BEAST v1.6.x XML Reference

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BEAST Documentation-> BEAST v1.6.x XML Reference

BEAST v1.6.0 Parser Library (2002-2010)

Release Version (updated on 17 September 2010 NZST)

The following is a list of valid elements in a beast file.

`<ACLikelihood>` element

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).

The element takes following attributes:

Attribute episodic is Boolean
true if model is branch length independent, false if length-dependent.
Attribute distribution is String
The distribution to use

The element has the following contents:

TreeModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
  
  The branch rates parameter
Element named <rootRate> containing:
- Parameter element (exactly one)
  
  The root rate parameter
Element named <variance> containing:
- Parameter element (exactly one)
  
  The standard deviation of the distribution

Example:

<ACLikelihood episodic="true" distribution="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel4"/>
 <rates>
   <matrixParameter idref="matrixParameter4"/>
 </rates>
 <rootRate>
   <maskedParameter idref="maskedParameter10"/>
 </rootRate>
 <variance>
   <matrixParameter idref="matrixParameter5"/>
 </variance>
</ACLikelihood>

`<addremoveARGEvent>` element

An operator that slides a subarg.

The element takes following attributes:

Attribute weight is Integer
Attribute size is Double
Attribute gaussian is Boolean
Attribute (optional) swapRates is Boolean
Attribute (optional) swapTraits is Boolean
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

ARGModel element (exactly one)

Example:

<addremoveARGEvent weight="1" size="1.0" gaussian="true" swapRates="true" swapTraits="true" autoOptimize="true">
  <argTreeModel idref="argTreeModel9"/>
</addremoveARGEvent>

`<alignment>` element

This element represents an alignment of molecular sequences.

The element has the following contents:

One of:
- Attribute dataType is String
  The data type
- DataType element (exactly one)

Sequence elements (one or more)

Example:

<!-- An alignment of three short DNA sequences -->
<alignment missing="-?" dataType="nucleotide">
  <sequence>
    <taxon idref="taxon1"/>
    ACGACTAGCATCGAGCTTCG--GATAGCAGGC
  </sequence>
  <sequence>
    <taxon idref="taxon2"/>
    ACGACTAGCATCGAGCTTCGG-GATAGCATGC
  </sequence>
  <sequence>
    <taxon idref="taxon3"/>
    ACG?CTAGAATCGAGCTTCGAGGATAGCATGC
  </sequence>
</alignment>

`<alignmentChunkOperator>` element

This element represents an operator that re-aligns a small chunk of an alignment.

The element takes following attributes:

Attribute weight is Double
Attribute iP is Double
tuning probability, values near zero resamples entire alignment and near 1.0 resamples single columns.
Attribute exponent is Double
tuning parameter, value of 1.0 samples random alignments, large values (e.g. 2.7) sample alignment peaked around 'best' alignment
Attribute gapPenalty is Double
tuning parameter, must be negative, large values penalize gaps more in the alignment proposal.

The element has the following contents:

TKF91Likelihood element (exactly one)

Example:

<alignmentChunkOperator weight="1.0" iP="1.0" exponent="1.0" gapPenalty="1.0">
  <tkf91Likelihood idref="tkf91Likelihood2"/>
</alignmentChunkOperator>

`<alsTreeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) storePartials is Boolean
Attribute integrateGainRate is Boolean

The element has the following contents:

Element named <immigrationRate> containing:
- Parameter element (exactly one)
PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
Element named <observationProcess> containing:
- Attribute type is String
- Attribute (optional) taxon is String

Example:

<alsTreeLikelihood useAmbiguities="true" storePartials="true" integrateGainRate="true">
  <convert idref="convert1"/>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel9"/>
  <categorySiteModel idref="categorySiteModel5"/>
 <observationProcess type="foo" taxon="foo"/>
</alsTreeLikelihood>

`<aminoAcidModel>` element

An empirical amino acid substitution model.

The element takes following attributes:

Attribute type is String
The type of empirical amino-acid rate matrix

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
  
  If the frequencies are omitted than the empirical frequencies associated with the selected model are used.

Example:

<aminoAcidModel type="WAG"/>

`<ancestralTrait>` element

A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging
Attribute (optional) traitName is String
The name of the trait to log

The element has the following contents:

TreeModel element (exactly one)
TreeTraitProvider element (exactly one)
Element named <mrca> containing:
- Taxa element (exactly one)

Example:

<ancestralTrait name="foo" traitName="foo">
  <treeModel idref="treeModel3"/>
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood1"/>
 <mrca>
   <taxa idref="taxa10"/>
 </mrca>
</ancestralTrait>

`<ancestralTrait>` element

A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging
Attribute (optional) traitName is String
The name of the trait to log

The element has the following contents:

TreeModel element (exactly one)
TreeTraitProvider element (exactly one)
Element named <mrca> containing:
- Taxa element (exactly one)

Example:

<ancestralTrait name="foo" traitName="foo">
  <treeModel idref="treeModel6"/>
  <ancestralTreeLikelihood idref="ancestralTreeLikelihood5"/>
 <mrca>
   <taxa idref="taxa1"/>
 </mrca>
</ancestralTrait>

`<ancestralTreeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) storePartials is Boolean
Attribute (optional) tagName is String
Attribute (optional) forceRescaling is Boolean
Attribute (optional) useMAP is Boolean
Attribute (optional) useMarginalLikelihood is Boolean

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
SubstitutionModel element (exactly one)

Example:

<ancestralTreeLikelihood useAmbiguities="true" storePartials="true" tagName="foo" forceRescaling="true" useMAP="true" useMarginalLikelihood="true">
  <convert idref="convert5"/>
  <treeModel idref="treeModel10"/>
  <sampleStateAndCategoryModel idref="sampleStateAndCategoryModel6"/>
  <TWOPHASEModel idref="TWOPHASEModel2"/>
</ancestralTreeLikelihood>

`<anyTipObservationProcess>` element

This element represents an instance of the AnyTipObservationProcess for ALSTreeLikelihood calculations

The element has the following contents:

TreeModel element (exactly one)
PatternList element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (exactly one)
Element named <deathRate> containing:
- Parameter element (exactly one)
Element named <immigrationRate> containing:
- Parameter element (exactly one)

Example:

<anyTipObservationProcess>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel3"/>
  <patterns idref="patterns1"/>
  <sampleStateAndCategoryModel idref="sampleStateAndCategoryModel3"/>
  <scaledTreeLengthModel idref="scaledTreeLengthModel1"/>
 <deathRate>
   <duplicatedParameter idref="duplicatedParameter6"/>
 </deathRate>
 <immigrationRate>
   <matrixParameter idref="matrixParameter3"/>
 </immigrationRate>
</anyTipObservationProcess>

`<arbitraryBranchRates>` element

This element returns an arbitrary rate model.The branch rates are drawn from an arbitrary distribution determine by the prior.

The element takes following attributes:

Attribute (optional) reciprocal is Boolean

The element has the following contents:

TreeModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
  
  The rate parameter

Example:

<arbitraryBranchRates reciprocal="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel2"/>
 <rates>
   <designMatrix idref="designMatrix1"/>
 </rates>
</arbitraryBranchRates>

`<argCoalescentLikelihood>` element

A coalescent likelihood for an ARG model

The element takes following attributes:

Attribute (optional) ancestralRestriction is Boolean

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <recombinationRate> containing:
- Parameter element (exactly one)
Element named <argModel> containing:
- ARGModel element (exactly one)

Example:

<argCoalescentLikelihood ancestralRestriction="true">
 <populationSize>
   <diagonalMatrix idref="diagonalMatrix9"/>
 </populationSize>
 <recombinationRate>
   <compoundParameter idref="compoundParameter7"/>
 </recombinationRate>
 <argModel>
   <argTreeModel idref="argTreeModel3"/>
 </argModel>
</argCoalescentLikelihood>

`<argDiscretizedBranchRates>` element

This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.

The element takes following attributes:

Attribute numRateCategories is Integer

The element has the following contents:

ARGModel element (exactly one)
Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
  
  The distribution model for rates among branches

Example:

<argDiscretizedBranchRates numRateCategories="1">
  <argTreeModel idref="argTreeModel6"/>
 <distribution>
   <onePGammaDistributionModel idref="onePGammaDistributionModel3"/>
 </distribution>
</argDiscretizedBranchRates>

`<ARGEventOperator>` element

An operator that slides a subarg.

The element takes following attributes:

Attribute addProbability is Double
The probability that the operator adds a new reassortment event
Attribute (optional) jointPartitioning is Boolean
Attribute (optional) tossSize is Integer
Attribute (optional) addProbability is Double
Attribute (optional) autoOptimize is Boolean
Attribute weight is Integer

The element has the following contents:

ARGModel element (exactly one)
ARGPartitionLikelihood element (exactly one)
ARGRatePrior element (zero or one)
Element named <internalNodes> containing:
- CompoundParameter element (exactly one)
Element named <internalNodesPlusRoot> containing:
- CompoundParameter element (exactly one)
Element named <nodeRates> containing:
- CompoundParameter element (exactly one)

Example:

<ARGEventOperator addProbability="1.0" jointPartitioning="true" tossSize="1" addProbability="1.0" autoOptimize="true" weight="1">
  <argTreeModel idref="argTreeModel1"/>
  <poissonPartitionLikelihood idref="poissonPartitionLikelihood6"/>
 <internalNodes>
   <matrixParameter idref="matrixParameter7"/>
 </internalNodes>
 <internalNodesPlusRoot>
   <matrixParameter idref="matrixParameter9"/>
 </internalNodesPlusRoot>
 <nodeRates>
   <diagonalMatrix idref="diagonalMatrix10"/>
 </nodeRates>
</ARGEventOperator>

`<argLocalClock>` element

null

Example:

<argLocalClock/>

`<argTreeModel>` element

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.

The element takes following attributes:

Attribute (optional) partitionType is String
Describes the partition structure of the model

The element has the following contents:

Tree element (exactly one)
Element named <rootHeight> containing:
- Parameter element (exactly one)
  
  A parameter definition with id only (cannot be a reference!)
Element named <nodeHeights> containing:
- Attribute (optional) rootNode is Boolean
  If true the root height is included in the parameter
- Attribute (optional) internalNodes is Boolean
  If true the internal node heights (minus the root) are included in the parameter
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)

Example:

<!-- the tree model as special sockets for attaching parameters to various aspects of the tree     -->
<!-- The treeModel below shows the standard setup with a parameter associated with the root height -->
<!-- a parameter associated with the internal node heights (minus the root height) and             -->
<!-- a parameter associates with all the internal node heights                                     -->
<!-- Notice that these parameters are overlapping                                                  -->
<!-- The parameters are subsequently used in operators to propose changes to the tree node heights -->
<treeModel id="treeModel1">
	<tree idref="startingTree"/>
	<rootHeight>
		<parameter id="treeModel1.rootHeight"/>
	</rootHeight>
	<nodeHeights internalNodes="true" rootNode="false">
		<parameter id="treeModel1.internalNodeHeights"/>
	</nodeHeights>
	<nodeHeights internalNodes="true" rootNode="true">
		<parameter id="treeModel1.allInternalNodeHeights"/>
	</nodeHeights>
</treeModel>

`<argNarrowExchange>` element

This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.

The element takes following attributes:

Attribute weight is Integer

The element has the following contents:

ARGModel element (exactly one)

Example:

<argNarrowExchange weight="1">
  <argTreeModel idref="argTreeModel3"/>
</argNarrowExchange>

`<argPartitionOperator>` element

An operator that picks a new partitioning uniformly at random.

The element takes following attributes:

Attribute weight is Integer
Attribute (optional) tossSize is Integer
Attribute (optional) tossAll is Boolean

The element has the following contents:

ARGModel element (exactly one)

Example:

<argPartitionOperator weight="1" tossSize="1" tossAll="true">
  <argTreeModel idref="argTreeModel8"/>
</argPartitionOperator>

`<argRatePrior>` element

null

Example:

<argRatePrior/>

`<argReassortmentNodeCount>` element

A statistic that returns the number of reassortment nodes in an ARG

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic for the purpose of logging

The element has the following contents:

ARGModel element (exactly one)

Example:

<argReassortmentNodeCount name="foo">
  <argTreeModel idref="argTreeModel8"/>
</argReassortmentNodeCount>

`<argSubtreeSlide>` element

An operator that slides a subtree.

The element takes following attributes:

Attribute weight is Integer
Attribute size is Double
Attribute gaussian is Boolean
Attribute (optional) swapRates is Boolean
Attribute (optional) swapTraits is Boolean
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

ARGModel element (exactly one)

Example:

<argSubtreeSlide weight="1" size="1.0" gaussian="true" swapRates="true" swapTraits="true" autoOptimize="true">
  <argTreeModel idref="argTreeModel9"/>
</argSubtreeSlide>

`<argSwapOperator>` element

Swaps nodes on a tree

The element takes following attributes:

Attribute weight is Integer
Attribute type is String
The mode of the operator

The element has the following contents:

ARGModel element (exactly one)

Example:

<argSwapOperator weight="1" type="bifurcationSwap">
  <argTreeModel idref="argTreeModel1"/>
</argSwapOperator>

`<argTimingStatistic>` element

The element takes following attributes:

Attribute (optional) name is String

The element has the following contents:

ARGModel element (exactly one)

Example:

<argTimingStatistic name="foo">
  <argTreeModel idref="argTreeModel9"/>
</argTimingStatistic>

`<argTotalLengthStatistic>` element

null

Example:

<argTotalLengthStatistic/>

`<argTraceAnalysis>` element

Analyses and reports on a trace consisting of trees.

The element takes following attributes:

Attribute fileName is String
name of a tree log file
Attribute (optional) burnIn is Integer

Example:

<argTraceAnalysis fileName="trees.log" burnIn="1"/>

`<argTreeCount>` element

Provides number of distinct loci trees

The element has the following contents:

ARGModel element (exactly one)

Example:

<argTreeCount>
  <argTreeModel idref="argTreeModel9"/>
</argTreeCount>

`<argTreeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) storePartials is Boolean
Attribute (optional) useScaling is Boolean

The element has the following contents:

PatternList element (exactly one)
ARGModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)

Example:

<argTreeLikelihood useAmbiguities="true" storePartials="true" useScaling="true">
  <convert idref="convert3"/>
  <argTreeModel idref="argTreeModel2"/>
  <categorySiteModel idref="categorySiteModel7"/>
</argTreeLikelihood>

`<argTreeModel>` element

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.

The element takes following attributes:

Attribute (optional) partitionType is String
Describes the partition structure of the model

The element has the following contents:

Tree element (exactly one)
Element named <rootHeight> containing:
- Parameter element (exactly one)
  
  A parameter definition with id only (cannot be a reference!)
Element named <nodeHeights> containing:
- Attribute (optional) rootNode is Boolean
  If true the root height is included in the parameter
- Attribute (optional) internalNodes is Boolean
  If true the internal node heights (minus the root) are included in the parameter
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)

Example:

<!-- the tree model as special sockets for attaching parameters to various aspects of the tree     -->
<!-- The treeModel below shows the standard setup with a parameter associated with the root height -->
<!-- a parameter associated with the internal node heights (minus the root height) and             -->
<!-- a parameter associates with all the internal node heights                                     -->
<!-- Notice that these parameters are overlapping                                                  -->
<!-- The parameters are subsequently used in operators to propose changes to the tree node heights -->
<treeModel id="treeModel1">
	<tree idref="startingTree"/>
	<rootHeight>
		<parameter id="treeModel1.rootHeight"/>
	</rootHeight>
	<nodeHeights internalNodes="true" rootNode="false">
		<parameter id="treeModel1.internalNodeHeights"/>
	</nodeHeights>
	<nodeHeights internalNodes="true" rootNode="true">
		<parameter id="treeModel1.allInternalNodeHeights"/>
	</nodeHeights>
</treeModel>

`<argUniformPrior>` element

A uniform prior for an ARG model

The element has the following contents:

ARGModel element (exactly one)

Example:

<argUniformPrior>
  <argTreeModel idref="argTreeModel5"/>
</argUniformPrior>

`<argWideExchange>` element

This element represents a wide exchange operator. This operator swaps two random subtrees.

The element takes following attributes:

Attribute weight is Integer

The element has the following contents:

ARGModel element (exactly one)

Example:

<argWideExchange weight="1">
  <argTreeModel idref="argTreeModel1"/>
</argWideExchange>

`<array>` element

This element returns an array of the objects it contains.

The element has the following contents:

Object elements (one or more)
Objects to be put in an array

Example:

<array>
  <treeTraceAnalysis idref="treeTraceAnalysis8"/>
  <normalDistributionModel idref="normalDistributionModel6"/>
  <operators idref="operators4"/>
</array>

`<ascertainedPatterns>` element

A weighted list of the unique site patterns (unique columns) in an alignment.

The element takes following attributes:

Attribute (optional) from is Integer
The site position to start at, default is 1 (the first position)
Attribute (optional) to is Integer
The site position to finish at, must be greater than from, default is length of given alignment
Attribute (optional) every is Integer
Determines how many sites are selected. A value of 3 will select every third site starting from from, default is 1 (every site)

The element has the following contents:

Element named <taxonList> containing:
- TaxonList element (exactly one)
Alignment element (exactly one)

<includePatterns from="Z" to="X"/>*:<excludePatterns from="Z" to="X"/>

Example:

<ascertainedPatterns from="1" to="1" every="1">
  <hypermutantAlignment idref="hypermutantAlignment8"/>
</ascertainedPatterns>

`<ASYMQUADModel>` element

This element represents an instance of the stepwise mutation model of microsatellite evolution.

The element takes following attributes:

Attribute (optional) isSubmodel is Boolean

The element has the following contents:

Microsatellite element (exactly one)
FrequencyModel element (zero or one)
Element named <ExpansionConstant> containing:
- Parameter element (exactly one)
Element named <ContractionConstant> containing:
- Parameter element (exactly one)
Element named <ExpansionLinear> containing:
- Parameter element (exactly one)
Element named <ContractionLinear> containing:
- Parameter element (exactly one)
Element named <ExpansionQuad> containing:
- Parameter element (exactly one)
Element named <ContractionQuad> containing:
- Parameter element (exactly one)

Example:

<ASYMQUADModel isSubmodel="true">
  <microsatellite idref="microsatellite3"/>
</ASYMQUADModel>

`<attr>` element

This element represents a name/value pair.

The element takes following attributes:

Attribute name is String
The name to give to this attribute

The element has the following contents:

Object element (exactly one)

Example:

<attr name="foo">
  <hypermutantErrorModel idref="hypermutantErrorModel6"/>
</attr>

`<attributePatterns>` element

A site pattern defined by an attribute in a set of taxa.

The element takes following attributes:

Attribute attribute is String

The element has the following contents:

One of:
- Attribute dataType is String
  The data type
- DataType element (exactly one)

TaxonList element (exactly one)
The taxon set

Example:

<attributePatterns attribute="foo">
  <extendedDataType idref="extendedDataType10"/>
  <attributePatterns idref="attributePatterns1"/>
</attributePatterns>

`<attributes>` element

This element represents an array of name/value pairs.

The element takes following attributes:

Attribute names is String;
Attribute values is String;

Example:

<attributes names="foo bar" values="foo bar"/>

`<avgPosteriorIBDReporter>` element

This element represents a reporter for average expected number of tips ibd conditional on observed patterns.

The element has the following contents:

TreeModel element (exactly one)
BranchRateModel element (zero or one)
AbstractSubstitutionModel element (exactly one)
Parameter element (exactly one)
NodePosteriorTreeLikelihood element (exactly one)

Example:

<avgPosteriorIBDReporter>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel5"/>
  <LINEARBIASModel idref="LINEARBIASModel8"/>
  <maskedParameter idref="maskedParameter6"/>
  ERROR!
</avgPosteriorIBDReporter>

`<ancestralTreeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) storePartials is Boolean
Attribute (optional) tagName is String
Attribute (optional) forceRescaling is Boolean
Attribute (optional) useMAP is Boolean
Attribute (optional) useMarginalLikelihood is Boolean

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
SubstitutionModel element (exactly one)

Example:

<ancestralTreeLikelihood useAmbiguities="true" storePartials="true" tagName="foo" forceRescaling="true" useMAP="true" useMarginalLikelihood="true">
  <ascertainedPatterns idref="ascertainedPatterns8"/>
  <treeModel idref="treeModel6"/>
  <siteModel idref="siteModel7"/>
  <MutationDeathModel idref="MutationDeathModel8"/>
</ancestralTreeLikelihood>

`<complexSubstitutionModel>` element

A general reversible model of sequence substitution for any data type with stochastic variable selection.

