statistic that has as its value the parsimony tree length of a set of a binary state defined by a set of taxa for a given tree
<passageBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<pathLikelihood>
Description:
A likelihood function used for estimating marginal likelihoods and Bayes factors using path sampling.
<patterns>
Description:
A weighted list of the unique site patterns (unique columns) in an alignment.
<patternSubSet>
Description:
A weighted list of the unique site patterns (unique columns) in an alignment.
<pcaCodonModel>
Description:
This element represents the PCA model of codon evolution.
<poissonPrior>
Description:
Calculates the prior probability of some data under a given poisson distribution.
<popGraph>
Description:
This element returns a statistic that is the population size at evenly spaced intervals over tree.
<popTreeModel>
Description:
Creates a Population Tree Model with specified divergence cut-off for population nodes
<productStatistic>
Description:
This element returns a statistic that is the product of the child statistics.
<randomDiscretizedBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<randomLocalClockModel>
Description:
This element returns an random local clock (RLC) model.Each branch either has a new rate or inherits the rate of the branch above it depending on the indicator vector, which is itself sampled.
<randomLocalYuleModel>
Description:
A speciation model of a Yule process whose rate can change at random nodes in the tree.
<randomWalk>
Description:
Describes a first-order random walk. No prior is assumed on the first data element
<rateEpochBranchRates>
Description:
This element provides a multiple epoch molecular clock model. All branches (or portions of them) have the same rate of molecular evolution within a given epoch. If parameters are used to sample transition times, these must be kept in ascending order by judicious use of bounds or priors.
<rateStatistic>
Description:
A statistic that returns the average of the branch rates
<ratioStatistic>
Description:
This element returns a statistic that is the ratio of the 2 child statistics.
<reciprocalStatistic>
Description:
This element returns a statistic that is the element-wise reciprocal of the child statistic.
<recombinationSimulator>
Description:
A SequenceSimulator that generates random sequences for a given tree, sitemodel and branch rate model
<RPNcalculator>
Description:
This element returns a statistic evaluated from arbitrary expression.
<SampleQuantileLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<sampleStateAndCategoryModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of rate categories and internal states.
<sampleStateModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of internal states.
<scaledTreeLengthModel>
Description:
This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).
<sequenceErrorModel>
Description:
This element returns a model that allows for post-mortem DNA damage.
<sequenceSimulator>
Description:
A SequenceSimulator that generates random sequences for a given tree, sitemodel and branch rate model
<singleTipObservationProcess>
Description:
This element represents an instance of the SingleTipObservationProcess for ALSTreeLikelihood calculations
<sp>
Description:
Taxon in a species tree
<species>
Description:
Binds taxa in gene trees with species information.
<speciesCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<speciesTree>
Description:
Species tree which includes demographic function per branch.
<speciesTreeStatistic>
Description:
A statistic that returns true if the given population tree is compatible with the species tree. Compatibility is defined as the compatibility of the timings of the events, so that incompatibility arises if two individuals in the population tree coalescent before their species do in the species tree.
<starTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<statistic>
Description:
A statistic of a given name from the specified object.
<strictClockBranchRates>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<subStatistic>
Description:
Allows you to choose specific dimensions of a given statistic
<sumStatistic>
Description:
This element returns a statistic that is the element-wise sum of the child statistics.
<taxa>
Description:
Defines a set of taxon objects.
<test>
Description:
This element represents a boolean statistic that returns 1 if the conditions are met and 0 otherwise.
<tipBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<tipHeightLikelihood>
Description:
Calculates the likelihood of the tipHeights given some parametric or empirical distribution.
<tkf91Likelihood>
Description:
Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. In particular all possible ancestral histories of insertions and deletions leading to the alignment of sequences at the tips are taken into account.
<tkf91Model>
Description:
The TKF91 (Thorne, Kishino & Felsenstein 1991) model of insertion-deletion.
<tmrcaStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<TN93Model>
Description:
This element represents an instance of the TN93 (Tamura and Nei 1993) model of nucleotide evolution.
<transmissionHistory>
Description:
Defines a transmission history
<transmissionStatistic>
Description:
A statistic that returns true if the given parasite tree is compatible with the host tree.
<tree>
Description:
This element represents a rooted binary tree and associated attributes.
<treeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<treeMetricStatistic>
Description:
A statistic that returns the distance between two trees. with method="topology", return a 0 for identity and a 1 for difference. With other methods return the distance metric associated with that method.
<treeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<treeShapeStatistics>
Description:
A statistic that reports a handful of tree shape statistics on the given target tree.
<twoEpoch>
Description:
A demographic model of two epochs.
<twoPartDistribution>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<TWOPHASEModel>
Description:
This element represents an instance of the Two Phase Model of microsatellite evolution.
<UCLikelihood>
Description:
This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.
<upgmaTree>
Description:
This element returns a UPGMA tree generated from the given distances.
<variableDemographic>
Description:
This element represents the likelihood of the tree given the population size vector.
<varianceStatistic>
Description:
This element returns a statistic that is the variance of the child statistics.
<vectorSlice>
Description:
A vector parameter constructed from a slice of component parameters.
<yangCodonModel>
Description:
This element represents the Yang model of codon evolution.
<yuleModel>
Description:
A speciation model of a simple constant rate Birth-death process.
Likelihood
Elements of this type include:
<ACLikelihood>
Description:
This element returns an object that can calculate the likelihood of rate changes in a tree under the assumption of distributed rate changes among lineages. Specifically, each branch is assumed to draw a rate from a distribution with mean of the rate in the parent branch and the given standard deviation (the variance can be optionally proportional to branch length).
<advancedTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<alsTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ancestralTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<antigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space.
<apspCoalescent>
Description:
Likelihood of a set of gene trees embedded in a allopolyploid species network.
<arbitraryBranchRates>
Description:
This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.
<argDiscretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<argTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ASYMQUADModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<avgPosteriorIBDReporter>
Description:
This element represents a reporter for average expected number of tips ibd conditional on observed patterns.
<benchmarker>
Description:
This element runs a benchmark on a series of likelihood calculators.
<betaPrior>
Description:
Calculates the prior probability of some data under a given beta distribution.
<binomialLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<booleanLikelihood>
Description:
A function that log likelihood of a set of boolean statistics. If all the statistics are true then it returns 0.0 otherwise -infinity.
<branchingLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<cachedPrior>
Description:
Calculates a cached likelihood of some data given some parametric or empirical distribution.
<coalescentLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<compoundBranchRateModel>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<compoundLikelihood>
Description:
A likelihood function which is simply the product of its component likelihood functions.
<continuousTraitRateModel>
Description:
This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.
<coulombPrior>
Description:
Calculates a prior density based on the force due to electrostatic charge between particles the given distance x.
<ctmcScalePrior>
Description:
This element represents the prior for CTMC scale parameter.
<decayingRateModel>
Description:
This element provides a clock model in which the rate of molecular evolution decays to a substitution rate in the past.
<dirichletPrior>
Description:
Calculates the likelihood of some data under a Dirichlet distribution.
<dirichletProcessLikelihood>
Description:
Calculates the likelihood of some items distributed into a number of classes under a Dirichlet drocess.
<discreteAntigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space. This is a discrete classifier form of the modelwhich assigns viruses to discrete antigenic classes.
<discreteTraitRateModel>
Description:
This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and gives the rate for each branch of the tree based on the child trait of that branch. The rates for each trait value are specified in a multidimensional parameter.
<discretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<DiscretizedLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<distributionLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<dummyLikelihood>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<dummyModel>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<exponentialMarkovLikelihood>
Description:
A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.
<exponentialPrior>
Description:
Calculates the prior probability of some data under a given exponential distribution.
<flatGeoSpatialPrior>
Description:
Calculates the likelihood of some data under a 2D geospatial distribution.
<gammaPrior>
Description:
Calculates the prior probability of some data under a given gamma distribution.
<glmModel>
Description:
Calculates the generalized linear model likelihood of the dependent parameters given one or more blocks of independent parameters and their design matrix.
<gmrfDensityComponent>
Description:
This element represents a single component (coalescent or field) of the GMRF Skyride.
<gmrfSkyrideLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gmrfTestLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gpSkytrackLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<ibdReporter>
Description:
This element represents a reporter for expected number of tips ibd.
<inhibitionLikelihood>
Description:
Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.
<invgammaPrior>
Description:
Calculates the prior probability of some data under a given inverse gamma distribution.
<oneOnXPrior>
Description:
Calculates the (improper) prior proportional to Prod_i (1/x_i) for the given statistic x.
<laplacePrior>
Description:
Calculates the prior probability of some data under a given laplace distribution.
<LINEARBIASModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<localClockModel>
Description:
This element returns a branch rate model that adds a delta to each terminal branch length.
<logNormalPrior>
Description:
Calculates the prior probability of some data under a given lognormal distribution.
<mixtureModelBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<msatBMA>
Description:
This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.
<mulMSCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<multidimensionalScalingLikelihood>
Description:
Provides the likelihood of pairwise distance given vectors of coordinatesfor points according to the multidimensional scaling scheme of XXX & Rafferty (xxxx).
<multivariateGammaPrior>
Description:
Calculates the likelihood of some data under a given multivariate-gamma distribution.
<multivariateNormalPrior>
Description:
Calculates the likelihood of some data under a given multivariate-normal distribution.
<nodePosteriorLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<normalPrior>
Description:
Calculates the prior probability of some data under a given normal distribution.
<passageBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<pathLikelihood>
Description:
A likelihood function used for estimating marginal likelihoods and Bayes factors using path sampling.
<poissonPrior>
Description:
Calculates the prior probability of some data under a given poisson distribution.
<randomDiscretizedBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<randomLocalClockModel>
Description:
This element returns an random local clock (RLC) model.Each branch either has a new rate or inherits the rate of the branch above it depending on the indicator vector, which is itself sampled.
<randomWalk>
Description:
Describes a first-order random walk. No prior is assumed on the first data element
<rateEpochBranchRates>
Description:
This element provides a multiple epoch molecular clock model. All branches (or portions of them) have the same rate of molecular evolution within a given epoch. If parameters are used to sample transition times, these must be kept in ascending order by judicious use of bounds or priors.
<SampleQuantileLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<scaledTreeLengthModel>
Description:
This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).
<speciesCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<strictClockBranchRates>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<tipBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<tipHeightLikelihood>
Description:
Calculates the likelihood of the tipHeights given some parametric or empirical distribution.