The element takes following attributes:

Attribute (optional) randomizeIndicator is Boolean
Attribute (optional) normalize is Boolean
Attribute (optional) maxConditionNumber is Double
Attribute (optional) mustBeConnected is Boolean
Attribute (optional) maxIterations is Integer
Attribute (optional) checkConditioning is Boolean

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <rootFrequencies> containing:
- FrequencyModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)

Example:

<complexSubstitutionModel dataType="amino acid" randomizeIndicator="true" normalize="true" maxConditionNumber="1.0" mustBeConnected="true" maxIterations="1" checkConditioning="true">
 <rootFrequencies>
   <frequencyModel idref="frequencyModel1"/>
 </rootFrequencies>
 <rates>
   <matrixParameter idref="matrixParameter9"/>
 </rates>
</complexSubstitutionModel>

`<DirichletSiteModel>` element

A SiteModel that has Dirichlet distributed rates across sites

The element has the following contents:

Element named <substitutionModel> containing:
- SubstitutionModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)

Example:

<DirichletSiteModel>
 <substitutionModel>
   <mkSubstitutionModel idref="mkSubstitutionModel10"/>
 </substitutionModel>
 <rates>
   <duplicatedParameter idref="duplicatedParameter7"/>
 </rates>
</DirichletSiteModel>

`<frequencyModel>` element

A model of equilibrium base frequencies.

The element takes following attributes:

Attribute (optional) normalize is Boolean

The element has the following contents:

PatternList element (zero or one)
Initial value
One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <frequencies> containing:
- Parameter element (exactly one)

Example:

<frequencyModel normalize="true" dataType="codon-yeast">
 <frequencies>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix7"/>
 </frequencies>
</frequencyModel>

`<siteModel>` element

A SiteModel that has a gamma distributed rates across sites

The element has the following contents:

Element named <substitutionModel> containing:
- SubstitutionModel element (exactly one)
One of:
- Element named <mutationRate> containing:
  - Parameter element (exactly one)
- Element named <relativeRate> containing:
  - Parameter element (exactly one)

Element named <gammaShape> containing:
- Attribute (optional) gammaCategories is Integer
- Parameter element (exactly one)
Element named <proportionInvariant> containing:
- Parameter element (exactly one)

Example:

<siteModel>
 <substitutionModel>
   <LINEARBIASModel idref="LINEARBIASModel6"/>
 </substitutionModel>
 <mutationRate>
   <parameter idref="parameter4"/>
 </mutationRate>
</siteModel>

`<benchmarker>` element

This element runs a benchmark on a series of likelihood calculators.

The element takes following attributes:

Attribute iterationCount is Integer

The element has the following contents:

Likelihood elements (one or more)

Example:

<benchmarker iterationCount="1">
  <discretizedBranchRates idref="discretizedBranchRates9"/>
</benchmarker>

`<betaSplittingModel>` element

The beta-splitting family of tree branching models (Aldous, 1996;2001).

The element has the following contents:

Element named <phi> containing:
- Parameter element (exactly one)
  
  A parameter that ranges from -infinity (comb-tree) to +infinity (balanced tree)
Element named <branchingTree> containing:
- Tree element (exactly one)

Example:

<betaSplittingModel>
 <phi>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix4"/>
 </phi>
 <branchingTree>
   <speciesTree idref="speciesTree9"/>
 </branchingTree>
</betaSplittingModel>

`<binaryCovarionModel>` element

A covarion substitution model on binary data and a hidden rate state with two rates.

The element has the following contents:

Element named <frequencies> containing:
- Parameter element (exactly one)
Element named <hiddenFrequencies> containing:
- Parameter element (exactly one)
Element named <alpha> containing:
- Parameter element (zero or one)
Element named <switchingRate> containing:
- Parameter element (zero or one)

Example:

<binaryCovarionModel>
 <frequencies>
   <maskedParameter idref="maskedParameter3"/>
 </frequencies>
 <hiddenFrequencies>
   <duplicatedParameter idref="duplicatedParameter5"/>
 </hiddenFrequencies>
 <alpha/>
 <switchingRate/>
</binaryCovarionModel>

`<binarySubstitutionModel>` element

A general reversible model of sequence substitution for binary data type.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)

Example:

<binarySubstitutionModel>
 <frequencies>
   <frequencyModel idref="frequencyModel9"/>
 </frequencies>
</binarySubstitutionModel>

`<binomialLikelihood>` element

Calculates the likelihood of some data given some parametric or empirical distribution.

The element has the following contents:

Element named <trials> containing:
- Parameter element (exactly one)
Element named <proportion> containing:
- Parameter element (exactly one)
Element named <counts> containing:
- Attribute values is Integer;

Example:

<binomialLikelihood>
 <trials>
   <parameter idref="parameter3"/>
 </trials>
 <proportion>
   <maskedParameter idref="maskedParameter2"/>
 </proportion>
 <counts values="1 2 4 8"/>
</binomialLikelihood>

`<birthDeathModel>` element

Gernhard (2008) model of speciation (equation at bottom of page 19 of draft).

The element takes following attributes:

Attribute (optional) type is String
Attribute (optional) conditionalOnRoot is Boolean
Attribute units is String
the units

The element has the following contents:

Element named <birthMinusDeathRate> containing:
- Parameter element (exactly one)
Element named <relativeDeathRate> containing:
- Parameter element (exactly one)
Element named <sampleRate> containing:
- Parameter element (exactly one)

Example:

<birthDeathModel type="foo" conditionalOnRoot="true" units="years">
 <birthMinusDeathRate>
   <diagonalMatrix idref="diagonalMatrix5"/>
 </birthMinusDeathRate>
 <relativeDeathRate>
   <maskedParameter idref="maskedParameter4"/>
 </relativeDeathRate>
</birthDeathModel>

`<bitFlipInSubstitutionModelOperator>` element

This element returns a bit-flip operator on a given indicatorParameter.

The element takes following attributes:

Attribute weight is Double
Attribute scaleFactor is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

Parameter element (zero or one)
BayesianStochasticSearchVariableSelection element (exactly one)

Example:

<bitFlipInSubstitutionModelOperator weight="1.0" scaleFactor="1.0" autoOptimize="true">
  ERROR!
</bitFlipInSubstitutionModelOperator>

`<bitFlipOperator>` element

This element returns a bit-flip operator on a given parameter.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) usesPriorOnSum is Boolean

The element has the following contents:

Parameter element (exactly one)

Example:

<bitFlipOperator weight="1.0" usesPriorOnSum="true">
  <diagonalMatrix idref="diagonalMatrix4"/>
</bitFlipOperator>

`<bitMoveOperator>` element

This element returns a bit-move operator on a given parameter.

The element takes following attributes:

Attribute weight is Double
Attribute numBitsToMove is Integer

The element has the following contents:

Element named <bits> containing:
- Parameter element (exactly one)
Element named <values> containing:
- Parameter element (exactly one)
  
  values parameter

Example:

<bitMoveOperator weight="1.0" numBitsToMove="1">
 <bits>
   <parameter idref="parameter1"/>
 </bits>
</bitMoveOperator>

`<bitSwapOperator>` element

This element returns a bit-swap operator on a given parameter and data.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) radius is Double

The element has the following contents:

Element named <data> containing:
- Statistic element (exactly one)
Element named <indicators> containing:
- Statistic element (exactly one)

Example:

<bitSwapOperator weight="1.0" radius="1.0">
 <data>
   <partitionStatistic idref="partitionStatistic9"/>
 </data>
 <indicators>
   <treeLengthStatistic idref="treeLengthStatistic5"/>
 </indicators>
</bitSwapOperator>

`<booleanLikelihood>` element

A function that log likelihood of a set of boolean statistics. If all the statistics are true then it returns 0.0 otherwise -infinity.

The element has the following contents:

BooleanStatistic elements (one or more)

Example:

<booleanLikelihood>
  <compatibilityStatistic idref="compatibilityStatistic5"/>
  <compatibilityStatistic idref="compatibilityStatistic2"/>
  <monotonicStatistic idref="monotonicStatistic3"/>
  <compatibilityStatistic idref="compatibilityStatistic5"/>
</booleanLikelihood>

`<branchDirections>` element

null

The element has the following contents:

SampledMultivariateTraitLikelihood element (exactly one)

Example:

<branchDirections>
  ERROR!
</branchDirections>

`<branchingLikelihood>` element

This element represents the likelihood of the tree given the demographic function.

The element has the following contents:

Element named <model> containing:
- BranchingModel element (exactly one)
Element named <branchingTree> containing:
- TreeModel element (exactly one)

Example:

<branchingLikelihood>
 <model>
   <betaSplittingModel idref="betaSplittingModel3"/>
 </model>
 <branchingTree>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel5"/>
 </branchingTree>
</branchingLikelihood>

`<branchMagnitudes>` element

null

The element takes following attributes:

Attribute (optional) scaleByLength is Boolean

The element has the following contents:

AbstractMultivariateTraitLikelihood element (exactly one)

Example:

<branchMagnitudes scaleByLength="true">
  <inhibitionLikelihood idref="inhibitionLikelihood3"/>
</branchMagnitudes>

`<BrownianMotion>` element

The element takes following attributes:

Attribute (optional) logUnits is Boolean

The element has the following contents:

One of:
- Element named <sigma> containing:
  - Double element (exactly one)
- Element named <sigma> containing:
  - Parameter element (exactly one)

VariableDemographicModel element (exactly one)

Example:

<BrownianMotion logUnits="true">
 <sigma>
   1.0
 </sigma>
  <variableDemographic idref="variableDemographic7"/>
</BrownianMotion>

`<cachedPrior>` element

Calculates a cached likelihood of some data given some parametric or empirical distribution.

The element has the following contents:

AbstractDistributionLikelihood element (exactly one)
Variable element (exactly one)

Example:

<cachedPrior>
  <cachedPrior idref="cachedPrior6"/>
  <diagonalMatrix idref="diagonalMatrix1"/>
</cachedPrior>

`<cartogramDiffusionModel>` element

Describes a bivariate diffusion process using cartogram distances.

The element takes following attributes:

Attribute (optional) cartogramFileName is String
Attribute xGridSize is Integer
Attribute yGridSize is Integer

The element has the following contents:

Parameter element (exactly one)
Element named <boundingBox> containing:
- Attribute minX is Double
- Attribute maxX is Double
- Attribute minY is Double
- Attribute maxY is Double

Example:

<cartogramDiffusionModel cartogramFileName="foo" xGridSize="1" yGridSize="1">
  <designMatrix idref="designMatrix10"/>
 <boundingBox minX="1.0" maxX="1.0" minY="1.0" maxY="1.0"/>
</cartogramDiffusionModel>

`<cataclysm>` element

A demographic model of exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <growthRate> containing:
- Parameter element (exactly one)
  
  The rate of exponential growth before the cataclysmic event.
Element named <spikeFactor> containing:
- Parameter element (exactly one)
  
  The factor larger the population size was at its height.
Element named <timeOfCataclysm> containing:
- Parameter element (exactly one)
  
  The time of the cataclysmic event that lead to exponential decline.

Example:

<cataclysm units="years">
 <populationSize>
   <maskedParameter idref="maskedParameter2"/>
 </populationSize>
 <growthRate>
   <compoundParameter idref="compoundParameter6"/>
 </growthRate>
 <spikeFactor>
   <diagonalMatrix idref="diagonalMatrix2"/>
 </spikeFactor>
 <timeOfCataclysm>
   <duplicatedParameter idref="duplicatedParameter4"/>
 </timeOfCataclysm>
</cataclysm>

`<categorySiteModel>` element

A SiteModel that has a gamma distributed rates across sites

The element has the following contents:

Element named <substitutionModel> containing:
- SubstitutionModel element (exactly one)
Element named <mutationRate> containing:
- Parameter element (exactly one)
Element named <rates> containing:
- Attribute (optional) relativeTo is Integer
- Parameter element (exactly one)
Element named <categories> containing:
- Attribute (optional) values is String
- Attribute (optional) states is String

Example:

<categorySiteModel>
 <substitutionModel>
   <positiveDefiniteSubstitutionModel idref="positiveDefiniteSubstitutionModel4"/>
 </substitutionModel>
 <mutationRate>
   <compoundParameter idref="compoundParameter8"/>
 </mutationRate>
</categorySiteModel>

`<centeredScale>` element

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.

The element takes following attributes:

Attribute weight is Double
Attribute scaleFactor is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

Parameter element (exactly one)

Example:

<centeredScale weight="1.0" scaleFactor="1.0" autoOptimize="true">
  <duplicatedParameter idref="duplicatedParameter8"/>
</centeredScale>

`<circle>` element

This element represents a regular circle polygon.

The element takes following attributes:

Attribute latitude is Double
Attribute longitude is Double
Attribute radius is Double
Attribute (optional) numberOfPoints is Integer

Example:

<circle latitude="1.0" longitude="1.0" radius="1.0" numberOfPoints="1"/>

`<coalescentIntervalStatistic>` element

The element has the following contents:

GMRFSkyrideLikelihood element (exactly one)

Example:

<coalescentIntervalStatistic>
  <gmrfTestLikelihood idref="gmrfTestLikelihood4"/>
</coalescentIntervalStatistic>

`<coalescentLikelihood>` element

This element represents the likelihood of the tree given the demographic function.

The element has the following contents:

Element named <model> containing:
- DemographicModel element (exactly one)
  
  The demographic model which describes the effective population size over time
Element named <populationTree> containing:
- Attribute (optional) factor is Double
- TreeModel element (exactly one)
  
  Tree(s) to compute likelihood for
Element named <include> containing:
- Taxa element (exactly one)
  
  An optional subset of taxa on which to calculate the likelihood (should be monophyletic)
Element named <exclude> containing:
- Taxa elements (one or more)
  
  One or more subsets of taxa which should be excluded from calculate the likelihood (should be monophyletic)

Example:

<coalescentLikelihood>
 <model>
   <scaledPiecewisePopulation idref="scaledPiecewisePopulation9"/>
 </model>
 <populationTree factor="1.0">
   <treeModel idref="treeModel9"/>
 </populationTree>
 <populationTree factor="1.0">
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel2"/>
 </populationTree>
</coalescentLikelihood>

`<coalescentTree>` element

This element returns a simulated tree under the given demographic model.

The element takes following attributes:

Attribute (optional) rescaleHeight is Double
Attempt to rescale the tree to the given root height
Attribute (optional) rootHeight is Double
'

The element has the following contents:

Tree elements (zero or more)
TaxonList elements (zero or more)
Element named <constrainedTaxa> containing:
- TaxonList elements (zero or more)
DemographicModel element (exactly one)

Example:

<coalescentTree rescaleHeight="1.0" rootHeight="1.0">
  <argTreeModel idref="argTreeModel5"/>
  <speciesTree idref="speciesTree7"/>
  <upgmaTree idref="upgmaTree8"/>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel1"/>
  <patterns idref="patterns2"/>
  <alignment idref="alignment8"/>
  <newick idref="newick5"/>
  <constantExponential idref="constantExponential7"/>
</coalescentTree>

`<column>` element

Specifies formating options for one or more columns in a log file.

The element takes following attributes:

Attribute (optional) label is String
The label of the column. If this is specified and more than one statistic is in this column, then the label will be appended by the index of the statistic to create individual column names
Attribute (optional) sf is Integer
Attribute (optional) dp is Integer
Attribute (optional) width is Integer
Attribute (optional) format is String

The element has the following contents:

Object elements (one or more)

Example:

<column label="foo" sf="1" dp="1" width="1" format="foo">
  <continuousTraitRateModel idref="continuousTraitRateModel3"/>
  <logML idref="logML10"/>
  <designMatrix idref="designMatrix10"/>
</column>

`<compatibilityStatistic>` element

A statistic that returns true if a pair of trees are compatible

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic for the purpose of logging

The element has the following contents:

Tree element (exactly one)
Element named <compatibleWith> containing:
- Tree element (exactly one)
Tree element (exactly one)

Example:

<compatibilityStatistic name="foo">
  <treeModel idref="treeModel8"/>
 <compatibleWith>
   <argTreeModel idref="argTreeModel4"/>
 </compatibleWith>
  <argTreeModel idref="argTreeModel7"/>
</compatibilityStatistic>

`<complexSubstitutionModel>` element

A general reversible model of sequence substitution for any data type with stochastic variable selection.

The element takes following attributes:

Attribute (optional) randomizeIndicator is Boolean
Attribute (optional) normalize is Boolean
Attribute (optional) maxConditionNumber is Double
Attribute (optional) mustBeConnected is Boolean
Attribute (optional) maxIterations is Integer
Attribute (optional) checkConditioning is Boolean

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <rootFrequencies> containing:
- FrequencyModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)

Example:

<complexSubstitutionModel randomizeIndicator="true" normalize="true" maxConditionNumber="1.0" mustBeConnected="true" maxIterations="1" checkConditioning="true">
  <hiddenNucleotides idref="hiddenNucleotides2"/>
 <rootFrequencies>
   <frequencyModel idref="frequencyModel2"/>
 </rootFrequencies>
 <rates>
   <maskedParameter idref="maskedParameter10"/>
 </rates>
</complexSubstitutionModel>

`<compoundBranchRateModel>` element

This element provides a strict clock model. All branches have the same rate of molecular evolution.

The element has the following contents:

BranchRateModel elements (one or more)
The component branch rate models

Example:

<compoundBranchRateModel>
  <localClockModel idref="localClockModel6"/>
  <arbitraryBranchRates idref="arbitraryBranchRates9"/>
  <argDiscretizedBranchRates idref="argDiscretizedBranchRates9"/>
</compoundBranchRateModel>

`<compoundLikelihood>` element

A likelihood function which is simply the product of its component likelihood functions.

The element takes following attributes:

Attribute (optional) threads is Integer

The element has the following contents:

Likelihood elements (one or more)

Example:

<compoundLikelihood threads="1">
  <coalescentLikelihood idref="coalescentLikelihood8"/>
  <speciesTreePopulationPrior idref="speciesTreePopulationPrior3"/>
</compoundLikelihood>

`<compoundParameter>` element

A multidimensional parameter constructed from its component parameters.

The element has the following contents:

Parameter elements (one or more)

Example:

<compoundParameter>
  <designMatrix idref="designMatrix4"/>
</compoundParameter>

`<compoundSymmetricMatrix>` element

A diagonal matrix parameter constructed from its diagonals.

The element takes following attributes:

Attribute (optional) asCorrelation is Boolean

The element has the following contents:

Element named <diagonal> containing:
- Parameter element (exactly one)
Element named <offDiagonal> containing:
- Parameter element (exactly one)

Example:

<compoundSymmetricMatrix asCorrelation="true">
 <diagonal>
   <designMatrix idref="designMatrix9"/>
 </diagonal>
 <offDiagonal>
   <compoundParameter idref="compoundParameter8"/>
 </offDiagonal>
</compoundSymmetricMatrix>

`<constantExponential>` element

A demographic model of constant population size followed by exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <growthPhaseStartTime> containing:
- Parameter element (exactly one)
One of:
- Element named <growthRate> containing:
  - Parameter element (exactly one)
    
    A value of zero represents a constant population size, negative values represent decline towards the present, positive numbers represents exponential growth towards the present. A random walk operator is recommended for this parameter with a starting value of 0.0 and no upper or lower limits.
- Element named <doublingTime> containing:
  - Parameter element (exactly one)
    
    This parameter determines the doubling time.

Example:

<constantExponential units="generations">
 <populationSize>
   <matrixParameter idref="matrixParameter1"/>
 </populationSize>
 <growthPhaseStartTime>
   <matrixParameter idref="matrixParameter7"/>
 </growthPhaseStartTime>
 <doublingTime>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix3"/>
 </doublingTime>
</constantExponential>

`<constantLogistic>` element

A demographic model of constant population size followed by logistic growth.

The element takes following attributes:

Attribute units is String
the units
Attribute alpha is Double

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <ancestralPopulationSize> containing:
- Parameter element (exactly one)
Element named <growthRate> containing:
- Parameter element (exactly one)
Element named <shape> containing:
- Parameter element (exactly one)

Example:

<constantLogistic units="substitutions" alpha="1.0">
 <populationSize>
   <diagonalMatrix idref="diagonalMatrix10"/>
 </populationSize>
 <ancestralPopulationSize>
   <maskedParameter idref="maskedParameter4"/>
 </ancestralPopulationSize>
 <growthRate>
   <designMatrix idref="designMatrix6"/>
 </growthRate>
 <shape>
   <designMatrix idref="designMatrix6"/>
 </shape>
</constantLogistic>

`<constantSize>` element

A demographic model representing a constant population size through time.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)

Example:

<constantSize units="years">
 <populationSize>
   <diagonalMatrix idref="diagonalMatrix1"/>
 </populationSize>
</constantSize>

`<constExpConst>` element

A demographic model of constant population size followed by exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <ancestralPopulationSize> containing:
- Parameter element (exactly one)
Element named <finalPhaseStartTime> containing:
- Parameter element (exactly one)
One of:
- Element named <growthRate> containing:
  - Parameter element (exactly one)
    
    A value of zero represents a constant population size, negative values represent decline towards the present, positive numbers represents exponential growth towards the present. A random walk operator is recommended for this parameter with a starting value of 0.0 and no upper or lower limits.
- Element named <doublingTime> containing:
  - Parameter element (exactly one)
    
    This parameter determines the doubling time.

Example:

<constExpConst units="days">
 <populationSize>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix4"/>
 </populationSize>
 <ancestralPopulationSize>
   <parameter idref="parameter10"/>
 </ancestralPopulationSize>
 <finalPhaseStartTime>
   <compoundParameter idref="compoundParameter3"/>
 </finalPhaseStartTime>
 <doublingTime>
   <maskedParameter idref="maskedParameter9"/>
 </doublingTime>
</constExpConst>

`<continuousTraitRateModel>` element

This element returns an trait rate model.The branch rates are an average of the rates provided by a node trait.