<tkf91Likelihood>
Description:
Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. In particular all possible ancestral histories of insertions and deletions leading to the alignment of sequences at the tips are taken into account.
<treeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<twoPartDistribution>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<TWOPHASEModel>
Description:
This element represents an instance of the Two Phase Model of microsatellite evolution.
<UCLikelihood>
Description:
This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.
Loggable
Elements of this type include:
<ACLikelihood>
Description:
This element returns an object that can calculate the likelihood of rate changes in a tree under the assumption of distributed rate changes among lineages. Specifically, each branch is assumed to draw a rate from a distribution with mean of the rate in the parent branch and the given standard deviation (the variance can be optionally proportional to branch length).
<advancedTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<alloppspecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<alsTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ancestralTrait>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<ancestralTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<antigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space.
<apspCoalescent>
Description:
Likelihood of a set of gene trees embedded in a allopolyploid species network.
<arbitraryBranchRates>
Description:
This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.
<argDiscretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<argTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<argTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ASYMQUADModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<avgPosteriorIBDReporter>
Description:
This element represents a reporter for average expected number of tips ibd conditional on observed patterns.
<benchmarker>
Description:
This element runs a benchmark on a series of likelihood calculators.
<betaPrior>
Description:
Calculates the prior probability of some data under a given beta distribution.
<binomialLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<booleanLikelihood>
Description:
A function that log likelihood of a set of boolean statistics. If all the statistics are true then it returns 0.0 otherwise -infinity.
<branchingLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<cachedPrior>
Description:
Calculates a cached likelihood of some data given some parametric or empirical distribution.
<coalescentLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<compoundBranchRateModel>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<compoundLikelihood>
Description:
A likelihood function which is simply the product of its component likelihood functions.
<compoundParameter>
Description:
A multidimensional parameter constructed from its component parameters.
<continuousTraitRateModel>
Description:
This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.
<correlation>
Description:
This element returns a precision that is the element-wise reciprocal of the child precision.
<coulombPrior>
Description:
Calculates a prior density based on the force due to electrostatic charge between particles the given distance x.
<ctmcScalePrior>
Description:
This element represents the prior for CTMC scale parameter.
<decayingRateModel>
Description:
This element provides a clock model in which the rate of molecular evolution decays to a substitution rate in the past.
<designMatrix>
Description:
A matrix parameter constructed from its component parameters.
<diagonalMatrix>
Description:
A diagonal matrix parameter constructed from its diagonals.
<differenceStatistic>
Description:
This element returns a statistic that is the difference of the 2 child statistics.
<dirichletPrior>
Description:
Calculates the likelihood of some data under a Dirichlet distribution.
<dirichletProcessLikelihood>
Description:
Calculates the likelihood of some items distributed into a number of classes under a Dirichlet drocess.
<discreteAntigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space. This is a discrete classifier form of the modelwhich assigns viruses to discrete antigenic classes.
<discreteTraitRateModel>
Description:
This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and gives the rate for each branch of the tree based on the child trait of that branch. The rates for each trait value are specified in a multidimensional parameter.
<discretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<DiscretizedLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<distributionLikelihood>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<dummyLikelihood>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<dummyModel>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<exponentialStatistic>
Description:
This element returns a statistic that is the element-wise exponentiation of the child statistic.
<exponentialMarkovLikelihood>
Description:
A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.
<exponentialPrior>
Description:
Calculates the prior probability of some data under a given exponential distribution.
<expressionStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<externalLengthStatistic>
Description:
A statistic that has as its value(s) the length of the external branch length(s) of a set of one or more taxa in a given tree
<flatGeoSpatialPrior>
Description:
Calculates the likelihood of some data under a 2D geospatial distribution.
<gammaPrior>
Description:
Calculates the prior probability of some data under a given gamma distribution.
<glmModel>
Description:
Calculates the generalized linear model likelihood of the dependent parameters given one or more blocks of independent parameters and their design matrix.
<gmrfDensityComponent>
Description:
This element represents a single component (coalescent or field) of the GMRF Skyride.
<gmrfHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<gmrfSkyrideLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gmrfTestLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gpSkytrackLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<ibdReporter>
Description:
This element represents a reporter for expected number of tips ibd.
<inhibitionLikelihood>
Description:
Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.
<invgammaPrior>
Description:
Calculates the prior probability of some data under a given inverse gamma distribution.
<oneOnXPrior>
Description:
Calculates the (improper) prior proportional to Prod_i (1/x_i) for the given statistic x.
<laplacePrior>
Description:
Calculates the prior probability of some data under a given laplace distribution.
<LINEARBIASModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<localClockModel>
Description:
This element returns a branch rate model that adds a delta to each terminal branch length.
<logarithmStatistic>
Description:
This element returns a statistic that is the element-wise natural logarithm of the child statistic.
<logNormalPrior>
Description:
Calculates the prior probability of some data under a given lognormal distribution.
<matrixInverse>
Description:
This element returns a statistic that is the matrix inverse of the child statistic.
<matrixParameter>
Description:
A matrix parameter constructed from its component parameters.
<meanStatistic>
Description:
This element returns a statistic that is the mean of the child statistics.
<mixtureModelBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<monophylyStatistic>
Description:
A statistic that returns true if a given set of taxa are monophyletic for a given tree
<mrcaTraitStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<msatBMA>
Description:
This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.
<mulMSCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<mulSpecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<multidimensionalScalingLikelihood>
Description:
Provides the likelihood of pairwise distance given vectors of coordinatesfor points according to the multidimensional scaling scheme of XXX & Rafferty (xxxx).
<multivariateGammaPrior>
Description:
Calculates the likelihood of some data under a given multivariate-gamma distribution.
<multivariateNormalPrior>
Description:
Calculates the likelihood of some data under a given multivariate-normal distribution.
<negativeStatistic>
Description:
This element returns a statistic that is the element-wise negation of the child statistic.
<nodeHeightsStatistic>
Description:
A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)
<nodePosteriorLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<normalPrior>
Description:
Calculates the prior probability of some data under a given normal distribution.
<notStatistic>
Description:
This element returns a statistic that is the element-wise inverse of the child statistic.
<parameter>
Description:
A real-valued parameter of one or more dimensions.
<parsimonyStateStatistic>
Description:
A statistic that has as its value the parsimony state reconstruction of a binary state defined by a set of taxa at a given MRCA of a tree
<parsimonyStatistic>
Description:
A statistic that has as its value the parsimony tree length of a set of a binary state defined by a set of taxa for a given tree
<passageBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<pathLikelihood>
Description:
A likelihood function used for estimating marginal likelihoods and Bayes factors using path sampling.
<poissonPrior>
Description:
Calculates the prior probability of some data under a given poisson distribution.
<popGraph>
Description:
This element returns a statistic that is the population size at evenly spaced intervals over tree.
<productStatistic>
Description:
This element returns a statistic that is the product of the child statistics.
<randomDiscretizedBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<randomLocalClockModel>
Description:
This element returns an random local clock (RLC) model.Each branch either has a new rate or inherits the rate of the branch above it depending on the indicator vector, which is itself sampled.
<randomWalk>
Description:
Describes a first-order random walk. No prior is assumed on the first data element
<rateEpochBranchRates>
Description:
This element provides a multiple epoch molecular clock model. All branches (or portions of them) have the same rate of molecular evolution within a given epoch. If parameters are used to sample transition times, these must be kept in ascending order by judicious use of bounds or priors.
<rateStatistic>
Description:
A statistic that returns the average of the branch rates
<ratioStatistic>
Description:
This element returns a statistic that is the ratio of the 2 child statistics.
<reciprocalStatistic>
Description:
This element returns a statistic that is the element-wise reciprocal of the child statistic.
<RPNcalculator>
Description:
This element returns a statistic evaluated from arbitrary expression.
<SampleQuantileLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<scaledTreeLengthModel>
Description:
This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).
<speciesCoalescent>
Description:
Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.
<speciesTreeStatistic>
Description:
A statistic that returns true if the given population tree is compatible with the species tree. Compatibility is defined as the compatibility of the timings of the events, so that incompatibility arises if two individuals in the population tree coalescent before their species do in the species tree.
<statistic>
Description:
A statistic of a given name from the specified object.
<strictClockBranchRates>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<subStatistic>
Description:
Allows you to choose specific dimensions of a given statistic
<sumStatistic>
Description:
This element returns a statistic that is the element-wise sum of the child statistics.
<test>
Description:
This element represents a boolean statistic that returns 1 if the conditions are met and 0 otherwise.
<tipBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<tipHeightLikelihood>
Description:
Calculates the likelihood of the tipHeights given some parametric or empirical distribution.
<tkf91Likelihood>
Description:
Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. In particular all possible ancestral histories of insertions and deletions leading to the alignment of sequences at the tips are taken into account.
<tmrcaStatistic>
Description:
A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree
<transmissionStatistic>
Description:
A statistic that returns true if the given parasite tree is compatible with the host tree.
<treeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<treeMetricStatistic>
Description:
A statistic that returns the distance between two trees. with method="topology", return a 0 for identity and a 1 for difference. With other methods return the distance metric associated with that method.
<treeShapeStatistics>
Description:
A statistic that reports a handful of tree shape statistics on the given target tree.
<twoPartDistribution>
Description:
Calculates the likelihood of some data given some parametric or empirical distribution.
<TWOPHASEModel>
Description:
This element represents an instance of the Two Phase Model of microsatellite evolution.
<UCLikelihood>
Description:
This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.
<varianceStatistic>
Description:
This element returns a statistic that is the variance of the child statistics.
<vectorSlice>
Description:
A vector parameter constructed from a slice of component parameters.
MCMCOperator
Elements of this type include:
<argNarrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<argWideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<bitFlipOperator>
Description:
This element returns a bit-flip operator on a given parameter.
<bitMoveOperator>
Description:
This element returns a bit-move operator on a given parameter.
<bitSwapOperator>
Description:
This element returns a bit-swap operator on a given parameter and data.
<centeredScale>
Description:
A centered-scale operator. This operator scales the the values of a multi-dimensional parameter so as to perserve the mean. It does this by expanding or conrtacting the parameter values around the mean.
<colouredNarrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<colouredOperator>
Description:
This element represents an arbitrary operator immediately followed by a re-colouring of the tree
<colouredWideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<deltaExchange>
Description:
This element returns a delta exchange operator on a given parameter.
<deltaMixOperator>
Description:
This element returns a scale operator on a given parameter.
<dirichletProcessOperator>
Description:
An operator that picks a new allocation of an item to a cluster under the Dirichlet process.