The element takes following attributes:

Attribute (optional) dimension is Integer
The dimension that supplies the rate

The element has the following contents:

Element named <rate> containing:
- Parameter element (exactly one)
  
  The rate parameter
Element named <ratio> containing:
- Parameter element (exactly one)
  
  The ratio parameter
SampledMultivariateTraitLikelihood element (zero or one)

Example:

<continuousTraitRateModel dimension="1"/>

`<convert>` element

Converts an alignment to the given data type.

The element takes following attributes:

Attribute dataType is String
The type of sequence data

The element has the following contents:

Alignment element (exactly one)

Example:

<convert dataType="codon">
  <alignment idref="alignment5"/>
</convert>

`<coordinates>` element

This element represents a set of (X,Y,Z) coordinates in KML format

The element has the following contents:

String element (exactly one)

Example:

<coordinates>
  foo
</coordinates>

`<correlation>` element

This element returns a precision that is the element-wise reciprocal of the child precision.

The element takes following attributes:

Attribute dimension1 is Integer
Attribute dimension2 is Integer

The element has the following contents:

MatrixParameter element (exactly one)

Example:

<correlation dimension1="1" dimension2="1">
  <matrixParameter idref="matrixParameter1"/>
</correlation>

`<CovarionHKYModel>` element

A covarion HKY model.

The element has the following contents:

Element named <kappa> containing:
- Parameter element (exactly one)
  A parameter representing the transition transversion bias
Element named <switchingRates> containing:
- Parameter element (exactly one)
  A parameter representing the rate of change between the different classes
Element named <hiddenClassRates> containing:
- Parameter element (exactly one)
  A parameter representing the rates of the hidden classes relative to the first hidden class.

Example:

<CovarionHKYModel>
 <kappa>
   <compoundParameter idref="compoundParameter4"/>
 </kappa>
 <switchingRates>
   <duplicatedParameter idref="duplicatedParameter10"/>
 </switchingRates>
 <hiddenClassRates>
   <matrixParameter idref="matrixParameter6"/>
 </hiddenClassRates>
</CovarionHKYModel>

`<covarionModel>` element

A covarion substitution model on binary data and a hidden rate state with two rates.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <alpha> containing:
- Parameter element (zero or one)
Element named <switchingRate> containing:
- Parameter element (zero or one)

Example:

<covarionModel>
 <frequencies>
   <frequencyModel idref="frequencyModel8"/>
 </frequencies>
 <alpha/>
 <switchingRate/>
</covarionModel>

`<CSVexport>` element

Write tabular data as an CSV file.

The element takes following attributes:

Attribute fileName is String
The name of a BEAST log file (can not include trees, which should be logged separately
Attribute (optional) separator is String
Values separator (default is tab)

The element has the following contents:

Element named <columns> containing:
- Attribute (optional) all is Boolean
  Dump all columns. default is TRUE when no columns are specified, FALSE otherwise
- Attribute (optional) rows is Boolean
  Write data in rows (default is columns)
- TabularData element (exactly one)
- Element named <CSVcolumn> containing:
  - Attribute name is String;
  - Parameter element (exactly one)
    
    column name
  A subset of columns from one source

Example:

<CSVexport fileName="foo" separator="foo">
 <columns all="true" rows="true">
   <logFileTrace idref="logFileTrace5"/>
  <CSVcolumn name="foo bar">
    <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
  </CSVcolumn>
  <CSVcolumn name="foo bar">
    <diagonalMatrix idref="diagonalMatrix4"/>
  </CSVcolumn>
  <CSVcolumn name="foo bar">
    <compoundParameter idref="compoundParameter6"/>
  </CSVcolumn>
 </columns>
 <columns all="true" rows="true">
   <VDAnalysis idref="VDAnalysis10"/>
  <CSVcolumn name="foo bar">
    <matrixParameter idref="matrixParameter7"/>
  </CSVcolumn>
 </columns>
 <columns all="true" rows="true">
   <logFileTrace idref="logFileTrace1"/>
  <CSVcolumn name="foo bar">
    <compoundParameter idref="compoundParameter8"/>
  </CSVcolumn>
  <CSVcolumn name="foo bar">
    <maskedParameter idref="maskedParameter5"/>
  </CSVcolumn>
 </columns>
 <columns all="true" rows="true">
   <VDAnalysis idref="VDAnalysis1"/>
  <CSVcolumn name="foo bar">
    <maskedParameter idref="maskedParameter10"/>
  </CSVcolumn>
  <CSVcolumn name="foo bar">
    <maskedParameter idref="maskedParameter10"/>
  </CSVcolumn>
  <CSVcolumn name="foo bar">
    <parameter idref="parameter10"/>
  </CSVcolumn>
 </columns>
</CSVexport>

`<ctmcScalePrior>` element

This element represents the prior for CTMC scale parameter.

The element has the following contents:

TreeModel element (exactly one)
Element named <ctmcScale> containing:
- Parameter element (exactly one)

Example:

<ctmcScalePrior>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel10"/>
 <ctmcScale>
   <duplicatedParameter idref="duplicatedParameter7"/>
 </ctmcScale>
</ctmcScalePrior>

`<date>` element

Specifies a date on a given timescale

The element takes following attributes:

Attribute value is String
The value of this date
Attribute (optional) origin is String
The origin of this time scale, which must be a valid calendar date
Attribute (optional) units is String
The units of the timescale
Attribute (optional) direction is String
The direction of the timescale

Example:

<!-- a date representing 10 years in the past                                 -->
<date value="10.0" units="years" direction="backwards"/>

<!-- a date representing 300 days after Jan 1st 1989                          -->
<date value="300.0" origin="01/01/89" units="days" direction="forwards"/>

`<deltaExchange>` element

This element returns a scale operator on a given parameter.

The element takes following attributes:

Attribute delta is Double
Attribute (optional) parameterWeights is Integer;
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) integer is Boolean

The element has the following contents:

Parameter element (exactly one)

Example:

<deltaExchange delta="1.0" parameterWeights="1 2 4 8" weight="1.0" autoOptimize="true" integer="true">
  <diagonalMatrix idref="diagonalMatrix6"/>
</deltaExchange>

`<designMatrix>` element

A matrix parameter constructed from its component parameters.

The element takes following attributes:

Attribute (optional) addIntercept is Boolean
Attribute (optional) form is String
Attribute (optional) colDimension is Integer
Attribute (optional) rowDimension is Integer

The element has the following contents:

Parameter elements (zero or more)

Example:

<designMatrix addIntercept="true" form="foo" colDimension="1" rowDimension="1">
  <parameter idref="parameter8"/>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix9"/>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
</designMatrix>

`<diagonalMatrix>` element

A diagonal matrix parameter constructed from its diagonals.

The element has the following contents:

Parameter element (exactly one)

Example:

<diagonalMatrix>
  <designMatrix idref="designMatrix10"/>
</diagonalMatrix>

`<differenceStatistic>` element

This element returns a statistic that is the difference of the 2 child statistics.

The element takes following attributes:

Attribute (optional) absolute is Boolean

The element has the following contents:

Statistic elements (exactly 2)
The two operand statistics

Example:

<differenceStatistic absolute="true">
  <duplicatedParameter idref="duplicatedParameter5"/>
  <matrixParameter idref="matrixParameter2"/>
</differenceStatistic>

`<differenceStatistic>` element

This element returns a statistic that is the difference of the 2 child statistics.

The element takes following attributes:

Attribute (optional) absolute is Boolean

The element has the following contents:

Statistic elements (exactly 2)
The two operand statistics

Example:

<differenceStatistic absolute="true">
  <RPNcalculator idref="RPNcalculator8"/>
  <negativeStatistic idref="negativeStatistic10"/>
</differenceStatistic>

`<diffusionRateStatistic>` element

A statistic that returns the average of the branch rates

The element takes following attributes:

Attribute (optional) name is String
Attribute (optional) greatCircleDistance is Boolean

The element has the following contents:

AbstractMultivariateTraitLikelihood elements (one or more)

Example:

<diffusionRateStatistic name="foo" greatCircleDistance="true">
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood2"/>
  <inhibitionLikelihood idref="inhibitionLikelihood9"/>
</diffusionRateStatistic>

`<dirichletPrior>` element

Calculates the likelihood of some data under an Inverse-Wishart distribution.

The element has the following contents:

Element named <countsParameter> containing:
- Parameter element (exactly one)

Example:

<dirichletPrior>
 <countsParameter>
   <maskedParameter idref="maskedParameter10"/>
 </countsParameter>
</dirichletPrior>

`<DirichletSiteModel>` element

A SiteModel that has Dirichlet distributed rates across sites

The element has the following contents:

Element named <substitutionModel> containing:
- SubstitutionModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)

Example:

<DirichletSiteModel>
 <substitutionModel>
   <yangCodonModel idref="yangCodonModel8"/>
 </substitutionModel>
 <rates>
   <maskedParameter idref="maskedParameter7"/>
 </rates>
</DirichletSiteModel>

`<dirtyLikelihood>` element

This element returns a operator that forces the entire model likelihood recomputation

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Likelihood element (exactly one)

Example:

<dirtyLikelihood weight="1.0">
  <discreteTraitRateModel idref="discreteTraitRateModel7"/>
</dirtyLikelihood>

`<discreteTraitRateModel>` element

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.

The element takes following attributes:

Attribute (optional) traitIndex is Integer
Attribute (optional) traitName is String

The element has the following contents:

TreeModel element (exactly one)
The tree model
One of:
- All of:***TreeTraitProvider element (exactly one)
  - The trait provider
  - One of:
    - Attribute dataType is String
      The type of general data
    - DataType element (exactly one)

- PatternList element (exactly one)

Element named <rate> containing:
- Parameter element (exactly one)
  
  The absolute rate of state 0
Element named <rates> containing:
- Parameter element (exactly one)
  
  The relative rates of state > 0
Element named <indicators> containing:
- Parameter element (exactly one)
  
  An index that links the state with a rate

Example:

<discreteTraitRateModel traitIndex="1" traitName="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel4"/>
 <rate>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix1"/>
 </rate>
</discreteTraitRateModel>

`<discretizedBranchRates>` element

This element returns an discretized relaxed clock model.The branch rates are drawn from a discretized parametric distribution.

The element takes following attributes:

Attribute (optional) singleRootRate is Boolean
Whether only a single rate should be used for the two children branches of the root
Attribute (optional) overSampling is Integer
The integer factor for oversampling the distribution model (1 means no oversampling)
Attribute (optional) normalize is Boolean
Whether the mean rate has to be normalized to a particular value
Attribute (optional) normalizeBranchRateTo is Double
The mean rate to normalize to, if normalizing
Attribute (optional) overSampling is Integer
The integer factor for oversampling the distribution model (1 means no oversampling)

The element has the following contents:

TreeModel element (exactly one)
Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
  
  The distribution model for rates among branches
Element named <rateCategories> containing:
- Parameter element (exactly one)
  
  The rate categories parameter

Example:

<discretizedBranchRates singleRootRate="true" overSampling="1" normalize="true" normalizeBranchRateTo="1.0" overSampling="1">
  <treeModel idref="treeModel1"/>
 <distribution>
   <exponentialDistributionModel idref="exponentialDistributionModel4"/>
 </distribution>
 <rateCategories>
   <parameter idref="parameter7"/>
 </rateCategories>
</discretizedBranchRates>

`<discretizedLocationOperator>` element

This element returns a multivariate Gibbs operator on traits for possible all nodes.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) onlyInternalNodes is Boolean
Attribute (optional) neighborhoodSize is Integer
Attribute (optional) randomize is Boolean

The element has the following contents:

AbstractMultivariateTraitLikelihood element (exactly one)

Example:

<discretizedLocationOperator weight="1.0" autoOptimize="true" onlyInternalNodes="true" neighborhoodSize="1" randomize="true">
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood8"/>
</discretizedLocationOperator>

`<distanceMatrix>` element

Constructs a distance matrix from a pattern list or alignment

The element takes following attributes:

Attribute correction is String
The type of distance correction used

The element has the following contents:

PatternList element (exactly one)

Example:

<distanceMatrix correction="F84">
  <sequenceSimulator idref="sequenceSimulator4"/>
</distanceMatrix>

`<distributionLikelihood>` element

Calculates the likelihood of some data given some parametric or empirical distribution.

The element has the following contents:

Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
Element named <data> containing:
- Attribute (optional) from is Integer
- Attribute (optional) to is Integer
- Statistic elements (one or more)

Example:

<distributionLikelihood>
 <distribution>
   <inverseGaussianDistributionModel idref="inverseGaussianDistributionModel9"/>
 </distribution>
 <data from="1" to="1">
   <treeMetricStatistic idref="treeMetricStatistic1"/>
   <sumStatistic idref="sumStatistic10"/>
   <speciesTreeStatistic idref="speciesTreeStatistic9"/>
   <notStatistic idref="notStatistic4"/>
 </data>
</distributionLikelihood>

`<double>` element

returns a Double. If a prompt attribute exists then the user is prompted for input, otherwise the character contents of the element are returned as a Double.

The element has the following contents:

One of:
- Attribute prompt is String
  A message displayed to the user when entering a value for this double
- Double element (exactly one)

Example:

<double>
  1.0
</double>

`<dummyLikelihood>` element

A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.

The element has the following contents:

Model element (exactly one)
A model element

Example:

<dummyLikelihood>
  <TN93Model idref="TN93Model8"/>
</dummyLikelihood>

`<dummyModel>` element

A function wraps a component model that would otherwise not be registered with the MCMC. Always returns a log likelihood of zero.

The element has the following contents:

Parameter elements (one or more)

Example:

<dummyModel>
  <maskedParameter idref="maskedParameter4"/>
  <diagonalMatrix idref="diagonalMatrix7"/>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix2"/>
</dummyModel>

`<duplicatedParameter>` element

A duplicated parameter.

The element has the following contents:

Parameter element (exactly one)
Element named <copies> containing:
- Parameter element (exactly one)

Example:

<duplicatedParameter>
  <designMatrix idref="designMatrix9"/>
 <copies>
   <designMatrix idref="designMatrix7"/>
 </copies>
</duplicatedParameter>

`<empiricalDistributionLikelihood>` element

Calculates the likelihood of some data given some empirically-generated distribution.

The element takes following attributes:

Attribute fileName is String
Attribute (optional) splineInterpolation is Boolean
Attribute (optional) degree is Integer
Attribute (optional) inverse is Boolean
Attribute (optional) readByColumn is Boolean

The element has the following contents:

Element named <data> containing:
- Attribute (optional) from is Integer
- Attribute (optional) to is Integer
- Attribute (optional) offset is Double
- Statistic elements (one or more)

Example:

<empiricalDistributionLikelihood fileName="foo" splineInterpolation="true" degree="1" inverse="true" readByColumn="true">
 <data from="1" to="1" offset="1.0">
   <reciprocalStatistic idref="reciprocalStatistic5"/>
 </data>
</empiricalDistributionLikelihood>

`<empiricalPiecewise>` element

This element represents a piecewise population model

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <intervalWidths> containing:
- Attribute values is Double;
Element named <populationSizes> containing:
- Parameter element (exactly one)
  
  The effective population sizes of each interval.
Element named <generationLength> containing:
- Parameter element (exactly one)
  
  The scale factor.
Element named <threshold> containing:
- Parameter element (exactly one)
  
  The threshold before counts occur.
Element named <lag> containing:
- Parameter element (exactly one)
  
  The lag between actual population sizes and genetic diversity.

Example:

<empiricalPiecewise units="days">
 <intervalWidths values="0.5 1.0"/>
 <populationSizes>
   <compoundParameter idref="compoundParameter3"/>
 </populationSizes>
 <generationLength>
   <compoundParameter idref="compoundParameter5"/>
 </generationLength>
 <threshold>
   <maskedParameter idref="maskedParameter7"/>
 </threshold>
 <lag>
   <compoundParameter idref="compoundParameter8"/>
 </lag>
</empiricalPiecewise>

`<empiricalTreeDistributionModel>` element

Read a list of trees from a NEXUS file.

The element takes following attributes:

Attribute fileName is String
The name of a NEXUS tree file

The element has the following contents:

TaxonList element (exactly one)

Example:

<empiricalTreeDistributionModel fileName="foo">
  <attributePatterns idref="attributePatterns2"/>
</empiricalTreeDistributionModel>

`<empiricalTreeDistributionOperator>` element

Operator which switches between trees in an empirical distribution.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) metropolisHastings is Boolean

The element has the following contents:

EmpiricalTreeDistributionModel element (exactly one)

Example:

<empiricalTreeDistributionOperator weight="1.0" metropolisHastings="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel5"/>
</empiricalTreeDistributionOperator>

`<exponentialStatistic>` element

This element returns a statistic that is the element-wise exponentiation of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<exponentialStatistic>
  <parsimonyStateStatistic idref="parsimonyStateStatistic8"/>
</exponentialStatistic>

`<expansion>` element

A demographic model of constant population size followed by exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <ancestralPopulationProportion> containing:
- Parameter element (exactly one)
One of:
- Element named <growthRate> containing:
  - Parameter element (exactly one)
    
    A value of zero represents a constant population size, negative values represent decline towards the present, positive numbers represents exponential growth towards the present. A random walk operator is recommended for this parameter with a starting value of 0.0 and no upper or lower limits.
- Element named <doublingTime> containing:
  - Parameter element (exactly one)
    
    This parameter determines the doubling time.

Example:

<expansion units="mutations">
 <populationSize>
   <duplicatedParameter idref="duplicatedParameter4"/>
 </populationSize>
 <ancestralPopulationProportion>
   <duplicatedParameter idref="duplicatedParameter2"/>
 </ancestralPopulationProportion>
 <growthRate>
   <matrixParameter idref="matrixParameter1"/>
 </growthRate>
</expansion>

`<expConstExp>` element

A demographic model of exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <relativePlateauSize> containing:
- Parameter element (exactly one)
  
  The size of plateau relative to modern population size.
Element named <relTimeModGrowth> containing:
- Parameter element (exactly one)
  
  The time spanned by modern growth phase relative to time back to start of plateau phase.
Element named <plateauStartTime> containing:
- Parameter element (exactly one)
  
  The time of the start of plateauPhase.
Element named <ancientGrowthRate> containing:
- Parameter element (exactly one)
  
  The growth rate of early growth phase

Example:

<expConstExp units="generations">
 <populationSize>
   <duplicatedParameter idref="duplicatedParameter10"/>
 </populationSize>
 <relativePlateauSize>
   <diagonalMatrix idref="diagonalMatrix3"/>
 </relativePlateauSize>
 <relTimeModGrowth>
   <designMatrix idref="designMatrix9"/>
 </relTimeModGrowth>
 <plateauStartTime>
   <matrixParameter idref="matrixParameter5"/>
 </plateauStartTime>
 <ancientGrowthRate>
   <parameter idref="parameter6"/>
 </ancientGrowthRate>
</expConstExp>

`<exponentialBranchLengthsPrior>` element

This element represents a tree prior assuming exponentially distributed branch lengths.

The element has the following contents:

TreeModel element (exactly one)

Example:

<exponentialBranchLengthsPrior>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel8"/>
</exponentialBranchLengthsPrior>

`<exponentialDistributionModel>` element

A model of an exponential distribution.

The element takes following attributes:

Attribute (optional) offset is Double

The element has the following contents:

One of:
- Element named <mean> containing:
  - Double element (exactly one)
- Element named <mean> containing:
  - Parameter element (exactly one)

Example:

<exponentialDistributionModel offset="1.0">
 <mean>
   1.0
 </mean>
</exponentialDistributionModel>

`<exponentialGrowth>` element

A demographic model of exponential growth.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
One of:
- Element named <growthRate> containing:
  - Parameter element (exactly one)
    
    A value of zero represents a constant population size, negative values represent decline towards the present, positive numbers represents exponential growth towards the present. A random walk operator is recommended for this parameter with a starting value of 0.0 and no upper or lower limits.
- Element named <doublingTime> containing:
  - Parameter element (exactly one)
    
    This parameter determines the doubling time.

Example:

<exponentialGrowth units="mutations">
 <populationSize>
   <compoundParameter idref="compoundParameter3"/>
 </populationSize>
 <doublingTime>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix8"/>
 </doublingTime>
</exponentialGrowth>

`<exponentialLogistic>` element

A demographic model of constant population size followed by logistic growth.

The element takes following attributes:

Attribute units is String
the units
Attribute alpha is Double

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <logisticGrowthRate> containing:
- Parameter element (exactly one)
Element named <logisticShape> containing:
- Parameter element (exactly one)
Element named <exponentialGrowthRate> containing:
- Parameter element (exactly one)
Element named <transitionTime> containing:
- Parameter element (exactly one)

Example:

<exponentialLogistic units="days" alpha="1.0">
 <populationSize>
   <maskedParameter idref="maskedParameter5"/>
 </populationSize>
 <logisticGrowthRate>
   <parameter idref="parameter4"/>
 </logisticGrowthRate>
 <logisticShape>
   <duplicatedParameter idref="duplicatedParameter2"/>
 </logisticShape>
 <exponentialGrowthRate>
   <matrixParameter idref="matrixParameter7"/>
 </exponentialGrowthRate>
 <transitionTime>
   <designMatrix idref="designMatrix5"/>
 </transitionTime>
</exponentialLogistic>

`<exponentialMarkovLikelihood>` element

A continuous state, discrete time markov chain in which each new state is an exponentially distributed variable with a mean of the previous state.