<dirtyLikelihood>
Description:
This element returns a operator that forces the entire model likelihood recomputation
<fixedColouredOperator>
Description:
This element (or a ColouredOperator) must wrap any operator that changes a parameter upon which the colouring proposal distribution depends
<GibbsPruneAndRegraft>
Description:
This element represents a Gibbs sampler implemented through a prune and regraft operator. This operator prunes a random subtree and regrafts it below a node chosen by an importance distribution which is the proportion of the likelihoods of the proposals.
<GibbsSubtreeSwap>
Description:
This element represents a Gibbs wide exchange operator. This operator swaps two subtrees chosen to their posterior probaility.
<gmrfBlockUpdateOperator>
Description:
This element returns a GMRF block-update operator for the joint distribution of the population sizes and precision parameter.
<ImportanceNarrowExchange>
Description:
This element represents a swap operator. This operator swaps a random subtree with its uncle.
<ImportancePruneAndRegraft>
Description:
This element represents a importance guided prune and regraft operator. This operator prunes a random subtree and regrafts it below a node chosen by an importance distribution.
<ImportanceSubtreeSwap>
Description:
This element represents a importance guided subtree swap operator. This operator swaps a random subtree with a second subtree guided by an importance distribution.
<traitGibbsOperator>
Description:
This element returns a multivariate Gibbs operator on traits for possible all nodes.
<jointOperator>
Description:
This element represents an arbitrary list of operators; only the first is optimizable
<latentLiabilityGibbsOperator>
Description:
This element returns a multivariate Gibbs operator on traits for tip nodes under a latent liability model.
<linkageGroupSwap>
Description:
This element represents an operator that swaps taxa among two linkage groups.
<microsatUpDownOperator>
Description:
This element represents an operator that scales two parameters in different directions. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. The up parameter is multipled by this scale and the down parameter is divided by this scale.
<moveLegs>
Description:
Operator which changes the way a tetraploid subtree joins the diploid tree.
<moveLinkageGroup>
Description:
Operator to reassign metagenomic reads from one linkage group to another
<mulTreeNodeReHeight>
Description:
Specialized Species tree operator, transform tree without breaking embedding of gene trees.
<mvnOperator>
Description:
This element returns a multivariate normal random walk operator on a given parameter.
<narrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<networkNodeReHeight>
Description:
Operator for allopolyploid species network: transforms network without breaking embedding of gene trees.
<nodeReHeight>
Description:
Specialized Species tree operator, transform tree without breaking embedding of gene trees.
<precisionGibbsOperator>
Description:
This element returns a multivariate normal random walk operator on a given parameter.
<rateExchange>
Description:
An operator that exchanges rates and traits on a tree.
<rateScaleOperator>
Description:
This element returns a rateScale operator on a given parameter.
<scaleOperator>
Description:
This element returns a scale operator on a given parameter.
<setOperator>
Description:
This element represents an operator on a set.
<swapOperator>
Description:
This element represents an operator that swaps values in a multi-dimensional parameter.
<teamOperator>
Description:
An arbitrary list of operators; A random subset of size N is aggregated in one operation. Operators may have unequal weights - in that case a subset probability of selection is proportional to the sum of it's members weights.
<tipStateSwapOperator>
Description:
This element represents an operator to swap tip states between two random tips.
<tipTraitSwapOperator>
Description:
This element represents an operator to swap tip traits between two random tips.
<traitRateGibbsOperator>
Description:
This element returns a multivariate Gibbs operator on traits for possible all nodes.
<treeBitRandomWalk>
Description:
This element returns a bit-random walk operator on a random indicator/variable pair in the tree.
<upDownOperator>
Description:
This element represents an operator that scales two parameters in different directions. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. The up parameter is multipled by this scale and the down parameter is divided by this scale.
<wideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<wilsonBalding>
Description:
An operator which performs the Wilson-Balding move on a tree
Model
Elements of this type include:
<ACLikelihood>
Description:
This element returns an object that can calculate the likelihood of rate changes in a tree under the assumption of distributed rate changes among lineages. Specifically, each branch is assumed to draw a rate from a distribution with mean of the rate in the parent branch and the given standard deviation (the variance can be optionally proportional to branch length).
<alloppspecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<alsTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ancestralTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<antigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space.
<anyTipObservationProcess>
Description:
This element represents an instance of the AnyTipObservationProcess for ALSTreeLikelihood calculations
<arbitraryBranchRates>
Description:
This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.
<argDiscretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<argTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<ASYMQUADModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<siteModel>
Description:
A SiteModel that has a gamma distributed rates across sites
<betaSplittingModel>
Description:
The beta-splitting family of tree branching models (Aldous, 1996;2001).
<binaryCovarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<birthDeathModel>
Description:
Gernhard (2008) model of speciation (equation at bottom of page 19 of draft).
<branchingLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<cataclysm>
Description:
A demographic model of exponential growth.
<coalescentLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<compoundBranchRateModel>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<constantExponential>
Description:
A demographic model of constant population size followed by exponential growth.
<constantLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<constantSize>
Description:
A demographic model representing a constant population size through time.
<constExpConst>
Description:
A demographic model of constant population size followed by exponential growth.
<continuousTraitRateModel>
Description:
This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.
<covarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<ctmcScalePrior>
Description:
This element represents the prior for CTMC scale parameter.
<decayingRateModel>
Description:
This element provides a clock model in which the rate of molecular evolution decays to a substitution rate in the past.
<discreteAntigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space. This is a discrete classifier form of the modelwhich assigns viruses to discrete antigenic classes.
<discreteTraitRateModel>
Description:
This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and gives the rate for each branch of the tree based on the child trait of that branch. The rates for each trait value are specified in a multidimensional parameter.
<discretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<DiscretizedLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<dummyModel>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<expansion>
Description:
A demographic model of constant population size followed by exponential growth.
<expConstExp>
Description:
A demographic model of exponential growth.
<exponentialLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<exponentialMarkovLikelihood>
Description:
A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.
<exponentialSawtooth>
Description:
A demographic model of succesive exponential growth and periodic population crashes.
<gammaSiteBMA>
Description:
A SiteModel that does BMA for a gamma distributed rates across sites
<glmSubstitutionModel>
Description:
A general model of sequence substitution for any data type where the rates come from the generalized linear model.
<gmrfSkyrideLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gmrfTestLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gpSkytrackLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gtrCovarionModel>
Description:
A covarion substitution model of langauge evolution with binary data and a hidden rate state with two rates.
<gtrModel>
Description:
A general reversible model of nucleotide sequence substitution.
<HiddenLinkageModel>
Description:
A model to describe missing information about linkage among several reads from a metagenome
<HKYModel>
Description:
This element represents an instance of the HKY85 (Hasegawa, Kishino & Yano, 1985) model of nucleotide evolution.
<inhibitionLikelihood>
Description:
Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.
<inverseGaussianDistributionModel>
Description:
Describes a inverse gaussian distribution with a given mean and shape (or standard deviation) that can be used in a distributionLikelihood element
<lewisMk>
Description:
A parser for Lewis' Mk model
<LINEARBIASModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<localClockModel>
Description:
This element returns a branch rate model that adds a delta to each terminal branch length.
<logNormalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<mixtureModel>
Description:
This element represents a finite mixture of likelihood models.
<mixtureModelBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<mkSubstitutionModel>
Description:
An Mk model of substitution. This model can also accomodate arbitrary orderings of changes.
<msatBMA>
Description:
This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.
<mulSpecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<mulSpeciesTree>
Description:
Multiply-labelled species tree which includes demographic function per branch.
<multidimensionalScalingLikelihood>
Description:
Provides the likelihood of pairwise distance given vectors of coordinatesfor points according to the multidimensional scaling scheme of XXX & Rafferty (xxxx).
<MutationDeathModel>
Description:
This element represents an instance of the MutationDeath model of CTMC evolution with deletions.
<normalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<ntdBMA>
Description:
A model that allows model averaging over nucleotide substitution models.
<passageBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<pcaCodonModel>
Description:
This element represents the PCA model of codon evolution.
<randomDiscretizedBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<randomLocalClockModel>
Description:
This element returns an random local clock (RLC) model.Each branch either has a new rate or inherits the rate of the branch above it depending on the indicator vector, which is itself sampled.
<randomLocalYuleModel>
Description:
A speciation model of a Yule process whose rate can change at random nodes in the tree.
<randomWalk>
Description:
Describes a first-order random walk. No prior is assumed on the first data element
<rateEpochBranchRates>
Description:
This element provides a multiple epoch molecular clock model. All branches (or portions of them) have the same rate of molecular evolution within a given epoch. If parameters are used to sample transition times, these must be kept in ascending order by judicious use of bounds or priors.
<SampleQuantileLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<sampleStateAndCategoryModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of rate categories and internal states.
<sampleStateModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of internal states.
<scaledTreeLengthModel>
Description:
This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).
<sequenceErrorModel>
Description:
This element returns a model that allows for post-mortem DNA damage.
<singleTipObservationProcess>
Description:
This element represents an instance of the SingleTipObservationProcess for ALSTreeLikelihood calculations
<species>
Description:
Binds taxa in gene trees with species information.
<speciesTree>
Description:
Species tree which includes demographic function per branch.
<starTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<strictClockBranchRates>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<tipBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<tkf91Likelihood>
Description:
Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. In particular all possible ancestral histories of insertions and deletions leading to the alignment of sequences at the tips are taken into account.
<tkf91Model>
Description:
The TKF91 (Thorne, Kishino & Felsenstein 1991) model of insertion-deletion.
<TN93Model>
Description:
This element represents an instance of the TN93 (Tamura and Nei 1993) model of nucleotide evolution.
<transmissionHistory>
Description:
Defines a transmission history
<treeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<treeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<twoEpoch>
Description:
A demographic model of two epochs.
<TWOPHASEModel>
Description:
This element represents an instance of the Two Phase Model of microsatellite evolution.
<UCLikelihood>
Description:
This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.
<variableDemographic>
Description:
This element represents the likelihood of the tree given the population size vector.
<yangCodonModel>
Description:
This element represents the Yang model of codon evolution.
<yuleModel>
Description:
A speciation model of a simple constant rate Birth-death process.
SimpleMCMCOperator
Elements of this type include:
<argNarrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<argWideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<bitFlipOperator>
Description:
This element returns a bit-flip operator on a given parameter.
<bitMoveOperator>
Description:
This element returns a bit-move operator on a given parameter.