The element takes following attributes:

Attribute (optional) jeffreys is Boolean
Attribute (optional) reverse is Boolean

The element has the following contents:

Element named <chainParameter> containing:
- Parameter element (exactly one)

Example:

<exponentialMarkovLikelihood jeffreys="true" reverse="true">
 <chainParameter>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix7"/>
 </chainParameter>
</exponentialMarkovLikelihood>

`<exponentialPrior>` element

Calculates the prior probability of some data under a given exponential distribution.

The element takes following attributes:

Attribute mean is Double
Attribute (optional) offset is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<exponentialPrior mean="1.0" offset="1.0">
  <speciesTreeStatistic idref="speciesTreeStatistic3"/>
  <treeLengthStatistic idref="treeLengthStatistic1"/>
  <negativeStatistic idref="negativeStatistic4"/>
  <argTimingStatistic idref="argTimingStatistic4"/>
</exponentialPrior>

`<exponentialSawtooth>` element

A demographic model of succesive exponential growth and periodic population crashes.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
Element named <growthRate> containing:
- Parameter element (exactly one)
  
  The rate of exponential growth during the growth phase.
Element named <wavelength> containing:
- Parameter element (exactly one)
  
  The wavelength between successive population crashes.
Element named <offset> containing:
- Parameter element (exactly one)
  
  The proportion of the last growth phase that is not achieved at the final sample time.

Example:

<exponentialSawtooth units="generations">
 <populationSize>
   <parameter idref="parameter5"/>
 </populationSize>
 <growthRate>
   <matrixParameter idref="matrixParameter6"/>
 </growthRate>
 <wavelength>
   <maskedParameter idref="maskedParameter7"/>
 </wavelength>
 <offset>
   <designMatrix idref="designMatrix5"/>
 </offset>
</exponentialSawtooth>

`<exponentialStatistic>` element

This element returns a statistic that is the element-wise exponentiation of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<exponentialStatistic>
  <varianceStatistic idref="varianceStatistic8"/>
</exponentialStatistic>

`<expressionStatistic>` element

This element returns a statistic that is the mean of the child statistics.

The element has the following contents:

Element named <expression> containing:
- String element (exactly one)
Element named <variables> containing:
- Statistic elements (one or more)

Example:

<expressionStatistic>
 <expression>
   foo
 </expression>
 <variables>
   <differenceStatistic idref="differenceStatistic5"/>
   <popGraph idref="popGraph9"/>
   <exponentialStatistic idref="exponentialStatistic10"/>
   <argTreeCount idref="argTreeCount1"/>
 </variables>
</expressionStatistic>

`<extendedDataType>` element

This element represents an instance of the MutationDeathType which extends a base datatype with an additional "death" state.

The element takes following attributes:

Attribute (optional) dataType is String
Base datatype name

The element has the following contents:

DataType element (zero or one)
Element named <deathState> containing:
- Attribute code is String
Element named <extantState> containing:
- Attribute code is String
<ambiguity code="Z" states="XY"/>

Example:

<extendedDataType dataType="codon-ascidianMitochondrial"/>

`<externalLengthStatistic>` element

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

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

TreeModel element (exactly one)
Taxa element (exactly one)

Example:

<externalLengthStatistic name="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel7"/>
  <taxa idref="taxa9"/>
</externalLengthStatistic>

`<FixedNodeheightSubtreePruneRegraft>` element

This element represents a FNPR operator. This operator swaps a random subtree with its uncle.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeModel element (exactly one)

Example:

<FixedNodeheightSubtreePruneRegraft weight="1.0">
  <treeModel idref="treeModel1"/>
</FixedNodeheightSubtreePruneRegraft>

`<flatGeoSpatialPrior>` element

Calculates the likelihood of some data under a 2D geospatial distribution.

The element takes following attributes:

Attribute (optional) taxon is String
Attribute (optional) inside is Boolean
Attribute (optional) union is Boolean

The element has the following contents:

One of:
- Attribute kmlFileName is String
- Polygon2D elements (one or more)

Element named <data> containing:
- Parameter elements (one or more)

Example:

<flatGeoSpatialPrior taxon="foo" inside="true" union="true" kmlFileName="foo">
 <data>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix9"/>
 </data>
</flatGeoSpatialPrior>

`<frequencyModel>` element

A model of equilibrium base frequencies.

The element takes following attributes:

Attribute (optional) normalize is Boolean

The element has the following contents:

PatternList element (zero or one)
Initial value
One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <frequencies> containing:
- Parameter element (exactly one)

Example:

<frequencyModel normalize="true">
  <hiddenNucleotides idref="hiddenNucleotides1"/>
 <frequencies>
   <duplicatedParameter idref="duplicatedParameter3"/>
 </frequencies>
</frequencyModel>

`<gammaDistributionModel>` element

A model of a gamma distribution.

The element has the following contents:

One of:
- Element named <shape> containing:
  - Double element (exactly one)
- Element named <shape> containing:
  - Parameter element (exactly one)

One of:
- Element named <scale> containing:
  - Double element (exactly one)
- Element named <scale> containing:
  - Parameter element (exactly one)

Example:

<gammaDistributionModel>
 <shape>
   <diagonalMatrix idref="diagonalMatrix9"/>
 </shape>
 <scale>
   1.0
 </scale>
</gammaDistributionModel>

`<gammaPrior>` element

Calculates the prior probability of some data under a given gamma distribution.

The element takes following attributes:

Attribute shape is Double
Attribute scale is Double
Attribute (optional) offset is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<gammaPrior shape="1.0" scale="1.0" offset="1.0">
  <nodeHeightsStatistic idref="nodeHeightsStatistic10"/>
</gammaPrior>

`<generalDataType>` element

Defines a general DataType for any number of states

The element has the following contents:

Identifiable elements (zero or more)

<state code="X"/>*:<alias code="Y" state="X"/>*:<ambiguity code="Z" states="XY"/>

Example:

<!-- The XML for a nucleotide data type under this scheme would be -->
<generalDataType id="nucleotides">
	<state code="A"/>
	<state code="C"/>
	<state code="G"/>
	<state code="T"/>
	<alias code="U" state="T"/>
	<ambiguity code="R" states="AG"/>
	<ambiguity code="Y" states="CT"/>
	<ambiguity code="?" states="ACGT"/>
	<ambiguity code="-" states="ACGT"/>
</generalDataType>

`<generalizedSkylineGibbsOperator>` element

This element returns a Gibbs operator for the joint distribution of population sizes.

The element takes following attributes:

Attribute (optional) linear is Boolean
Attribute weight is Double
Attribute lower is Double
Attribute upper is Double
Attribute (optional) Jeffreys is Boolean
Attribute (optional) reverse is Boolean
Attribute (optional) exponentialMarkov is Boolean
Attribute shape is Double

The element has the following contents:

BayesianSkylineLikelihood element (exactly one)
Parameter element (exactly one)

Example:

<generalizedSkylineGibbsOperator linear="true" weight="1.0" lower="1.0" upper="1.0" Jeffreys="true" reverse="true" exponentialMarkov="true" shape="1.0">
  <generalizedSkyLineLikelihood idref="generalizedSkyLineLikelihood7"/>
  <diagonalMatrix idref="diagonalMatrix10"/>
</generalizedSkylineGibbsOperator>

`<generalizedSkyLineLikelihood>` element

This element represents the likelihood of the tree given the population size vector.

The element has the following contents:

One of:
- Attribute linear is Boolean
- Attribute type is String

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <groupSizes> containing:
- Parameter element (exactly one)
Element named <populationTree> containing:
- TreeModel element (exactly one)

Example:

<generalizedSkyLineLikelihood type="foo">
 <populationSizes>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
 </populationSizes>
 <groupSizes>
   <parameter idref="parameter3"/>
 </groupSizes>
 <populationTree>
   <treeModel idref="treeModel10"/>
 </populationTree>
</generalizedSkyLineLikelihood>

`<generalizedSkylinePopSizeStatistic>` element

The pop sizes at the given times

Example:

<generalizedSkylinePopSizeStatistic/>

`<generalSubstitutionModel>` element

A general reversible model of sequence substitution for any data type.

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)

Example:

<generalSubstitutionModel>
  <hiddenNucleotides idref="hiddenNucleotides1"/>
 <frequencies>
   <frequencyModel idref="frequencyModel1"/>
 </frequencies>
 <rates>
   <duplicatedParameter idref="duplicatedParameter7"/>
 </rates>
</generalSubstitutionModel>

`<GibbsPruneAndRegraft>` element

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.

The element takes following attributes:

Attribute weight is Double
Attribute pruned is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<GibbsPruneAndRegraft weight="1.0" pruned="true">
  <treeModel idref="treeModel2"/>
</GibbsPruneAndRegraft>

`<GibbsSubtreeSwap>` element

This element represents a Gibbs wide exchange operator. This operator swaps two subtrees chosen to their posterior probaility.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) pruned is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<GibbsSubtreeSwap weight="1.0" pruned="true">
  <treeModel idref="treeModel4"/>
</GibbsSubtreeSwap>

`<glmModel>` element

Calculates the generalized linear model likelihood of the dependent parameters given one or more blocks of independent parameters and their design matrix.

The element takes following attributes:

Attribute family is String
Attribute (optional) checkIdentifiability is Boolean

The element has the following contents:

Element named <dependentVariables> containing:
- Parameter element (exactly one)
Element named <independentVariables> containing:
- Parameter element (zero or one)
- DesignMatrix element (exactly one)
- Element named <indicator> containing:
  - Parameter element (exactly one)
Element named <randomEffects> containing:
- Parameter element (exactly one)

Example:

<glmModel family="foo" checkIdentifiability="true">
 <independentVariables>
   <designMatrix idref="designMatrix9"/>
 </independentVariables>
 <independentVariables>
   <designMatrix idref="designMatrix5"/>
 </independentVariables>
 <randomEffects>
   <parameter idref="parameter8"/>
 </randomEffects>
</glmModel>

`<glmSubstitutionModel>` element

A general model of sequence substitution for any data type where the rates come from the generalized linear model.

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <rootFrequencies> containing:
- FrequencyModel element (exactly one)
GeneralizedLinearModel element (exactly one)

Example:

<glmSubstitutionModel dataType="codon-euplotidNuclear">
 <rootFrequencies>
   <frequencyModel idref="frequencyModel4"/>
 </rootFrequencies>
  <multivariateOUModel idref="multivariateOUModel7"/>
</glmSubstitutionModel>

`<gmrfBivariateCurveAnalysis>` element

Integrates two curves

The element takes following attributes:

Attribute fileName1 is String
Attribute fileName2 is String
Attribute endTime is String
Attribute (optional) burnIn is Integer

Example:

<gmrfBivariateCurveAnalysis fileName1="foo" fileName2="foo" endTime="foo" burnIn="1"/>

`<gmrfBlockUpdateOperator>` element

This element returns a GMRF block-update operator for the joint distribution of the population sizes and precision parameter.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) stopValue is Double
Attribute (optional) maxIterations is Integer
Attribute (optional) trialVersion is Boolean

The element has the following contents:

GMRFSkyrideLikelihood element (exactly one)

Example:

<gmrfBlockUpdateOperator scaleFactor="1.0" weight="1.0" autoOptimize="true" stopValue="1.0" maxIterations="1" trialVersion="true">
  <gmrfSkyrideLikelihood idref="gmrfSkyrideLikelihood3"/>
</gmrfBlockUpdateOperator>

`<gmrfFixedEffectsGibbsOperator>` element

This element returns a Gibbs operator for regression coefficients in a GMRF.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

MultivariateDistributionLikelihood element (exactly one)
Parameter element (exactly one)
GMRFSkyrideLikelihood element (exactly one)

Example:

<gmrfFixedEffectsGibbsOperator weight="1.0">
  <multivariateNormalPrior idref="multivariateNormalPrior7"/>
  <matrixParameter idref="matrixParameter5"/>
  <gmrfSkyrideLikelihood idref="gmrfSkyrideLikelihood5"/>
</gmrfFixedEffectsGibbsOperator>

`<gmrfHeightsStatistic>` element

A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)

The element takes following attributes:

Attribute (optional) name is String

The element has the following contents:

GMRFSkyrideLikelihood element (exactly one)

Example:

<gmrfHeightsStatistic name="foo">
  <gmrfTestLikelihood idref="gmrfTestLikelihood5"/>
</gmrfHeightsStatistic>

`<gmrfPopSizeStatistic>` element

The pop sizes at the given times

The element takes following attributes:

Attribute (optional) from is Double
Attribute (optional) to is Double
Attribute (optional) number is Integer
Attribute (optional) time is Double;

The element has the following contents:

GMRFSkyrideLikelihood element (exactly one)

Example:

<gmrfPopSizeStatistic from="1.0" to="1.0" number="1" time="0.5 1.0">
  <gmrfSkyrideLikelihood idref="gmrfSkyrideLikelihood7"/>
</gmrfPopSizeStatistic>

`<gmrfSkyrideLikelihood>` element

This element represents the likelihood of the tree given the population size vector.

The element takes following attributes:

Attribute (optional) rescaleByRootHeight is Boolean
Attribute (optional) randomizeTree is Boolean
Attribute (optional) timeAwareSmoothing is Boolean

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <precisionParameter> containing:
- Parameter element (exactly one)
Element named <populationTree> containing:
- TreeModel elements (one or more)
Element named <groupSizes> containing:
- Parameter element (exactly one)

Example:

<gmrfSkyrideLikelihood rescaleByRootHeight="true" randomizeTree="true" timeAwareSmoothing="true">
 <populationSizes>
   <compoundParameter idref="compoundParameter2"/>
 </populationSizes>
 <precisionParameter>
   <diagonalMatrix idref="diagonalMatrix3"/>
 </precisionParameter>
 <populationTree>
   <treeModel idref="treeModel4"/>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel8"/>
 </populationTree>
</gmrfSkyrideLikelihood>

`<gmrfTestLikelihood>` element

This element represents the likelihood of the tree given the population size vector.

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <precisionParameter> containing:
- Parameter element (exactly one)
Element named <lambdaParameter> containing:
- Parameter element (exactly one)

Example:

<gmrfTestLikelihood>
 <populationSizes>
   <compoundParameter idref="compoundParameter2"/>
 </populationSizes>
 <precisionParameter>
   <compoundParameter idref="compoundParameter8"/>
 </precisionParameter>
 <lambdaParameter>
   <diagonalMatrix idref="diagonalMatrix2"/>
 </lambdaParameter>
</gmrfTestLikelihood>

`<greatCircleDiffusionModel>` element

Describes a bivariate diffusion process using great circle distances.

The element has the following contents:

Parameter element (exactly one)
Element named <diffusionCoefficient> containing:
- Parameter element (exactly one)

Example:

<greatCircleDiffusionModel>
  <parameter idref="parameter3"/>
</greatCircleDiffusionModel>

`<gtrCovarionModel>` element

A covarion substitution model of langauge evolution with binary data and a hidden rate state with two rates.

The element has the following contents:

Element named <rateAC> containing:
- Parameter element (exactly one)
  
  relative rate of A<->C substitution
Element named <rateAG> containing:
- Parameter element (exactly one)
  
  relative rate of A<->G substitution
Element named <rateAT> containing:
- Parameter element (exactly one)
  
  relative rate of A<->T substitution
Element named <rateCG> containing:
- Parameter element (exactly one)
  
  relative rate of C<->G substitution
Element named <rateCT> containing:
- Parameter element (exactly one)
  
  relative rate of C<->T substitution
Element named <rateGT> containing:
- Parameter element (exactly one)
  
  relative rate of G<->T substitution
Element named <hiddenClassRates> containing:
- Parameter element (exactly one)
Element named <switchingRates> containing:
- Parameter element (exactly one)
Element named <frequencies> containing:
- FrequencyModel element (exactly one)

Example:

<gtrCovarionModel>
 <hiddenClassRates>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix7"/>
 </hiddenClassRates>
 <switchingRates>
   <maskedParameter idref="maskedParameter2"/>
 </switchingRates>
 <frequencies>
   <frequencyModel idref="frequencyModel3"/>
 </frequencies>
</gtrCovarionModel>

`<gtrModel>` element

A general reversible model of nucleotide sequence substitution.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <rateAC> containing:
- Variable element (exactly one)
Element named <rateAG> containing:
- Variable element (exactly one)
Element named <rateAT> containing:
- Variable element (exactly one)
Element named <rateCG> containing:
- Variable element (exactly one)
Element named <rateCT> containing:
- Variable element (exactly one)
Element named <rateGT> containing:
- Variable element (exactly one)

Example:

<!-- A general time reversible model for DNA.                                          -->
<!-- This element must have parameters for exactly five of the six rates               -->
<!-- The sixth rate has an implied value of 1.0 and all other rates are relative to it -->
<!-- This example parameterizes the rate matrix relative to the A<->G transition       -->
<gtrModel id="gtr1">
	<frequencies> <frequencyModel idref="freqs"/> </frequencies>
	<rateAC> <parameter id="rateAC" value="1.0"/> </rateAC>
	<rateAT> <parameter id="rateAT" value="1.0"/> </rateAT>
	<rateCG> <parameter id="rateCG" value="1.0"/> </rateCG>
	<rateCT> <parameter id="rateCT" value="1.0"/> </rateCT>
	<rateGT> <parameter id="rateGT" value="1.0"/> </rateGT>
</gtrModel>

`<hiddenNucleotides>` element

A nucleotide data type that allows hidden substitution classes

The element takes following attributes:

Attribute classCount is Integer

Example:

<hiddenNucleotides classCount="1"/>

`<hierarchicalPartitionLikelihood>` element

null

The element has the following contents:

ARGModel element (exactly one)

Example:

<hierarchicalPartitionLikelihood>
  <argTreeModel idref="argTreeModel3"/>
</hierarchicalPartitionLikelihood>

`<HKYModel>` element

This element represents an instance of the HKY85 (Hasegawa, Kishino & Yano, 1985) model of nucleotide evolution.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <kappa> containing:
- Variable element (exactly one)

Example:

<HKYModel>
 <frequencies>
   <frequencyModel idref="frequencyModel7"/>
 </frequencies>
 <kappa>
   <compoundParameter idref="compoundParameter10"/>
 </kappa>
</HKYModel>

`<hypermutantAlignment>` element

Converts an alignment so that 'A's at specific APOBEC targeted contexts are set to an A/G ambiguity code.

The element takes following attributes:

Attribute type is String
The type of APOBEC molecule being modelled

The element has the following contents:

Alignment element (exactly one)

Example:

<hypermutantAlignment type="hA3G">
  <convert idref="convert4"/>
</hypermutantAlignment>

`<hypermutantErrorModel>` element

This element returns a model that allows for APOBEC-type RNA editing.

The element takes following attributes:

Attribute (optional) unlinkedRates is Boolean

The element has the following contents:

HypermutantAlignment element (exactly one)
Element named <hypermutationRate> containing:
- Parameter element (exactly one)
  
  The hypermutation rate per target site per sequence
Element named <hypermutationIndicators> containing:
- Parameter element (exactly one)
  
  A binary indicator of whether the sequence is hypermutated

Example:

<hypermutantErrorModel unlinkedRates="true">
  ERROR!
 <hypermutationRate>
   <compoundParameter idref="compoundParameter3"/>
 </hypermutationRate>
 <hypermutationIndicators>
   <diagonalMatrix idref="diagonalMatrix4"/>
 </hypermutationIndicators>
</hypermutantErrorModel>

`<ibdReporter>` element

This element represents a reporter for expected number of tips ibd.

The element has the following contents:

TreeModel element (exactly one)
BranchRateModel element (zero or one)
AbstractSubstitutionModel element (exactly one)
Parameter element (exactly one)

Example:

<ibdReporter>
  <treeModel idref="treeModel4"/>
  <lewisMk idref="lewisMk5"/>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
</ibdReporter>

`<ImportanceNarrowExchange>` element

This element represents a swap operator. This operator swaps a random subtree with its uncle.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) epsilon is Double

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)

Example:

<ImportanceNarrowExchange weight="1.0" epsilon="1.0">
  <ascertainedPatterns idref="ascertainedPatterns6"/>
  <treeModel idref="treeModel5"/>
</ImportanceNarrowExchange>

`<ImportancePruneAndRegraft>` element

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.

The element takes following attributes:

Attribute weight is Double
Attribute samples is Integer

The element has the following contents:

TreeModel element (exactly one)

Example:

<ImportancePruneAndRegraft weight="1.0" samples="1">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel9"/>
</ImportancePruneAndRegraft>

`<ImportanceSubtreeSwap>` element

This element represents a importance guided subtree swap operator. This operator swaps a random subtree with a second subtree guided by an importance distribution.