<bitSwapOperator>
Description:
This element returns a bit-swap operator on a given parameter and data.
<centeredScale>
Description:
A centered-scale operator. This operator scales the the values of a multi-dimensional parameter so as to perserve the mean. It does this by expanding or conrtacting the parameter values around the mean.
<colouredNarrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<colouredWideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<dirichletProcessOperator>
Description:
An operator that picks a new allocation of an item to a cluster under the Dirichlet process.
<dirtyLikelihood>
Description:
This element returns a operator that forces the entire model likelihood recomputation
<ImportanceNarrowExchange>
Description:
This element represents a swap operator. This operator swaps a random subtree with its uncle.
<ImportancePruneAndRegraft>
Description:
This element represents a importance guided prune and regraft operator. This operator prunes a random subtree and regrafts it below a node chosen by an importance distribution.
<ImportanceSubtreeSwap>
Description:
This element represents a importance guided subtree swap operator. This operator swaps a random subtree with a second subtree guided by an importance distribution.
<jointOperator>
Description:
This element represents an arbitrary list of operators; only the first is optimizable
<linkageGroupSwap>
Description:
This element represents an operator that swaps taxa among two linkage groups.
<microsatUpDownOperator>
Description:
This element represents an operator that scales two parameters in different directions. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. The up parameter is multipled by this scale and the down parameter is divided by this scale.
<moveLegs>
Description:
Operator which changes the way a tetraploid subtree joins the diploid tree.
<moveLinkageGroup>
Description:
Operator to reassign metagenomic reads from one linkage group to another
<mulTreeNodeReHeight>
Description:
Specialized Species tree operator, transform tree without breaking embedding of gene trees.
<narrowExchange>
Description:
This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.
<networkNodeReHeight>
Description:
Operator for allopolyploid species network: transforms network without breaking embedding of gene trees.
<nodeReHeight>
Description:
Specialized Species tree operator, transform tree without breaking embedding of gene trees.
<rateExchange>
Description:
An operator that exchanges rates and traits on a tree.
<rateScaleOperator>
Description:
This element returns a rateScale operator on a given parameter.
<scaleOperator>
Description:
This element returns a scale operator on a given parameter.
<setOperator>
Description:
This element represents an operator on a set.
<swapOperator>
Description:
This element represents an operator that swaps values in a multi-dimensional parameter.
<teamOperator>
Description:
An arbitrary list of operators; A random subset of size N is aggregated in one operation. Operators may have unequal weights - in that case a subset probability of selection is proportional to the sum of it's members weights.
<tipStateSwapOperator>
Description:
This element represents an operator to swap tip states between two random tips.
<tipTraitSwapOperator>
Description:
This element represents an operator to swap tip traits between two random tips.
<upDownOperator>
Description:
This element represents an operator that scales two parameters in different directions. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. The up parameter is multipled by this scale and the down parameter is divided by this scale.
<wideExchange>
Description:
This element represents a wide exchange operator. This operator swaps two random subtrees.
<wilsonBalding>
Description:
An operator which performs the Wilson-Balding move on a tree
StatisticList
Elements of this type include:
<ACLikelihood>
Description:
This element returns an object that can calculate the likelihood of rate changes in a tree under the assumption of distributed rate changes among lineages. Specifically, each branch is assumed to draw a rate from a distribution with mean of the rate in the parent branch and the given standard deviation (the variance can be optionally proportional to branch length).
<alloppspecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<alsTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<ancestralTreeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<antigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space.
<anyTipObservationProcess>
Description:
This element represents an instance of the AnyTipObservationProcess for ALSTreeLikelihood calculations
<arbitraryBranchRates>
Description:
This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.
<argDiscretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<argTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<ASYMQUADModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<siteModel>
Description:
A SiteModel that has a gamma distributed rates across sites
<betaSplittingModel>
Description:
The beta-splitting family of tree branching models (Aldous, 1996;2001).
<binaryCovarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<birthDeathModel>
Description:
Gernhard (2008) model of speciation (equation at bottom of page 19 of draft).
<branchingLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<cataclysm>
Description:
A demographic model of exponential growth.
<coalescentLikelihood>
Description:
This element represents the likelihood of the tree given the demographic function.
<compoundBranchRateModel>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<constantExponential>
Description:
A demographic model of constant population size followed by exponential growth.
<constantLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<constantSize>
Description:
A demographic model representing a constant population size through time.
<constExpConst>
Description:
A demographic model of constant population size followed by exponential growth.
<continuousTraitRateModel>
Description:
This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.
<covarionModel>
Description:
A covarion substitution model on binary data and a hidden rate state with two rates.
<ctmcScalePrior>
Description:
This element represents the prior for CTMC scale parameter.
<decayingRateModel>
Description:
This element provides a clock model in which the rate of molecular evolution decays to a substitution rate in the past.
<discreteAntigenicTraitLikelihood>
Description:
Provides the likelihood of immunological assay data such as Hemagglutinin inhibition (HI) given vectors of coordinatesfor viruses and sera/antisera in some multidimensional 'antigenic' space. This is a discrete classifier form of the modelwhich assigns viruses to discrete antigenic classes.
<discreteTraitRateModel>
Description:
This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and gives the rate for each branch of the tree based on the child trait of that branch. The rates for each trait value are specified in a multidimensional parameter.