The element takes following attributes:

Attribute weight is Double
Attribute samples is Integer

The element has the following contents:

TreeModel element (exactly one)

Example:

<ImportanceSubtreeSwap weight="1.0" samples="1">
  <treeModel idref="treeModel2"/>
</ImportanceSubtreeSwap>

`<inhibitionLikelihood>` element

Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.

The element has the following contents:

TreeModel element (exactly one)
MatrixParameter element (exactly one)
Element named <precision> containing:
- Parameter element (exactly one)

Example:

<inhibitionLikelihood>
  <treeModel idref="treeModel10"/>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix8"/>
 <precision>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix7"/>
 </precision>
</inhibitionLikelihood>

`<integer>` element

returns an Integer. If a prompt attribute exists then the user is prompted for input, otherwise the character contents of the element are returned as an Integer.

The element has the following contents:

One of:
- Attribute prompt is String
  A message displayed to the user when entering a value for this integer
- Integer element (exactly one)

Example:

<integer>
  1
</integer>

`<traitGibbsOperator>` element

This element returns a multivariate Gibbs operator on traits for possible all nodes.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) onlyInternalNodes is Boolean
Attribute (optional) onlyTipsWithPriors is Boolean

The element has the following contents:

SampledMultivariateTraitLikelihood element (exactly one)
MultivariateDistributionLikelihood elements (zero or more)
Element named <rootPrior> containing:
- MultivariateDistributionLikelihood element (exactly one)
GeoSpatialCollectionModel element (zero or one)

Example:

<traitGibbsOperator weight="1.0" onlyInternalNodes="true" onlyTipsWithPriors="true">
  ERROR!
</traitGibbsOperator>

`<invgammaPrior>` element

Calculates the prior probability of some data under a given inverse gamma distribution.

The element takes following attributes:

Attribute shape is Double
Attribute scale is Double
Attribute offset is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<invgammaPrior shape="1.0" scale="1.0" offset="1.0">
  <exponentialStatistic idref="exponentialStatistic1"/>
  <gmrfHeightsStatistic idref="gmrfHeightsStatistic3"/>
</invgammaPrior>

`<inverseGaussianDistributionModel>` element

Describes a inverse gaussian distribution with a given mean and shape (or standard deviation) that can be used in a distributionLikelihood element

The element takes following attributes:

Attribute (optional) offset is Double

The element has the following contents:

Element named <mean> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

Element named <stdev> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

Element named <shape> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

Example:

<inverseGaussianDistributionModel offset="1.0">
 <mean>
   <diagonalMatrix idref="diagonalMatrix1"/>
 </mean>
</inverseGaussianDistributionModel>

`<invgammaPrior>` element

Calculates the prior probability of some data under a given inverse gamma distribution.

The element takes following attributes:

Attribute shape is Double
Attribute scale is Double
Attribute offset is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<invgammaPrior shape="1.0" scale="1.0" offset="1.0">
  <speciesTreeStatistic idref="speciesTreeStatistic6"/>
  <statistic idref="statistic8"/>
  <monophylyStatistic idref="monophylyStatistic8"/>
  <maskedParameter idref="maskedParameter4"/>
</invgammaPrior>

`<oneOnXPrior>` element

Calculates the (improper) prior proportional to Prod_i (1/x_i) for the given statistic x.

The element has the following contents:

One of:
- Statistic elements (one or more)
- Element named <data> containing:
  - Statistic elements (one or more)

Example:

<oneOnXPrior>
 <data>
   <matrixParameter idref="matrixParameter2"/>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix9"/>
   <test idref="test5"/>
 </data>
</oneOnXPrior>

`<jointOperator>` element

This element represents an arbitrary list of operators; only the first is optimizable

The element takes following attributes:

Attribute weight is Double
Attribute (optional) targetAcceptance is Double

The element has the following contents:

SimpleMCMCOperator elements (one or more)

Example:

<jointOperator weight="1.0" targetAcceptance="1.0">
  <argSubtreeSlide idref="argSubtreeSlide7"/>
  <jointOperator idref="jointOperator8"/>
  <argPartitionOperator idref="argPartitionOperator7"/>
</jointOperator>

`<kStateType>` element

Parser for k-state model.

The element takes following attributes:

Attribute stateCount is Integer
Attribute (optional) startWith is Integer

Example:

<kStateType stateCount="1" startWith="1"/>

`<laplacePrior>` element

Calculates the prior probability of some data under a given laplace distribution.

The element takes following attributes:

Attribute mean is Double
Attribute stdev is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<laplacePrior mean="1.0" stdev="1.0">
  <reciprocalStatistic idref="reciprocalStatistic8"/>
  <correlation idref="correlation3"/>
  <designMatrix idref="designMatrix6"/>
  <treeMetricStatistic idref="treeMetricStatistic10"/>
</laplacePrior>

`<lewisMk>` element

A parser for Lewis' Mk model

The element takes following attributes:

Attribute (optional) totalOrder is Boolean

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <order> containing:
- Attribute state is String
- Attribute adjacentTo is String

Example:

<lewisMk totalOrder="true">
 <frequencies>
   <frequencyModel idref="frequencyModel5"/>
 </frequencies>
</lewisMk>

`<compoundLikelihood>` element

A likelihood function which is simply the product of its component likelihood functions.

The element takes following attributes:

Attribute (optional) threads is Integer

The element has the following contents:

Likelihood elements (one or more)

Example:

<compoundLikelihood threads="1">
  <arbitraryBranchRates idref="arbitraryBranchRates8"/>
</compoundLikelihood>

`<lineageCountStatistic>` element

The element has the following contents:

OldAbstractCoalescentLikelihood element (exactly one)

Example:

<lineageCountStatistic>
  <gmrfSkyrideLikelihood idref="gmrfSkyrideLikelihood10"/>
</lineageCountStatistic>

`<LINEARBIASModel>` element

This element represents an instance of the stepwise mutation model of microsatellite evolution.

The element takes following attributes:

Attribute (optional) estimateSubmodelParameters is String
whether or not to esitmate the parameters of the submodel
Attribute (optional) logistics is Boolean
Attribute (optional) isSubmodel is Boolean

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <Submodel> containing:
- OnePhaseModel element (exactly one)
Microsatellite element (exactly one)
Element named <BiasConstant> containing:
- Parameter element (exactly one)
Element named <BiasLinear> containing:
- Parameter element (exactly one)

Example:

<LINEARBIASModel estimateSubmodelParameters="foo" logistics="true" isSubmodel="true">
 <Submodel>
   <LINEARBIASModel idref="LINEARBIASModel8"/>
 </Submodel>
  <microsatellite idref="microsatellite10"/>
</LINEARBIASModel>

`<localClockModel>` element

This element returns a branch rate model that adds a delta to each terminal branch length.

The element has the following contents:

TreeModel element (exactly one)
Element named <rate> containing:
- Parameter element (exactly one)
  
  The molecular evolutionary rate parameter
Element named <externalBranches> containing:
- Attribute (optional) relative is Boolean
- Taxa element (exactly one)
  A local clock that will be applied only to the external branches for these taxa
- Parameter element (exactly one)
  The rate parameter
Element named <clade> containing:
- Attribute (optional) relative is Boolean
- Attribute (optional) includeStem is Boolean
  determines whether or not the stem branch above this clade is included in the siteModel (default false).
- Attribute (optional) excludeClade is Boolean
  determines whether to exclude actual branches of the clade from the siteModel (default false).
- Taxa element (exactly one)
  A set of taxa which defines a clade to apply a different site model to
- Parameter element (exactly one)
  The rate parameter
Element named <backbone> containing:
- Attribute (optional) relative is Boolean
- Taxa element (exactly one)
  A local clock that will be applied only to the 'backbone' branches defined by these taxa
- Parameter element (exactly one)
  The rate parameter

Example:

<localClockModel>
  <treeModel idref="treeModel2"/>
 <rate>
   <matrixParameter idref="matrixParameter9"/>
 </rate>
 <backbone relative="true">
   <taxa idref="taxa2"/>
   <matrixParameter idref="matrixParameter7"/>
 </backbone>
 <backbone relative="true">
   <taxa idref="taxa4"/>
   <designMatrix idref="designMatrix5"/>
 </backbone>
</localClockModel>

`<location>` element

Specifies a location with an optional longitude and latitude

The element takes following attributes:

Attribute (optional) description is String
A description of this location
Attribute (optional) longitude is String
The longitude in degrees, minutes, seconds or decimal degrees
Attribute (optional) latitude is String
The latitude in degrees, minutes, seconds or decimal degrees

Example:

<location description="foo" longitude="foo" latitude="foo"/>

`<log>` element

Logs one or more items at a given frequency to the screen or to a file

The element takes following attributes:

Attribute logEvery is Integer
Attribute (optional) overwrite is Boolean
Attribute (optional) fileName is String
The name of the file to send log output to. If no file name is specified then log is sent to standard output
Attribute (optional) title is String
The title of the log

The element has the following contents:

At least one of:**Columns elements (one or more)
- Loggable elements (one or more)
- Object elements (one or more)

Example:

<log logEvery="1" overwrite="true" fileName="foo" title="foo">
  <column idref="column7"/>
  <column idref="column10"/>
  <column idref="column8"/>
  <column idref="column9"/>
</log>

`<logAllTraits>` element

null

The element has the following contents:

TreeModel element (exactly one)
The tree which is to be logged

Example:

<logAllTraits>
  <treeModel idref="treeModel9"/>
</logAllTraits>

`<logArg>` element

Logs an ARG to a file

The element takes following attributes:

Attribute logEvery is Integer
Attribute format is String
The type logger's output type
Attribute (optional) fileName is String
The name of the file to send log output to. If no file name is specified then log is sent to standard output
Attribute (optional) title is String
The title of the log

The element has the following contents:

ARGModel element (exactly one)
The ARG which is to be logged

Example:

<!-- The logArg element takes an argModel to be logged -->
<logArg logEvery="100" fileName="log.args">
	<argModel idref="treeModel1"/>
</logArg>

`<logArgTree>` element

Logs a tree to a file

The element takes following attributes:

Attribute logEvery is Integer
Attribute partition is Integer
Attribute (optional) fileName is String
The name of the file to send log output to. If no file name is specified then log is sent to standard output
Attribute (optional) title is String
The title of the log
Attribute (optional) nexusFormat is Boolean
Whether to use the NEXUS format for the tree log
Attribute (optional) branchLengths is String
What units should the branch lengths be in

The element has the following contents:

ARGModel element (exactly one)
The ARG which is to be logged
BranchRateModel element (zero or one)
ColourSamplerModel element (zero or one)
Likelihood element (zero or one)

Example:

<!-- The logArgTree element takes an argTreeModel to be logged -->
<logArgTree logEvery="100" fileName="log.trees" nexusFormat="true">
	<treeModel idref="treeModel1"/>
</logArgTree>

`<logarithmStatistic>` element

This element returns a statistic that is the element-wise natural logarithm of the child statistic.

The element takes following attributes:

Attribute (optional) base is Double
An optional base for the logarithm (default is the natural logarithm, base e)

The element has the following contents:

Statistic element (exactly one)

Example:

<logarithmStatistic base="1.0">
  <compatibilityStatistic idref="compatibilityStatistic2"/>
</logarithmStatistic>

`<logarithmStatistic>` element

This element returns a statistic that is the element-wise natural logarithm of the child statistic.

The element takes following attributes:

Attribute (optional) base is Double
An optional base for the logarithm (default is the natural logarithm, base e)

The element has the following contents:

Statistic element (exactly one)

Example:

<logarithmStatistic base="1.0">
  <nodeHeightsStatistic idref="nodeHeightsStatistic8"/>
</logarithmStatistic>

`<logFileTrace>` element

reconstruct population graph from variable dimension run.

The element takes following attributes:

Attribute fileName is String
trace log.
Attribute (optional) burnIn is Integer
The number of states (not sampled states, but actual states) that are discarded from the beginning of the trace before doing the analysis

Example:

<logFileTrace fileName="foo" burnIn="1"/>

`<loggableStatistic>` element

Allows you to choose specific dimensions of a given statistic

The element has the following contents:

Loggable element (exactly one)

Example:

<loggableStatistic>
  <parsimonyStatistic idref="parsimonyStatistic3"/>
</loggableStatistic>

`<logisticGrowth>` element

Logistic growth demographic model.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <populationSize> containing:
- Parameter element (exactly one)
  
  This parameter represents the carrying capacity (maximum population size). If the shape is very large then the current day population size will be very close to the carrying capacity.
One of:
- Element named <growthRate> containing:
  - Parameter element (exactly one)
    
    This parameter determines the rate of growth during the exponential phase. See exponentialGrowth for details.
- Element named <doublingTime> containing:
  - Parameter element (exactly one)
    
    This parameter determines the doubling time at peak growth rate.

Element named <t50> containing:
- Parameter element (exactly one)
  
  This parameter represents the time in the past when the population had half of the carrying capacity (population size). It is therefore a positive number with the same units as divergence times. A scale operator is recommended with a starting value near zero. A lower bound of zero should be employed and an upper bound is required!

Example:

<logisticGrowth units="substitutions">
 <populationSize>
   <designMatrix idref="designMatrix10"/>
 </populationSize>
 <doublingTime>
   <designMatrix idref="designMatrix2"/>
 </doublingTime>
 <t50>
   <maskedParameter idref="maskedParameter5"/>
 </t50>
</logisticGrowth>

`<logML>` element

Logs one or more items every time the given likelihood improves

The element takes following attributes:

Attribute (optional) logEvery is Integer

The element has the following contents:

Element named <ml> containing:
- Likelihood element (exactly one)
At least one of:**Columns elements (one or more)
- Loggable elements (one or more)

Example:

<logML logEvery="1">
 <ml>
   <ovariableSkyLineLikelihood idref="ovariableSkyLineLikelihood4"/>
 </ml>
  <column idref="column3"/>
  <column idref="column4"/>
</logML>

`<logNormalDistributionModel>` element

Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element

The element takes following attributes:

Attribute (optional) meanInRealSpace is Boolean
Attribute (optional) offset is Double

The element has the following contents:

Element named <mean> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

One of:
- Element named <stdev> containing:
  - One of:
    - Parameter element (exactly one)
    - Double element (exactly one)

- Element named <precision> containing:
  - One of:
    - Parameter element (exactly one)
    - Double element (exactly one)

Example:

<logNormalDistributionModel meanInRealSpace="true" offset="1.0">
 <mean>
   1.0
 </mean>
 <precision>
   <diagonalMatrix idref="diagonalMatrix7"/>
 </precision>
</logNormalDistributionModel>

`<logNormalPrior>` element

Calculates the prior probability of some data under a given lognormal distribution.

The element takes following attributes:

Attribute mean is Double
Attribute stdev is Double
Attribute (optional) offset is Double
Attribute (optional) meanInRealSpace is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<logNormalPrior mean="1.0" stdev="1.0" offset="1.0" meanInRealSpace="true">
  <rateCovarianceStatistic idref="rateCovarianceStatistic1"/>
  <lineageCountStatistic idref="lineageCountStatistic1"/>
  <speciesTreeStatistic idref="speciesTreeStatistic3"/>
  <expressionStatistic idref="expressionStatistic1"/>
</logNormalPrior>

`<logRandomWalkOperator>` element

This element returns a scale operator on a given parameter.

The element takes following attributes:

Attribute window is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) scaleAll is Boolean
Attribute (optional) scaleAllIndependently is Boolean

The element has the following contents:

Parameter element (exactly one)

Example:

<logRandomWalkOperator window="1.0" weight="1.0" autoOptimize="true" scaleAll="true" scaleAllIndependently="true">
  <parameter idref="parameter7"/>
</logRandomWalkOperator>

`<logTree>` element

Logs a tree to a file

The element takes following attributes:

Attribute (optional) logEvery is Integer
Attribute (optional) overwrite is Boolean
Attribute (optional) fileName is String
The name of the file to send log output to. If no file name is specified then log is sent to standard output
Attribute (optional) title is String
The title of the log
Attribute (optional) nexusFormat is Boolean
Whether to use the NEXUS format for the tree log
Attribute (optional) sortTranslationTable is Boolean
Whether the translation table is sorted.
Attribute (optional) branchLengths is String
What units should the branch lengths be in
Attribute (optional) mapNamesToNumbers is Boolean
Attribute (optional) dp is Integer

The element has the following contents:

Tree element (exactly one)
The tree which is to be logged
BranchRates element (zero or one)
TreeColouringProvider element (zero or one)
Likelihood element (zero or one)
TreeAttributeProvider elements (zero or more)
TreeTraitProvider elements (zero or more)
TreeLogger$LogUpon element (zero or one)

Example:

<!-- The logTree element takes a treeModel to be logged -->
<logTree logEvery="100" fileName="log.trees" nexusFormat="true">
	<treeModel idref="treeModel1"/>
</logTree>

`<marginalLikelihoodAnalysis>` element

Performs a trace analysis. Estimates the mean of the various statistics in the given log file.

The element takes following attributes:

Attribute fileName is String
The traceName of a BEAST log file (can not include trees, which should be logged separately
Attribute (optional) burnIn is Integer

The element has the following contents:

Element named <likelihoodColumn> containing:
- Attribute name is String
  The column name

Example:

<marginalLikelihoodAnalysis fileName="foo" burnIn="1">
 <likelihoodColumn name="foo"/>
</marginalLikelihoodAnalysis>

`<ancestralTreeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) storePartials is Boolean
Attribute (optional) tagName is String
Attribute (optional) forceRescaling is Boolean
Attribute (optional) useMAP is Boolean
Attribute (optional) useMarginalLikelihood is Boolean

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
SubstitutionModel element (exactly one)

Example:

<ancestralTreeLikelihood useAmbiguities="true" storePartials="true" tagName="foo" forceRescaling="true" useMAP="true" useMarginalLikelihood="true">
  <sequenceSimulator idref="sequenceSimulator8"/>
  <treeModel idref="treeModel3"/>
  <DirichletSiteModel idref="DirichletSiteModel9"/>
  <aminoAcidModel idref="aminoAcidModel2"/>
</ancestralTreeLikelihood>

`<maskedParameter>` element

A masked parameter.

The element takes following attributes:

Attribute (optional) complement is Boolean

The element has the following contents:

Parameter element (exactly one)
Element named <mask> containing:
- Parameter element (exactly one)

Example:

<maskedParameter complement="true">
  <maskedParameter idref="maskedParameter9"/>
 <mask>
   <designMatrix idref="designMatrix10"/>
 </mask>
</maskedParameter>

`<matrixParameter>` element

A matrix parameter constructed from its component parameters.

The element has the following contents:

Parameter elements (one or more)

Example:

<matrixParameter>
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix4"/>
</matrixParameter>

`<mcmc>` element

This element returns an MCMC chain and runs the chain as a side effect.

The element takes following attributes:

Attribute chainLength is Integer
Attribute (optional) autoOptimize is Boolean
Attribute (optional) autoOptimizeDelay is Integer
Attribute (optional) preBurnin is Integer
Attribute (optional) temperature is Double
Attribute (optional) fullEvaluation is Integer
Attribute (optional) minOpsFullEvaluations is Integer
Attribute (optional) spawn is Boolean
Attribute (optional) name is String
Attribute (optional) operatorAnalysis is String

The element has the following contents:

OperatorSchedule element (exactly one)
Likelihood element (exactly one)
Logger elements (one or more)

Example:

<mcmc chainLength="1" autoOptimize="true" autoOptimizeDelay="1" preBurnin="1" temperature="1.0" fullEvaluation="1" minOpsFullEvaluations="1" spawn="true" name="foo" operatorAnalysis="foo">
  <operators idref="operators9"/>
  <booleanLikelihood idref="booleanLikelihood8"/>
  <log idref="log4"/>
</mcmc>

`<meanStatistic>` element

This element returns a statistic that is the mean of the child statistics.

The element has the following contents:

Statistic elements (one or more)

Example:

<meanStatistic>
  <meanStatistic idref="meanStatistic9"/>
  <notStatistic idref="notStatistic8"/>
  <treeLengthStatistic idref="treeLengthStatistic7"/>
</meanStatistic>

`<mergePatterns>` element

A weighted list of the unique site patterns (unique columns) in an alignment.

The element has the following contents:

SiteList elements (one or more)

Example:

<mergePatterns>
  <convert idref="convert2"/>
  <hypermutantAlignment idref="hypermutantAlignment9"/>
</mergePatterns>

`<microsatellite>` element

This element represents a microsatellite data type.

The element has the following contents:

All of:**Attribute min is Integer
- Attribute max is Integer
- Attribute unitLength is Integer

Example:

<microsatellite min="0" max="20" unitLength="2"/>

`<microsatellitePattern>` element

This element represents a microsatellite pattern.

The element takes following attributes:

Attribute id is String
the name of the locus
Attribute (optional) printDetails is Boolean
Attribute (optional) printMsatPatContent is Boolean

The element has the following contents:

Taxa element (exactly one)
Microsatellite element (exactly one)
Element named <microsatSeq> containing:
- String element (exactly one)
  A string of numbers representing the microsatellite lengths for a locus

Example:

<microsatellitePattern id="foo" printDetails="true" printMsatPatContent="true">
  <taxa idref="taxa9"/>
  <microsatellite idref="microsatellite7"/>
 <microsatSeq>
   1,2,3,4,5,67,100
 </microsatSeq>
</microsatellitePattern>

`<microsatelliteSamplerTreeLikelihood>` element

this parser returns an object of the TreeMicrosatelliteSamplerLikelihood class

The element has the following contents:

MicrosatelliteSamplerTreeModel element (exactly one)
MicrosatelliteModel element (exactly one)
Element named <mutationRate> containing:
- Parameter element (exactly one)
BranchRateModel element (zero or one)

Example:

<microsatelliteSamplerTreeLikelihood>
  <microsatelliteSamplerTreeModel idref="microsatelliteSamplerTreeModel9"/>
  <LINEARBIASModel idref="LINEARBIASModel8"/>
</microsatelliteSamplerTreeLikelihood>

`<microsatelliteSamplerTreeModel>` element

This parser returns a TreeMicrosatelliteSamplerModel Object

The element takes following attributes:

Attribute (optional) provideInternalNodeValues is Boolean

The element has the following contents:

Element named <tree> containing:
- TreeModel element (exactly one)
Element named <internalValues> containing:
- Parameter element (exactly one)
Element named <externalValues> containing:
- Patterns element (exactly one)

Example:

<microsatelliteSamplerTreeModel provideInternalNodeValues="true">
 <tree>
   <treeModel idref="treeModel10"/>
 </tree>
 <internalValues>
   <matrixParameter idref="matrixParameter5"/>
 </internalValues>
 <externalValues>
   <microsatellitePattern idref="microsatellitePattern10"/>
 </externalValues>
</microsatelliteSamplerTreeModel>

`<microsatelliteSimulator>` element

This parser facilliates simulation of microsatellites given a tree and infinitesimal rate model

The element has the following contents:

Microsatellite element (exactly one)
Taxa element (exactly one)
Tree element (exactly one)
MicrosatelliteModel element (exactly one)
BranchRateModel element (zero or one)

Example:

<microsatelliteSimulator>
  <microsatellite idref="microsatellite2"/>
  <taxa idref="taxa4"/>
  <neighborJoiningTree idref="neighborJoiningTree6"/>
  <LINEARBIASModel idref="LINEARBIASModel3"/>
</microsatelliteSimulator>

`<microsatUpDownOperator>` element

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.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

Element named <up> containing:
- Parameter element (zero or one)
Element named <down> containing:
- Parameter element (zero or one)

Example:

<microsatUpDownOperator scaleFactor="1.0" weight="1.0" autoOptimize="true">
 <up/>
 <up/>
 <down/>
 <down/>
 <down/>
</microsatUpDownOperator>

`<mixedDistributionLikelihood>` element

Calculates the likelihood of some data given some mix of parametric distributions.

The element has the following contents:

Element named <distribution0> containing:
- ParametricDistributionModel element (exactly one)
Element named <distribution1> containing:
- ParametricDistributionModel element (exactly one)
Element named <data> containing:
- Statistic element (exactly one)
Element named <indicators> containing:
- Statistic element (exactly one)

Example:

<mixedDistributionLikelihood>
 <distribution0>
   <gammaDistributionModel idref="gammaDistributionModel9"/>
 </distribution0>
 <distribution1>
   <normalDistributionModel idref="normalDistributionModel5"/>
 </distribution1>
 <data>
   <gmrfHeightsStatistic idref="gmrfHeightsStatistic6"/>
 </data>
 <indicators>
   <monotonicStatistic idref="monotonicStatistic9"/>
 </indicators>
</mixedDistributionLikelihood>

`<mixtureCartogramDiffusionModel>` element

Describes a bivariate diffusion process using cartogram distances.

The element has the following contents:

Parameter element (exactly one)
Element named <mixture> containing:
- Parameter element (exactly one)
Element named <boundingBox> containing:
- Attribute minX is Double
- Attribute maxX is Double
- Attribute minY is Double
- Attribute maxY is Double

Example:

<mixtureCartogramDiffusionModel>
  <maskedParameter idref="maskedParameter7"/>
 <mixture>
   <maskedParameter idref="maskedParameter6"/>
 </mixture>
 <boundingBox minX="1.0" maxX="1.0" minY="1.0" maxY="1.0"/>
</mixtureCartogramDiffusionModel>

`<mixtureModel>` element

This element represents a discrete mixture of tree likelihood models.

The element takes following attributes:

Attribute (optional) normalize is Boolean

The element has the following contents:

Likelihood elements ( or more)
Parameter element (exactly one)

Example:

<mixtureModel normalize="true">
  <cachedPrior idref="cachedPrior7"/>
  <dirichletPrior idref="dirichletPrior1"/>
  <diagonalMatrix idref="diagonalMatrix7"/>
</mixtureModel>

`<mixtureModelBranchRates>` element

This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.

The element takes following attributes:

Attribute (optional) singleRootRate is Boolean
Whether only a single rate should be used for the two children branches of the root
Attribute (optional) normalize is Boolean
Whether the mean rate has to be normalized to a particular value
Attribute (optional) normalizeBranchRateTo is Double
The mean rate to normalize to, if normalizing
Attribute (optional) useQuantilesForRates is Boolean
Whether or not to use quantiles to represent rates. If false then rates are not drawn specifically from any of the distributions

The element has the following contents:

TreeModel element (exactly one)
Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
  
  The distribution model for rates among branches
Element named <distributionIndex> containing:
- Parameter element (exactly one)
  
  Operator that switches between the distributions of the branch rate distribution model
Element named <rateCategoryQuantiles> containing:
- Parameter element (exactly one)
  
  The quantiles for

Example:

<mixtureModelBranchRates singleRootRate="true" normalize="true" normalizeBranchRateTo="1.0" useQuantilesForRates="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel6"/>
 <distribution>
   <uniformDistributionModel idref="uniformDistributionModel6"/>
 </distribution>
 <distribution>
   <uniformDistributionModel idref="uniformDistributionModel9"/>
 </distribution>
 <distribution>
   <uniformDistributionModel idref="uniformDistributionModel4"/>
 </distribution>
 <distributionIndex>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
 </distributionIndex>
 <rateCategoryQuantiles>
   <designMatrix idref="designMatrix2"/>
 </rateCategoryQuantiles>
</mixtureModelBranchRates>

`<mkSubstitutionModel>` element

An Mk model of substitution. This model can also accomodate arbitrary orderings of changes.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)

Example:

<mkSubstitutionModel>
 <frequencies>
   <frequencyModel idref="frequencyModel7"/>
 </frequencies>
</mkSubstitutionModel>

`<modelSpecificPseudoPrior>` element

Calculates the likelihood of some data given some parametric or empirical distribution.

Example:

<modelSpecificPseudoPrior/>

`<monophylyStatistic>` element

A statistic that returns true if a given set of taxa are monophyletic for a given tree

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic for the purpose of logging

The element has the following contents:

Tree element (exactly one)
Element named <mrca> containing:
- One of:
  - Taxon elements (one or more)
  - Taxa element (exactly one)

Element named <ignore> containing:
- One of:
  - Taxon elements (one or more)
  - Taxa element (exactly one)

- An optional list of taxa to ignore from the test of monophyly

Example:

<monophylyStatistic name="foo">
  <newick idref="newick1"/>
 <mrca>
   <taxon idref="taxon9"/>
 </mrca>
</monophylyStatistic>

`<monotonicStatistic>` element

The element takes following attributes:

Attribute (optional) order is String
Attribute (optional) strictlyMonotic is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<monotonicStatistic order="foo" strictlyMonotic="true">
  <loggableStatistic idref="loggableStatistic6"/>
  <differenceStatistic idref="differenceStatistic7"/>
  <monotonicStatistic idref="monotonicStatistic10"/>
  <expressionStatistic idref="expressionStatistic8"/>
</monotonicStatistic>

`<mrcaTraitStatistic>` element

A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging
Attribute trait is String
The name of the trait (can be rate)
Attribute (optional) rate is Boolean

The element has the following contents:

TreeModel element (exactly one)
Element named <mrca> containing:
- Taxa element (exactly one)

Example:

<mrcaTraitStatistic name="foo" trait="foo" rate="true">
  <treeModel idref="treeModel5"/>
 <mrca>
   <taxa idref="taxa2"/>
 </mrca>
</mrcaTraitStatistic>

`<msatAvgSubsetModel>` element

This element represents an instance of the Microsatellite Averaging Model of microsatellite evolution.

The element takes following attributes:

Attribute (optional) logit is Boolean

The element has the following contents:

Microsatellite element (exactly one)
Element named <models> containing:
- Element named <model> containing:
  - Attribute binary is String
  - Attribute code is String
Element named <rateProps> containing:
- Element named <rateProp> containing:
  - Attribute inModels is Integer;
  - Parameter element (exactly one)
Element named <biasConsts> containing:
- Element named <biasConst> containing:
  - Attribute inModels is Integer;
  - Parameter element (exactly one)
Element named <biasLins> containing:
- Element named <biasLin> containing:
  - Attribute inModels is Integer;
  - Parameter element (exactly one)
Element named <geos> containing:
- Element named <geo> containing:
  - Attribute inModels is Integer;
  - Parameter element (exactly one)
Element named <modelChoose> containing:
- Parameter element (exactly one)
Element named <modelIndicator> containing:
- Parameter element (exactly one)

Example:

<msatAvgSubsetModel logit="true">
  <microsatellite idref="microsatellite3"/>
 <models>
  <model binary="foo" code="foo"/>
  <model binary="foo" code="foo"/>
 </models>
 <rateProps>
  <rateProp inModels="1 2 4 8">
    <diagonalMatrix idref="diagonalMatrix8"/>
  </rateProp>
  <rateProp inModels="1 2 4 8">
    <designMatrix idref="designMatrix7"/>
  </rateProp>
  <rateProp inModels="1 2 4 8">
    <maskedParameter idref="maskedParameter10"/>
  </rateProp>
 </rateProps>
 <biasConsts>
  <biasConst inModels="1 2 4 8">
    <designMatrix idref="designMatrix5"/>
  </biasConst>
  <biasConst inModels="1 2 4 8">
    <designMatrix idref="designMatrix6"/>
  </biasConst>
  <biasConst inModels="1 2 4 8">
    <matrixParameter idref="matrixParameter8"/>
  </biasConst>
 </biasConsts>
 <biasLins>
  <biasLin inModels="1 2 4 8">
    <maskedParameter idref="maskedParameter1"/>
  </biasLin>
 </biasLins>
 <geos>
  <geo inModels="1 2 4 8">
    <matrixParameter idref="matrixParameter10"/>
  </geo>
  <geo inModels="1 2 4 8">
    <compoundSymmetricMatrix idref="compoundSymmetricMatrix5"/>
  </geo>
 </geos>
 <modelChoose>
   <maskedParameter idref="maskedParameter7"/>
 </modelChoose>
 <modelIndicator>
   <duplicatedParameter idref="duplicatedParameter3"/>
 </modelIndicator>
</msatAvgSubsetModel>

`<msatModelSelectOperator>` element

This element returns a microsatellite averaging operator on a given parameter.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <modelChoose> containing:
- Parameter element (exactly one)
Element named <modelIndicators> containing:
- Parameter elements (one or more)

Example:

<msatModelSelectOperator weight="1.0">
 <modelChoose>
   <matrixParameter idref="matrixParameter2"/>
 </modelChoose>
 <modelIndicators>
   <duplicatedParameter idref="duplicatedParameter7"/>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix7"/>
 </modelIndicators>
</msatModelSelectOperator>

`<msatModelSwitchOperator>` element

This element returns a microsatellite averaging operator on a given parameter.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <modelChoose> containing:
- Parameter element (exactly one)
Element named <dependencies> containing:
- Parameter element (exactly one)

Example:

<msatModelSwitchOperator weight="1.0">
 <modelChoose>
   <diagonalMatrix idref="diagonalMatrix8"/>
 </modelChoose>
 <dependencies>
   <designMatrix idref="designMatrix8"/>
 </dependencies>
</msatModelSwitchOperator>

`<multiLociDistance>` element

Constructs a distance matrix from a pattern list or alignment

The element has the following contents:

DistanceMatrix elements (one or more)

Example:

<multiLociDistance>
  <distanceMatrix idref="distanceMatrix7"/>
  <distanceMatrix idref="distanceMatrix6"/>
</multiLociDistance>

`<multivariateDiffusionModel>` element

Describes a multivariate normal diffusion process.

The element has the following contents:

Element named <precisionMatrix> containing:
- MatrixParameter element (exactly one)

Example:

<multivariateDiffusionModel>
 <precisionMatrix>
   <matrixParameter idref="matrixParameter5"/>
 </precisionMatrix>
</multivariateDiffusionModel>

`<multivariateGammaPrior>` element

Calculates the likelihood of some data under a given multivariate-gamma distribution.

The element has the following contents:

One of:
- Element named <shapeParameter> containing:
  - Parameter element (exactly one)
- Element named <meanParameter> containing:
  - Parameter element (exactly one)

One of:
- Element named <scaleParameter> containing:
  - Parameter element (exactly one)
- Element named <coefficientOfVariation> containing:
  - Parameter element (exactly one)

Element named <data> containing:
- Parameter elements (one or more)

Example:

<multivariateGammaPrior>
 <meanParameter>
   <compoundParameter idref="compoundParameter10"/>
 </meanParameter>
 <coefficientOfVariation>
   <designMatrix idref="designMatrix10"/>
 </coefficientOfVariation>
 <data>
   <compoundParameter idref="compoundParameter4"/>
   <compoundParameter idref="compoundParameter6"/>
   <duplicatedParameter idref="duplicatedParameter4"/>
 </data>
</multivariateGammaPrior>

`<multivariateInverseWishartPrior>` element

Calculates the likelihood of some data under an Inverse-Wishart distribution.

The element takes following attributes:

Attribute df is Double

The element has the following contents:

Element named <scaleMatrix> containing:
- MatrixParameter element (exactly one)

Example:

<multivariateInverseWishartPrior df="1.0">
 <scaleMatrix>
   <diagonalMatrix idref="diagonalMatrix9"/>
 </scaleMatrix>
</multivariateInverseWishartPrior>

`<multivariateNormalPrior>` element

Calculates the likelihood of some data under a given multivariate-normal distribution.

The element has the following contents:

Element named <meanParameter> containing:
- Parameter element (exactly one)
Element named <precisionParameter> containing:
- MatrixParameter element (exactly one)
Element named <data> containing:
- Parameter elements (one or more)

Example:

<multivariateNormalPrior>
 <meanParameter>
   <maskedParameter idref="maskedParameter1"/>
 </meanParameter>
 <precisionParameter>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix4"/>
 </precisionParameter>
</multivariateNormalPrior>

`<multivariateOUModel>` element

Describes a multivariate OU process

The element has the following contents:

SubstitutionModel element (exactly one)
MatrixParameter element (exactly one)
Element named <data> containing:
- Parameter element (exactly one)
Element named <times> containing:
- Parameter element (exactly one)
Element named <design> containing:
- Parameter element (exactly one)
Element named <independentVariables> containing:
- MatrixParameter element (exactly one)

Example:

<multivariateOUModel>
  <substitutionEpochModel idref="substitutionEpochModel2"/>
  <diagonalMatrix idref="diagonalMatrix5"/>
 <data>
   <diagonalMatrix idref="diagonalMatrix5"/>
 </data>
 <times>
   <compoundParameter idref="compoundParameter6"/>
 </times>
 <design>
   <maskedParameter idref="maskedParameter4"/>
 </design>
</multivariateOUModel>

`<multivariateTDiffusionModel>` element

Describes a multivariate t-distribution diffusion process.

The element has the following contents:

Element named <precisionParameter> containing:
- Parameter element (exactly one)
Element named <dfParameter> containing:
- Parameter element (exactly one)

Example:

<multivariateTDiffusionModel>
 <precisionParameter>
   <designMatrix idref="designMatrix1"/>
 </precisionParameter>
 <dfParameter>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix6"/>
 </dfParameter>
</multivariateTDiffusionModel>

`<multivariateTraitLikelihood>` element

Provides the likelihood of a continuous trait evolving on a tree by a given diffusion model.

The element takes following attributes:

Attribute traitName is String
The name of the trait for which a likelihood should be calculated
Attribute (optional) integrateInternalTraits is Boolean
Attribute (optional) cut is Double;
Attribute (optional) reportAsMultivariate is Boolean
Attribute (optional) useTreeLength is Boolean
Attribute (optional) scaleByTime is Boolean
Attribute (optional) reciprocalRates is Boolean
Attribute (optional) randomSample is Integer

The element has the following contents:

Element named <traitParameter> containing:
- Parameter element (exactly one)
MultivariateDistributionLikelihood element (zero or one)
Element named <conjugateRootPrior> containing:
- Element named <meanParameter> containing:
  - Parameter element (exactly one)
- Element named <priorSampleSize> containing:
  - Parameter element (exactly one)
MultivariateDiffusionModel element (exactly one)
TreeModel element (exactly one)
BranchRateModel element (zero or one)
Parameter element (zero or one)
Element named <randomize> containing:
- Attribute (optional) lower is Double
- Attribute (optional) upper is Double
- Parameter element (exactly one)
Element named <jitter> containing:
- Attribute window is Double;
- Attribute (optional) duplicatesOnly is Boolean
- Parameter element (exactly one)
Element named <check> containing:
- Parameter element (exactly one)

Example:

<multivariateTraitLikelihood traitName="foo" integrateInternalTraits="true" cut="0.5 1.0" reportAsMultivariate="true" useTreeLength="true" scaleByTime="true" reciprocalRates="true" randomSample="1">
 <traitParameter>
   <compoundParameter idref="compoundParameter6"/>
 </traitParameter>
  <greatCircleDiffusionModel idref="greatCircleDiffusionModel5"/>
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel5"/>
</multivariateTraitLikelihood>

`<multivariateWishartPrior>` element

Calculates the likelihood of some data under a Wishart distribution.

The element takes following attributes:

Attribute (optional) nonInformative is Boolean
Attribute (optional) df is Integer

The element has the following contents:

Element named <scaleMatrix> containing:
- MatrixParameter element (exactly one)
Element named <data> containing:
- MatrixParameter elements (one or more)

Example:

<multivariateWishartPrior nonInformative="true" df="1">
 <data>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix5"/>
   <matrixParameter idref="matrixParameter5"/>
 </data>
</multivariateWishartPrior>

`<MutationDeathModel>` element

This element represents an instance of the MutationDeath model of CTMC evolution with deletions.

The element has the following contents:

AbstractSubstitutionModel element (zero or one)
Parameter element (exactly one)
MutationDeathType element (exactly one)
Element named <mutationRate> containing:
- Parameter element (exactly one)

Example:

<MutationDeathModel>
  <designMatrix idref="designMatrix10"/>
  <extendedDataType idref="extendedDataType9"/>
</MutationDeathModel>

`<mvouOperator>` element

This element returns junk.

The element takes following attributes:

Attribute mixingFactor is Double
Attribute priorDf is Integer
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

MatrixParameter element (exactly one)

Example:

<mvouOperator mixingFactor="1.0" priorDf="1" weight="1.0" autoOptimize="true">
  <compoundSymmetricMatrix idref="compoundSymmetricMatrix9"/>
</mvouOperator>

`<narrowExchange>` element

This element represents a narrow exchange operator. This operator swaps a random subtree with its uncle.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeModel element (exactly one)

Example:

<narrowExchange weight="1.0">
  <treeModel idref="treeModel4"/>
</narrowExchange>

`<NearestNeighborInterchange>` element

This element represents a NNI operator. This operator swaps a random subtree with its uncle.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeModel element (exactly one)

Example:

<NearestNeighborInterchange weight="1.0">
  <treeModel idref="treeModel9"/>
</NearestNeighborInterchange>

`<negativeStatistic>` element

This element returns a statistic that is the element-wise negation of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<negativeStatistic>
  <argReassortmentNodeCount idref="argReassortmentNodeCount2"/>
</negativeStatistic>

`<negativeStatistic>` element

This element returns a statistic that is the element-wise negation of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<negativeStatistic>
  <externalLengthStatistic idref="externalLengthStatistic3"/>
</negativeStatistic>

`<negativeStatistic>` element

This element returns a statistic that is the element-wise negation of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<negativeStatistic>
  <argTotalLengthStatistic idref="argTotalLengthStatistic4"/>
</negativeStatistic>

`<neighborJoiningTree>` element

This element returns a neighbour-joining tree generated from the given distances.

The element has the following contents:

DistanceMatrix element (exactly one)

Example:

<neighborJoiningTree>
  <distanceMatrix idref="distanceMatrix5"/>
</neighborJoiningTree>

`<newARGEvent>` element

An operator that slides a subarg.