<discretizedBranchRates>
Description:
This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.
<DiscretizedLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<dummyModel>
Description:
A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.
<expansion>
Description:
A demographic model of constant population size followed by exponential growth.
<expConstExp>
Description:
A demographic model of exponential growth.
<exponentialLogistic>
Description:
A demographic model of constant population size followed by logistic growth.
<exponentialMarkovLikelihood>
Description:
A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.
<exponentialSawtooth>
Description:
A demographic model of succesive exponential growth and periodic population crashes.
<gammaSiteBMA>
Description:
A SiteModel that does BMA for a gamma distributed rates across sites
<gmrfSkyrideLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gmrfTestLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gpSkytrackLikelihood>
Description:
This element represents the likelihood of the tree given the population size vector.
<gtrCovarionModel>
Description:
A covarion substitution model of langauge evolution with binary data and a hidden rate state with two rates.
<HiddenLinkageModel>
Description:
A model to describe missing information about linkage among several reads from a metagenome
<HKYModel>
Description:
This element represents an instance of the HKY85 (Hasegawa, Kishino & Yano, 1985) model of nucleotide evolution.
<inhibitionLikelihood>
Description:
Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.
<inverseGaussianDistributionModel>
Description:
Describes a inverse gaussian distribution with a given mean and shape (or standard deviation) that can be used in a distributionLikelihood element
<lewisMk>
Description:
A parser for Lewis' Mk model
<LINEARBIASModel>
Description:
This element represents an instance of the stepwise mutation model of microsatellite evolution.
<localClockModel>
Description:
This element returns a branch rate model that adds a delta to each terminal branch length.
<logNormalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<mixtureModelBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<mkSubstitutionModel>
Description:
An Mk model of substitution. This model can also accomodate arbitrary orderings of changes.
<msatBMA>
Description:
This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.
<mulSpecies>
Description:
Binds taxa to gene trees with information about possibly allopolyploid species.
<mulSpeciesTree>
Description:
Multiply-labelled species tree which includes demographic function per branch.
<multidimensionalScalingLikelihood>
Description:
Provides the likelihood of pairwise distance given vectors of coordinatesfor points according to the multidimensional scaling scheme of XXX & Rafferty (xxxx).
<MutationDeathModel>
Description:
This element represents an instance of the MutationDeath model of CTMC evolution with deletions.
<normalDistributionModel>
Description:
Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element
<ntdBMA>
Description:
A model that allows model averaging over nucleotide substitution models.
<passageBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<pcaCodonModel>
Description:
This element represents the PCA model of codon evolution.
<randomDiscretizedBranchRates>
Description:
This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.
<randomLocalClockModel>
Description:
This element returns an random local clock (RLC) model.Each branch either has a new rate or inherits the rate of the branch above it depending on the indicator vector, which is itself sampled.
<randomLocalYuleModel>
Description:
A speciation model of a Yule process whose rate can change at random nodes in the tree.
<randomWalk>
Description:
Describes a first-order random walk. No prior is assumed on the first data element
<rateEpochBranchRates>
Description:
This element provides a multiple epoch molecular clock model. All branches (or portions of them) have the same rate of molecular evolution within a given epoch. If parameters are used to sample transition times, these must be kept in ascending order by judicious use of bounds or priors.
<SampleQuantileLociRates>
Description:
This element returns an discretized loci rate model.The loci rates are drawn from a discretized parametric distribution.
<sampleStateAndCategoryModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of rate categories and internal states.
<sampleStateModel>
Description:
A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of internal states.
<scaledTreeLengthModel>
Description:
This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).
<sequenceErrorModel>
Description:
This element returns a model that allows for post-mortem DNA damage.
<singleTipObservationProcess>
Description:
This element represents an instance of the SingleTipObservationProcess for ALSTreeLikelihood calculations
<species>
Description:
Binds taxa in gene trees with species information.
<speciesTree>
Description:
Species tree which includes demographic function per branch.
<starTreeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<strictClockBranchRates>
Description:
This element provides a strict clock model. All branches have the same rate of molecular evolution.
<tipBranchRateModel>
Description:
This element returns a branch rate model that has a different rate for external branches than internal.
<tkf91Likelihood>
Description:
Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. In particular all possible ancestral histories of insertions and deletions leading to the alignment of sequences at the tips are taken into account.
<tkf91Model>
Description:
The TKF91 (Thorne, Kishino & Felsenstein 1991) model of insertion-deletion.
<TN93Model>
Description:
This element represents an instance of the TN93 (Tamura and Nei 1993) model of nucleotide evolution.
<transmissionHistory>
Description:
Defines a transmission history
<treeLikelihood>
Description:
This element represents the likelihood of a patternlist on a tree given the site model.
<treeModel>
Description:
This element represents a model of the tree. The tree model includes and attributes of the nodes including the age (or height) and the rate of evolution at each node in the tree.
<twoEpoch>
Description:
A demographic model of two epochs.
<TWOPHASEModel>
Description:
This element represents an instance of the Two Phase Model of microsatellite evolution.
<UCLikelihood>
Description:
This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.
<variableDemographic>
Description:
This element represents the likelihood of the tree given the population size vector.
<yangCodonModel>
Description:
This element represents the Yang model of codon evolution.
<yuleModel>
Description:
A speciation model of a simple constant rate Birth-death process.