The element takes following attributes:

Attribute weight is Integer
Attribute size is Double
Attribute gaussian is Boolean
Attribute (optional) swapRates is Boolean
Attribute (optional) swapTraits is Boolean
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

ARGModel element (exactly one)

Example:

<newARGEvent weight="1" size="1.0" gaussian="true" swapRates="true" swapTraits="true" autoOptimize="true">
  <argTreeModel idref="argTreeModel9"/>
</newARGEvent>

`<newick>` element

Constructs a tree from a NEWICK format tree description

The element takes following attributes:

Attribute (optional) usingDates is Boolean
Attribute (optional) rescaleHeight is Double
Attempt to rescale the tree to the given root height
Attribute (optional) rescaleLength is Double
Attempt to rescale the tree to the given total length
Attribute (optional) units is String
The branch length units of this tree

The element has the following contents:

String element (exactly one)
The NEWICK format tree. Tip labels are taken to be Taxon IDs

Example:

<newick units="years"> ((A:1.0, B:1.0):1.0,(C:2.0, D:2.0):1.0); </newick>

`<node>` element

This element represents a node in a tree.

The element takes following attributes:

Attribute (optional) height is Double
the age of the node
Attribute (optional) rate is Double
the relative rate of evolution at this node - default is 1.0

The element has the following contents:

One of:
- Taxon element (exactly one)
  The taxon of this leaf node
- SimpleNode elements (exactly 2)
  The children of this internal node

Example:

<node height="1.0" rate="1.0">
  <node idref="node7"/>
  <node idref="node3"/>
</node>

`<nodeHeightsStatistic>` element

A statistic that returns the heights of each internal node in increasing order (or groups them by a group size parameter)

The element takes following attributes:

Attribute (optional) name is String

The element has the following contents:

TreeModel element (exactly one)
Parameter element (zero or one)

Example:

<nodeHeightsStatistic name="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel1"/>
</nodeHeightsStatistic>

`<nodePosteriorLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) allowMissingTaxa is Boolean

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
SubstitutionModel element (exactly one)

Example:

<nodePosteriorLikelihood useAmbiguities="true" allowMissingTaxa="true">
  <convert idref="convert4"/>
  <treeModel idref="treeModel3"/>
  <siteModel idref="siteModel7"/>
  <covarionModel idref="covarionModel10"/>
</nodePosteriorLikelihood>

`<nodeReHeight>` element

Specialized Species tree operator, transform tree without breaking embedding of gene trees.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

SpeciesBindings element (exactly one)
SpeciesTreeModel element (exactly one)

Example:

<nodeReHeight weight="1.0">
  <species idref="species1"/>
  <speciesTree idref="speciesTree3"/>
</nodeReHeight>

`<normalDistributionModel>` element

Describes a normal distribution with a given mean and standard deviation that can be used in a distributionLikelihood element

The element has the following contents:

Element named <mean> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

One of:
- Element named <stdev> containing:
  - One of:
    - Parameter element (exactly one)
    - Double element (exactly one)

- Element named <precision> containing:
  - One of:
    - Parameter element (exactly one)
    - Double element (exactly one)

Example:

<normalDistributionModel>
 <mean>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix10"/>
 </mean>
 <stdev>
   1.0
 </stdev>
</normalDistributionModel>

`<normalGammaPrecisionGibbsOperator>` element

This element returns a operator on the precision parameter of a normal model with gamma prior.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <likelihood> containing:
- DistributionLikelihood element (exactly one)
Element named <prior> containing:
- DistributionLikelihood element (exactly one)

Example:

<normalGammaPrecisionGibbsOperator weight="1.0">
 <likelihood>
   <cachedPrior idref="cachedPrior3"/>
 </likelihood>
 <prior>
   <distributionLikelihood idref="distributionLikelihood8"/>
 </prior>
</normalGammaPrecisionGibbsOperator>

`<normalNormalMeanGibbsOperator>` element

This element returns a operator on the mean parameter of a normal model with normal prior.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <likelihood> containing:
- DistributionLikelihood element (exactly one)
Element named <prior> containing:
- DistributionLikelihood element (exactly one)

Example:

<normalNormalMeanGibbsOperator weight="1.0">
 <likelihood>
   <twoPartDistribution idref="twoPartDistribution10"/>
 </likelihood>
 <prior>
   <twoPartDistribution idref="twoPartDistribution6"/>
 </prior>
</normalNormalMeanGibbsOperator>

`<normalPrior>` element

Calculates the prior probability of some data under a given normal distribution.

The element takes following attributes:

Attribute mean is Double
Attribute stdev is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<normalPrior mean="1.0" stdev="1.0">
  <logarithmStatistic idref="logarithmStatistic8"/>
  <rateCovarianceStatistic idref="rateCovarianceStatistic8"/>
  <monotonicStatistic idref="monotonicStatistic6"/>
  <argTotalLengthStatistic idref="argTotalLengthStatistic1"/>
</normalPrior>

`<notStatistic>` element

This element returns a statistic that is the element-wise inverse of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<notStatistic>
  <argReassortmentNodeCount idref="argReassortmentNodeCount5"/>
</notStatistic>

`<notStatistic>` element

This element returns a statistic that is the element-wise inverse of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<notStatistic>
  <argReassortmentNodeCount idref="argReassortmentNodeCount9"/>
</notStatistic>

`<oneOnXPrior>` element

Calculates the (improper) prior proportional to Prod_i (1/x_i) for the given statistic x.

The element has the following contents:

One of:
- Statistic elements (one or more)
- Element named <data> containing:
  - Statistic elements (one or more)

Example:

<oneOnXPrior>
  <argTreeCount idref="argTreeCount6"/>
  <treeShapeStatistics idref="treeShapeStatistics5"/>
</oneOnXPrior>

`<onePGammaDistributionModel>` element

A model of a one parameter gamma distribution.

The element has the following contents:

One of:
- Element named <shape> containing:
  - Double element (exactly one)
- Element named <shape> containing:
  - Parameter element (exactly one)

Example:

<onePGammaDistributionModel>
 <shape>
   <designMatrix idref="designMatrix5"/>
 </shape>
</onePGammaDistributionModel>

`<operators>` element

A simple operator scheduler

The element takes following attributes:

Attribute (optional) sequential is Boolean
Attribute (optional) optimizationSchedule is String

The element has the following contents:

MCMCOperator elements (one or more)

Example:

<operators sequential="true" optimizationSchedule="foo">
  <argSwapOperator idref="argSwapOperator8"/>
</operators>

`<optimizer>` element

This element returns a maximum likelihood heuristic optimizer and runs the optimization as a side effect.

The element takes following attributes:

Attribute chainLength is Integer

The element has the following contents:

OperatorSchedule element (exactly one)
Likelihood element (exactly one)
Logger elements (one or more)

Example:

<optimizer chainLength="1">
  <operators idref="operators7"/>
  <speciesCoalescent idref="speciesCoalescent4"/>
  <logArgTree idref="logArgTree6"/>
  <logArg idref="logArg2"/>
  <logML idref="logML6"/>
</optimizer>

`<Ornstein-Uhlenbeck>` element

The element takes following attributes:

Attribute (optional) logUnits is Boolean
Attribute (optional) normalize is Boolean

The element has the following contents:

One of:
- Element named <mean> containing:
  - Double element (exactly one)
- Element named <mean> containing:
  - Parameter element (exactly one)

One of:
- Element named <sigma> containing:
  - Double element (exactly one)
- Element named <sigma> containing:
  - Parameter element (exactly one)

One of:
- Element named <lambda> containing:
  - Double element (exactly one)
- Element named <lambda> containing:
  - Parameter element (exactly one)

VariableDemographicModel element (zero or one)
Element named <data> containing:
- Statistic element (exactly one)
Element named <times> containing:
- Statistic element (exactly one)

Example:

<Ornstein-Uhlenbeck logUnits="true" normalize="true">
 <mean>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix9"/>
 </mean>
 <sigma>
   1.0
 </sigma>
 <lambda>
   1.0
 </lambda>
</Ornstein-Uhlenbeck>

`<ovariableSkyLineLikelihood>` element

This element represents the likelihood of the tree given the population size vector.

The element takes following attributes:

Attribute (optional) type is Boolean
Attribute logUnits is Boolean

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <indicators> containing:
- Parameter element (exactly one)
Element named <populationTree> containing:
- TreeModel element (exactly one)

Example:

<ovariableSkyLineLikelihood type="true" logUnits="true">
 <populationSizes>
   <maskedParameter idref="maskedParameter1"/>
 </populationSizes>
 <indicators>
   <designMatrix idref="designMatrix4"/>
 </indicators>
 <populationTree>
   <treeModel idref="treeModel10"/>
 </populationTree>
</ovariableSkyLineLikelihood>

`<parameter>` element

A real-valued parameter of one or more dimensions.

The element takes following attributes:

Attribute (optional) value is Double;
Attribute (optional) dimension is Integer
Attribute (optional) upper is Double;
Attribute (optional) lower is Double;

The element has the following contents:

Element named <randomize> containing:
- Distribution element (exactly one)

Example:

<parameter value="0.5 1.0" dimension="1" upper="0.5 1.0" lower="0.5 1.0"/>

`<parsimonyStateStatistic>` element

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

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic for the purposes of logging

The element has the following contents:

TreeModel element (exactly one)
Element named <state> containing:
- Taxa element (exactly one)
Element named <mrca> containing:
- Taxa element (exactly one)

Example:

<parsimonyStateStatistic name="foo">
  <treeModel idref="treeModel6"/>
 <state>
   <taxa idref="taxa5"/>
 </state>
 <mrca>
   <taxa idref="taxa8"/>
 </mrca>
</parsimonyStateStatistic>

`<parsimonyStatistic>` element

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

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

TreeModel element (exactly one)
Element named <state> containing:
- Taxa element (exactly one)

Example:

<parsimonyStatistic name="foo">
  <treeModel idref="treeModel8"/>
 <state>
   <taxa idref="taxa2"/>
 </state>
</parsimonyStatistic>

`<partitionStatistic>` element

null

Example:

<partitionStatistic/>

`<patterns>` element

A weighted list of the unique site patterns (unique columns) in an alignment.

The element takes following attributes:

Attribute (optional) from is Integer
The site position to start at, default is 1 (the first position)
Attribute (optional) to is Integer
The site position to finish at, must be greater than from, default is length of given alignment
Attribute (optional) every is Integer
Determines how many sites are selected. A value of 3 will select every third site starting from from, default is 1 (every site)
Attribute (optional) strip is Boolean
Strip out completely ambiguous sites
Attribute (optional) unique is Boolean
Return a weight list of unique patterns

The element has the following contents:

Element named <taxonList> containing:
- TaxonList element (exactly one)
Alignment element (exactly one)

Example:

<patterns from="1" to="1" every="1" strip="true" unique="true">
  <hypermutantAlignment idref="hypermutantAlignment7"/>
</patterns>

`<patternSubSet>` element

A weighted list of the unique site patterns (unique columns) in an alignment.

The element takes following attributes:

Attribute (optional) subSet is Integer
Which subset of patterns to use (out of subSetCount)
Attribute (optional) subSetCount is Integer
The number of subsets

The element has the following contents:

SiteList element (exactly one)

Example:

<patternSubSet subSet="1" subSetCount="1">
  <alignment idref="alignment10"/>
</patternSubSet>

`<piecewisePopulation>` element

This element represents a piecewise population model

The element takes following attributes:

Attribute (optional) linear is Boolean

The element has the following contents:

One of:
- Element named <epochSizes> containing:
  - Parameter element (exactly one)
- All of:***Element named <populationSize> containing:
  - - Parameter element (exactly one)
  - Element named <growthRates> containing:
    - Parameter element (exactly one)

Element named <epochWidths> containing:
- Attribute widths is Double;

Example:

<piecewisePopulation linear="true">
 <epochSizes>
   <parameter idref="parameter2"/>
 </epochSizes>
 <epochWidths widths="0.5 1.0"/>
</piecewisePopulation>

`<poissonPartitionLikelihood>` element

null

The element takes following attributes:

Attribute mean is Double

The element has the following contents:

ARGModel element (exactly one)

Example:

<poissonPartitionLikelihood mean="1.0">
  <argTreeModel idref="argTreeModel6"/>
</poissonPartitionLikelihood>

`<poissonPrior>` element

Calculates the prior probability of some data under a given poisson distribution.

The element takes following attributes:

Attribute mean is Double
Attribute offset is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<poissonPrior mean="1.0" offset="1.0">
  <generalizedSkylinePopSizeStatistic idref="generalizedSkylinePopSizeStatistic8"/>
  <loggableStatistic idref="loggableStatistic4"/>
</poissonPrior>

`<polygon>` element

This element represents a polygon.

The element takes following attributes:

Attribute (optional) closed is Boolean
Attribute (optional) fillValue is Double

The element has the following contents:

One of:
- KMLCoordinates element (exactly one)
- Polygon2D element (exactly one)

Example:

<polygon closed="true" fillValue="1.0">
  <polygon idref="polygon1"/>
</polygon>

`<poolSwapOperator>` element

.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

ValuesPool element (exactly one)

Example:

<poolSwapOperator weight="1.0">
  ERROR!
</poolSwapOperator>

`<popGraph>` element

This element returns a statistic that is the population size at evenly spaced intervals over tree.

The element takes following attributes:

Attribute time is Double

The element has the following contents:

VariableDemographicModel element (exactly one)

Example:

<popGraph time="1.0">
  <variableDemographic idref="variableDemographic9"/>
</popGraph>

`<positiveDefiniteSubstitutionModel>` element

A general reversible model of sequence substitution for any data type with stochastic variable selection.

The element has the following contents:

MatrixParameter element (exactly one)

Example:

<positiveDefiniteSubstitutionModel>
  <designMatrix idref="designMatrix7"/>
</positiveDefiniteSubstitutionModel>

`<compoundLikelihood>` element

A likelihood function which is simply the product of its component likelihood functions.

The element takes following attributes:

Attribute (optional) threads is Integer

The element has the following contents:

Likelihood elements (one or more)

Example:

<compoundLikelihood threads="1">
  <booleanLikelihood idref="booleanLikelihood5"/>
  <ancestralTreeLikelihood idref="ancestralTreeLikelihood2"/>
</compoundLikelihood>

`<precisionGibbsOperator>` element

This element returns a multivariate normal random walk operator on a given parameter.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

AbstractMultivariateTraitLikelihood element (exactly one)
MultivariateDistributionLikelihood element (exactly one)

Example:

<precisionGibbsOperator weight="1.0">
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood4"/>
  <multivariateNormalPrior idref="multivariateNormalPrior10"/>
</precisionGibbsOperator>

`<compoundLikelihood>` element

A likelihood function which is simply the product of its component likelihood functions.

The element takes following attributes:

Attribute (optional) threads is Integer

The element has the following contents:

Likelihood elements (one or more)

Example:

<compoundLikelihood threads="1">
  <ancestralTreeLikelihood idref="ancestralTreeLikelihood1"/>
  <UCLikelihood idref="UCLikelihood6"/>
  <UCLikelihood idref="UCLikelihood4"/>
</compoundLikelihood>

`<productStatistic>` element

This element returns a statistic that is the product of the child statistics.

The element takes following attributes:

Attribute (optional) elementwise is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<productStatistic elementwise="true">
  <rateStatistic idref="rateStatistic4"/>
</productStatistic>

`<productStatistic>` element

This element returns a statistic that is the product of the child statistics.

The element takes following attributes:

Attribute (optional) elementwise is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<productStatistic elementwise="true">
  <differenceStatistic idref="differenceStatistic5"/>
  <reciprocalStatistic idref="reciprocalStatistic6"/>
  <matrixParameter idref="matrixParameter8"/>
</productStatistic>

`<property>` element

This element returns an object representing the named property of the given child object.

The element takes following attributes:

Attribute name is String
name of the property

The element has the following contents:

Object element (exactly one)

Example:

<property name="length">
  <uniformPartitionLikelihood idref="uniformPartitionLikelihood1"/>
</property>

`<randomDiscretizedBranchRates>` element

This element returns a random discretized relaxed clock model.The branch rates are drawn from a continuous parametric distribution.

The element takes following attributes:

Attribute (optional) singleRootRate is Boolean
Whether only a single rate should be used for the two children branches of the root
Attribute (optional) normalize is Boolean
Whether the mean rate has to be normalized to a particular value
Attribute (optional) normalizeBranchRateTo is Double
The mean rate to normalize to, if normalizing

The element has the following contents:

TreeModel element (exactly one)
Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
  
  The distribution model for rates among branches
Element named <rateCategoryQuantiles> containing:
- Parameter element (exactly one)
  
  The quantiles for

Example:

<randomDiscretizedBranchRates singleRootRate="true" normalize="true" normalizeBranchRateTo="1.0">
  <treeModel idref="treeModel9"/>
 <distribution>
   <inverseGaussianDistributionModel idref="inverseGaussianDistributionModel2"/>
 </distribution>
 <rateCategoryQuantiles>
   <parameter idref="parameter2"/>
 </rateCategoryQuantiles>
</randomDiscretizedBranchRates>

`<randomLocalClockModel>` element

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.

The element takes following attributes:

Attribute ratesAreMultipliers is Boolean

The element has the following contents:

TreeModel element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)
  
  The rate change indicators parameter
Element named <rates> containing:
- Parameter element (exactly one)
  
  The rates parameter
Element named <clockRate> containing:
- Parameter element (exactly one)
  
  The mean rate across all local clocks

Example:

<randomLocalClockModel ratesAreMultipliers="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel3"/>
 <rateIndicator>
   <designMatrix idref="designMatrix7"/>
 </rateIndicator>
 <rates>
   <duplicatedParameter idref="duplicatedParameter9"/>
 </rates>
</randomLocalClockModel>

`<randomLocalLogger>` element

A speciation model of a Yule process whose rate can evolve down the tree.

The element takes following attributes:

Attribute logEvery is Integer
Attribute fileName is String

The element has the following contents:

TreeModel element (exactly one)
RandomLocalTreeVariable element (exactly one)

Example:

<randomLocalLogger logEvery="1" fileName="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel3"/>
  <randomLocalClockModel idref="randomLocalClockModel1"/>
</randomLocalLogger>

`<randomLocalYuleModel>` element

A speciation model of a Yule process whose rate can change at random nodes in the tree.

The element takes following attributes:

Attribute ratesAsMultipliers is Boolean
Attribute (optional) dp is Integer
Attribute units is String
the units

The element has the following contents:

Element named <birthRates> containing:
- Parameter element (exactly one)
Element named <indicators> containing:
- Parameter element (exactly one)
Element named <meanRate> containing:
- Parameter element (exactly one)

Example:

<randomLocalYuleModel ratesAsMultipliers="true" dp="1" units="days">
 <birthRates>
   <maskedParameter idref="maskedParameter1"/>
 </birthRates>
 <indicators>
   <maskedParameter idref="maskedParameter9"/>
 </indicators>
 <meanRate>
   <matrixParameter idref="matrixParameter10"/>
 </meanRate>
</randomLocalYuleModel>

`<randomTaxaSample>` element

Randomly samples n taxa from a collection of N taxa

The element takes following attributes:

Attribute sample is Integer

The element has the following contents:

Taxa element (exactly one)

Example:

<randomTaxaSample sample="1">
  <taxa idref="taxa5"/>
</randomTaxaSample>

`<randomWalk>` element

Describes a first-order random walk. No prior is assumed on the first data element

The element takes following attributes:

Attribute (optional) logScale is Boolean

The element has the following contents:

Parameter element (exactly one)
One of:
- ParametricDistributionModel element (exactly one)
- DistributionLikelihood element (exactly one)

Example:

<randomWalk logScale="true">
  <maskedParameter idref="maskedParameter6"/>
  <normalDistributionModel idref="normalDistributionModel7"/>
</randomWalk>

`<randomWalkIntegerNodeHeightWeightedOperator>` element

This element returns a random walk node height weighted operator on a given parameter.

The element takes following attributes:

Attribute windowSize is Double
Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)
Element named <internalNodeHeights> containing:
- Parameter element (exactly one)

Example:

<randomWalkIntegerNodeHeightWeightedOperator windowSize="1.0" weight="1.0">
  <parameter idref="parameter2"/>
 <internalNodeHeights>
   <duplicatedParameter idref="duplicatedParameter2"/>
 </internalNodeHeights>
</randomWalkIntegerNodeHeightWeightedOperator>

`<randomWalkIntegerOperator>` element

This element returns a random walk operator on a given parameter.

The element takes following attributes:

Attribute windowSize is Double
Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)

Example:

<randomWalkIntegerOperator windowSize="1.0" weight="1.0">
  <parameter idref="parameter10"/>
</randomWalkIntegerOperator>

`<randomWalkIntegerSetSizeWeightedOperator>` element

This element returns a random walk set size weighted operator on a given parameter.

The element takes following attributes:

Attribute windowSize is Double
Attribute weight is Double
Attribute baseSetSize is Double

The element has the following contents:

Parameter element (exactly one)
MicrosatelliteSamplerTreeModel element (exactly one)

Example:

<randomWalkIntegerSetSizeWeightedOperator windowSize="1.0" weight="1.0" baseSetSize="1.0">
  <maskedParameter idref="maskedParameter7"/>
  <microsatelliteSamplerTreeModel idref="microsatelliteSamplerTreeModel5"/>
</randomWalkIntegerSetSizeWeightedOperator>

`<randomWalkOnMapOperator>` element

This element returns a random walk operator on a given map.

The element takes following attributes:

Attribute windowSize is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

MapDiffusionModel element (exactly one)
Parameter element (exactly one)

Example:

<randomWalkOnMapOperator windowSize="1.0" weight="1.0" autoOptimize="true">
  ERROR!
  <compoundParameter idref="compoundParameter2"/>
</randomWalkOnMapOperator>

`<randomWalkOperator>` element

This element returns a random walk operator on a given parameter.

The element takes following attributes:

Attribute windowSize is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) boundaryCondition is String

The element has the following contents:

Parameter element (exactly one)

Example:

<randomWalkOperator windowSize="1.0" weight="1.0" autoOptimize="true" boundaryCondition="reflecting">
  <diagonalMatrix idref="diagonalMatrix7"/>
</randomWalkOperator>

`<rateBitExchangeOperator>` element

This element returns a bit-flip operator on a given parameter.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <bits> containing:
- Parameter element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)

Example:

<rateBitExchangeOperator weight="1.0">
 <bits>
   <diagonalMatrix idref="diagonalMatrix10"/>
 </bits>
 <rates>
   <matrixParameter idref="matrixParameter3"/>
 </rates>
</rateBitExchangeOperator>

`<rateCovarianceStatistic>` element

A statistic that has as its value the covariance of parent and child branch rates

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

TreeModel element (exactly one)
BranchRateModel element (exactly one)

Example:

<rateCovarianceStatistic name="foo">
  <treeModel idref="treeModel5"/>
  <rateEpochBranchRates idref="rateEpochBranchRates7"/>
</rateCovarianceStatistic>

`<rateEpochBranchRates>` element

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.

The element takes following attributes:

Attribute (optional) continuousNormalization is Boolean
Special rate normalization for a Brownian diffusion process

The element has the following contents:

Element named <epoch> containing:
- Attribute (optional) transitionTime is Double
  The time of transition between this epoch and the previous one
- Parameter element (exactly one)
  The evolutionary rate parameter for this epoch
- Element named <transitionTime> containing:
  - Parameter element (exactly one)
    
    The transition time parameter for this epoch
  An epoch that lasts until transitionTime
Element named <rate> containing:
- Parameter element (exactly one)
  
  The ancestral molecular evolutionary rate parameter
Element named <rootHeight> containing:
- Parameter element (exactly one)
  The tree root height
  Parameterization may require the root height

Example:

<rateEpochBranchRates continuousNormalization="true">
 <epoch transitionTime="1.0">
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix5"/>
 </epoch>
 <rate>
   <duplicatedParameter idref="duplicatedParameter1"/>
 </rate>
</rateEpochBranchRates>

`<rateExchange>` element

An operator that exchanges rates and traits on a tree.

The element takes following attributes:

Attribute weight is Double
Attribute swapRates is Boolean
Attribute swapTraits is Boolean
Attribute swapAtRoot is Boolean
Attribute moveHeight is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<rateExchange weight="1.0" swapRates="true" swapTraits="true" swapAtRoot="true" moveHeight="true">
  <treeModel idref="treeModel6"/>
</rateExchange>

`<rateSampleOperator>` element

This element returns a rateSample operator on a given parameter.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) sampleAll is Boolean

The element has the following contents:

TreeModel element (exactly one)
RateEvolutionLikelihood element (zero or one)

Example:

<rateSampleOperator weight="1.0" sampleAll="true">
  <treeModel idref="treeModel2"/>
</rateSampleOperator>

`<rateScaleOperator>` element

This element returns a rateScale operator on a given parameter.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) noRoot is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<rateScaleOperator scaleFactor="1.0" weight="1.0" autoOptimize="true" noRoot="true">
  <treeModel idref="treeModel7"/>
</rateScaleOperator>

`<rateStatistic>` element

A statistic that returns the average of the branch rates

The element takes following attributes:

Attribute internal is Boolean
Attribute external is Boolean
Attribute mode is String
This attribute determines how the rates are summarized, can be one of (mean, variance, coefficientOfVariance)
Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

TreeModel element (exactly one)
BranchRateModel element (exactly one)

Example:

<rateStatistic internal="true" external="true" mode="coefficientOfVariation" name="foo">
  <treeModel idref="treeModel8"/>
  <strictClockBranchRates idref="strictClockBranchRates1"/>
</rateStatistic>

`<rateVarianceScaleOperator>` element

This element returns a rateScale operator on a given parameter.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

TreeModel element (exactly one)
Parameter element (exactly one)

Example:

<rateVarianceScaleOperator scaleFactor="1.0" weight="1.0" autoOptimize="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel2"/>
  <duplicatedParameter idref="duplicatedParameter1"/>
</rateVarianceScaleOperator>

`<ratioStatistic>` element

This element returns a statistic that is the ratio of the 2 child statistics.

The element has the following contents:

Statistic elements (exactly 2)
The two operand statistics

Example:

<ratioStatistic>
  <argTimingStatistic idref="argTimingStatistic3"/>
  <generalizedSkylinePopSizeStatistic idref="generalizedSkylinePopSizeStatistic4"/>
</ratioStatistic>

`<ratioStatistic>` element

This element returns a statistic that is the ratio of the 2 child statistics.

The element has the following contents:

Statistic elements (exactly 2)
The two operand statistics

Example:

<ratioStatistic>
  <externalLengthStatistic idref="externalLengthStatistic7"/>
  <varianceStatistic idref="varianceStatistic4"/>
</ratioStatistic>

`<reciprocalStatistic>` element

This element returns a statistic that is the element-wise reciprocal of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<reciprocalStatistic>
  <statistic idref="statistic8"/>
</reciprocalStatistic>

`<reciprocalStatistic>` element

This element returns a statistic that is the element-wise reciprocal of the child statistic.

The element has the following contents:

Statistic element (exactly one)

Example:

<reciprocalStatistic>
  <negativeStatistic idref="negativeStatistic7"/>
</reciprocalStatistic>

`<regressionGibbsEffectOperator>` element

This element returns a multivariate Gibbs operator on an internal node trait.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)
MultivariateDistributionLikelihood element (exactly one)
LinearRegression element (exactly one)
Element named <indicator> containing:
- Parameter element (exactly one)

Example:

<regressionGibbsEffectOperator weight="1.0">
  <maskedParameter idref="maskedParameter5"/>
  <multivariateGammaPrior idref="multivariateGammaPrior3"/>
  ERROR!
</regressionGibbsEffectOperator>

`<regressionGibbsPrecisionOperator>` element

This element returns a multivariate Gibbs operator on an internal node trait.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)
DistributionLikelihood element (exactly one)
LinearRegression element (exactly one)

Example:

<regressionGibbsPrecisionOperator weight="1.0">
  <compoundParameter idref="compoundParameter6"/>
  <cachedPrior idref="cachedPrior5"/>
  ERROR!
</regressionGibbsPrecisionOperator>

`<regressionMetropolizedIndicatorOperator>` element

This element returns a multivariate Gibbs operator on an internal node trait.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)
MultivariateDistributionLikelihood element (exactly one)
LinearRegression element (exactly one)
Element named <indicator> containing:
- Parameter element (exactly one)
Element named <mask> containing:
- Parameter element (exactly one)

Example:

<regressionMetropolizedIndicatorOperator weight="1.0">
  <compoundParameter idref="compoundParameter7"/>
  <multivariateNormalPrior idref="multivariateNormalPrior3"/>
  ERROR!
 <indicator>
   <duplicatedParameter idref="duplicatedParameter10"/>
 </indicator>
</regressionMetropolizedIndicatorOperator>

`<report>` element

Generates a report using the given text and elements

The element takes following attributes:

Attribute (optional) type is String
The format of the report
Attribute (optional) title is String
The title of the report
Attribute (optional) fileName is String

The element has the following contents:

Object elements (one or more)
An arbitrary mixture of text and elements to report

Example:

<report type="XHTML" title="Report" fileName="foo">
  <randomWalkOnMapOperator idref="randomWalkOnMapOperator1"/>
  <argUniformPrior idref="argUniformPrior2"/>
  <NearestNeighborInterchange idref="NearestNeighborInterchange2"/>
</report>

`<RPNcalculator>` element

This element returns a statistic evaluated from arbitrary expression.

The element has the following contents:

Element named <expression> containing:
- String element (exactly one)
Element named <variable> containing:
- Statistic element (exactly one)

Example:

<RPNcalculator>
 <expression>
   foo
 </expression>
 <variable>
   <parsimonyStatistic idref="parsimonyStatistic6"/>
 </variable>
 <variable>
   <logarithmStatistic idref="logarithmStatistic10"/>
 </variable>
 <variable>
   <RPNcalculator idref="RPNcalculator2"/>
 </variable>
</RPNcalculator>

`<sampleNonActiveOperator>` element

This element returns a Gibbs operator for the joint distribution of population sizes.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
Element named <indicators> containing:
- Parameter element (exactly one)
Element named <data> containing:
- Parameter element (exactly one)

Example:

<sampleNonActiveOperator weight="1.0">
 <distribution>
   <logNormalDistributionModel idref="logNormalDistributionModel8"/>
 </distribution>
 <indicators>
   <duplicatedParameter idref="duplicatedParameter6"/>
 </indicators>
 <data>
   <matrixParameter idref="matrixParameter3"/>
 </data>
</sampleNonActiveOperator>

`<sampleStateAndCategoryModel>` element

A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of rate categories and internal states.

The element has the following contents:

Element named <mutationRate> containing:
- Parameter element (exactly one)
Element named <categoriesParameter> containing:
- Parameter element (exactly one)
SubstitutionModel elements (one or more)

Example:

<sampleStateAndCategoryModel>
 <mutationRate>
   <parameter idref="parameter7"/>
 </mutationRate>
 <categoriesParameter>
   <maskedParameter idref="maskedParameter2"/>
 </categoriesParameter>
  <gtrModel idref="gtrModel4"/>
  <CovarionHKYModel idref="CovarionHKYModel3"/>
  <aminoAcidModel idref="aminoAcidModel2"/>
</sampleStateAndCategoryModel>

`<sampleStateModel>` element

A SiteModel that has a discrete distribution of substitution models over sites, designed for sampling of internal states.

The element has the following contents:

Element named <mutationRate> containing:
- Parameter element (exactly one)
Element named <proportions> containing:
- Parameter element (exactly one)
SubstitutionModel elements (one or more)

Example:

<sampleStateModel>
 <mutationRate>
   <matrixParameter idref="matrixParameter5"/>
 </mutationRate>
 <proportions>
   <matrixParameter idref="matrixParameter5"/>
 </proportions>
  <positiveDefiniteSubstitutionModel idref="positiveDefiniteSubstitutionModel8"/>
  <MutationDeathModel idref="MutationDeathModel4"/>
  <yangCodonModel idref="yangCodonModel3"/>
</sampleStateModel>

`<scaledPiecewisePopulation>` element

This element represents a piecewise population model

The element takes following attributes:

Attribute units is String
the units
Attribute linear is Boolean

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <populationTree> containing:
- TreeModel element (exactly one)

Example:

<scaledPiecewisePopulation units="years" linear="true">
 <populationSizes>
   <diagonalMatrix idref="diagonalMatrix8"/>
 </populationSizes>
 <populationTree>
   <treeModel idref="treeModel10"/>
 </populationTree>
</scaledPiecewisePopulation>

`<scaledTreeLengthModel>` element

This element returns a branch rate model that scales the total length of the tree to specified valued (default=1.0).

The element has the following contents:

Element named <scalingFactor> containing:
- Parameter element (exactly one)
TreeModel element (exactly one)

Example:

<scaledTreeLengthModel>
  <treeModel idref="treeModel7"/>
</scaledTreeLengthModel>

`<scaleOperator>` element

This element returns a scale operator on a given parameter.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute (optional) scaleAll is Boolean
Attribute (optional) scaleAllIndependently is Boolean
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean
Attribute (optional) df is Integer

The element has the following contents:

Parameter element (exactly one)
Element named <indicators> containing:
- Attribute (optional) pickoneprob is Double
- Parameter element (exactly one)

Example:

<scaleOperator scaleFactor="1.0" scaleAll="true" scaleAllIndependently="true" weight="1.0" autoOptimize="true" df="1">
  <compoundParameter idref="compoundParameter4"/>
</scaleOperator>

`<selectorOperator>` element

.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)

Example:

<selectorOperator weight="1.0">
  <matrixParameter idref="matrixParameter8"/>
</selectorOperator>

`<sequence>` element

A biomolecular sequence.

The element has the following contents:

Taxon element (exactly one)
String element (exactly one)
A character string representing the aligned molecular sequence

Example:

<sequence>
  <taxon idref="taxon3"/>
  ACGACTAGCATCGAGCTTCG--GATAGCATGC
</sequence>

`<sequenceErrorModel>` element

This element returns a model that allows for post-mortem DNA damage.

The element takes following attributes:

Attribute (optional) type is String

The element has the following contents:

Element named <baseErrorRate> containing:
- Parameter element (exactly one)
  
  The base error rate per site per sequence
Element named <ageRelatedErrorRate> containing:
- Parameter element (exactly one)
  
  The error rate per site per unit time
Element named <indicators> containing:
- Parameter element (exactly one)
  
  A binary indicator of whether the sequence has errors
One of:
- Element named <include> containing:
  - TaxonList element (exactly one)
    
    A set of taxa to which to apply the damage model to
- Element named <exclude> containing:
  - TaxonList element (exactly one)
    
    A set of taxa to which to not apply the damage model to

Example:

<sequenceErrorModel type="foo">
 <include>
   <patternSubSet idref="patternSubSet2"/>
 </include>
</sequenceErrorModel>

`<sequenceSimulator>` element

A SequenceSimulator that generates random sequences for a given tree, sitemodel and branch rate model

The element takes following attributes:

Attribute replications is Integer

The element has the following contents:

Tree element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)

Example:

<sequenceSimulator replications="1">
  <newick idref="newick10"/>
  <sampleStateModel idref="sampleStateModel3"/>
</sequenceSimulator>

`<setOperator>` element

This element represents an operator on a set.

The element takes following attributes:

Attribute set is Double;
Attribute weight is Double

The element has the following contents:

Parameter element (exactly one)

Example:

<setOperator set="0.5 1.0" weight="1.0">
  <compoundParameter idref="compoundParameter8"/>
</setOperator>

`<singleTipObservationProcess>` element

This element represents an instance of the SingleTipObservationProcess for ALSTreeLikelihood calculations

The element has the following contents:

TreeModel element (exactly one)
PatternList element (exactly one)
Taxon element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (exactly one)
Element named <deathRate> containing:
- Parameter element (exactly one)
Element named <immigrationRate> containing:
- Parameter element (exactly one)

Example:

<singleTipObservationProcess>
  <treeModel idref="treeModel3"/>
  <convert idref="convert10"/>
  <taxon idref="taxon2"/>
  <categorySiteModel idref="categorySiteModel6"/>
  <continuousTraitRateModel idref="continuousTraitRateModel5"/>
 <deathRate>
   <diagonalMatrix idref="diagonalMatrix1"/>
 </deathRate>
 <immigrationRate>
   <parameter idref="parameter4"/>
 </immigrationRate>
</singleTipObservationProcess>

`<siteModel>` element

A SiteModel that has a gamma distributed rates across sites

The element has the following contents:

Element named <substitutionModel> containing:
- SubstitutionModel element (exactly one)
One of:
- Element named <mutationRate> containing:
  - Parameter element (exactly one)
- Element named <relativeRate> containing:
  - Parameter element (exactly one)

Element named <gammaShape> containing:
- Attribute (optional) gammaCategories is Integer
- Parameter element (exactly one)
Element named <proportionInvariant> containing:
- Parameter element (exactly one)

Example:

<siteModel>
 <substitutionModel>
   <binarySubstitutionModel idref="binarySubstitutionModel2"/>
 </substitutionModel>
 <relativeRate>
   <designMatrix idref="designMatrix6"/>
 </relativeRate>
</siteModel>

`<gmrfSkyrideLikelihood>` element

This element represents the likelihood of the tree given the population size vector.

The element takes following attributes:

Attribute (optional) rescaleByRootHeight is Boolean
Attribute (optional) randomizeTree is Boolean
Attribute (optional) timeAwareSmoothing is Boolean

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <precisionParameter> containing:
- Parameter element (exactly one)
Element named <populationTree> containing:
- TreeModel elements (one or more)
Element named <groupSizes> containing:
- Parameter element (exactly one)

Example:

<gmrfSkyrideLikelihood rescaleByRootHeight="true" randomizeTree="true" timeAwareSmoothing="true">
 <populationSizes>
   <parameter idref="parameter3"/>
 </populationSizes>
 <precisionParameter>
   <duplicatedParameter idref="duplicatedParameter6"/>
 </precisionParameter>
 <populationTree>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel9"/>
   <treeModel idref="treeModel10"/>
 </populationTree>
</gmrfSkyrideLikelihood>

`<slidingPatternsOperator>` element

This element returns a sliding window operator on alignment sites.

The element takes following attributes:

Attribute windowSize is Integer
Attribute weight is Integer
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

Element named <breakPoints> containing:
- Parameter element (exactly one)
SitePatterns elements ( to 100)

Example:

<slidingPatternsOperator windowSize="1" weight="1" autoOptimize="true">
 <breakPoints>
   <diagonalMatrix idref="diagonalMatrix5"/>
 </breakPoints>
  ERROR!
  ERROR!
</slidingPatternsOperator>

`<sp>` element

Taxon in a species tree

The element has the following contents:

Taxon elements (one or more)

Example:

<sp>
  <taxon idref="taxon10"/>
  <sp idref="sp8"/>
  <taxon idref="taxon4"/>
  <taxon idref="taxon2"/>
</sp>

`<speciationLikelihood>` element

This element represents the likelihood of the tree given the speciation.

The element has the following contents:

Element named <model> containing:
- SpeciationModel element (exactly one)
Element named <speciesTree> containing:
- Tree element (exactly one)
Element named <include> containing:
- Taxa elements (one or more)
  
  One or more subsets of taxa which should be included from calculate the likelihood (the remaining taxa are excluded)
Element named <exclude> containing:
- Taxa elements (one or more)
  
  One or more subsets of taxa which should be excluded from calculate the likelihood (which is calculated on the remaining subtree)

Example:

<speciationLikelihood>
 <model>
   <yuleModel idref="yuleModel4"/>
 </model>
 <speciesTree>
   <neighborJoiningTree idref="neighborJoiningTree3"/>
 </speciesTree>
</speciationLikelihood>

`<species>` element

Binds taxa in gene trees with species information.

The element has the following contents:

SpeciesBindings$SPinfo elements ( or more)
Element named <geneTrees> containing:
- TreeModel elements (zero or more)
- Element named <gtree> containing:
  - Attribute ploidy is Double
  - TreeModel element (exactly one)

Example:

<species>
  <sp idref="sp7"/>
  <sp idref="sp1"/>
  <sp idref="sp4"/>
  <sp idref="sp1"/>
 <geneTrees>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel5"/>
   <treeModel idref="treeModel3"/>
   <treeModel idref="treeModel10"/>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel8"/>
  <gtree ploidy="1.0">
    <treeModel idref="treeModel6"/>
  </gtree>
  <gtree ploidy="1.0">
    <treeModel idref="treeModel7"/>
  </gtree>
  <gtree ploidy="1.0">
    <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel1"/>
  </gtree>
  <gtree ploidy="1.0">
    <treeModel idref="treeModel6"/>
  </gtree>
 </geneTrees>
</species>

`<speciesCoalescent>` element

Compute coalecent log-liklihood of a set of gene trees embedded inside one species tree.

The element has the following contents:

SpeciesBindings element (exactly one)
SpeciesTreeModel element (exactly one)

Example:

<speciesCoalescent>
  <species idref="species2"/>
  <speciesTree idref="speciesTree8"/>
</speciesCoalescent>

`<speciesTree>` element

Species tree which includes demographic function per branch.

The element takes following attributes:

Attribute (optional) bmPrior is Boolean
Attribute (optional) constantRoot is Boolean
Attribute (optional) constantPopulation is Boolean

The element has the following contents:

SpeciesBindings element (exactly one)
Tree element (zero or one)
Element named <sppSplitPopulations> containing:
- Attribute (optional) value is Double
- Parameter element (exactly one)
Element named <coalescentPointsPopulations> containing:
- Attribute (optional) value is Double
- Parameter element (exactly one)
Element named <coalescentPointsIndicators> containing:
- Parameter element (exactly one)

Example:

<speciesTree bmPrior="true" constantRoot="true" constantPopulation="true">
  <species idref="species1"/>
 <sppSplitPopulations value="1.0">
   <diagonalMatrix idref="diagonalMatrix10"/>
 </sppSplitPopulations>
</speciesTree>

`<speciesTreePopulationPrior>` element

The element has the following contents:

SpeciesTreeModel element (exactly one)
Element named <tipsDistribution> containing:
- ParametricDistributionModel element (exactly one)
Element named <sigma> containing:
- Parameter element (exactly one)

Example:

<speciesTreePopulationPrior>
  <speciesTree idref="speciesTree1"/>
 <tipsDistribution>
   <normalDistributionModel idref="normalDistributionModel3"/>
 </tipsDistribution>
 <sigma>
   <designMatrix idref="designMatrix3"/>
 </sigma>
</speciesTreePopulationPrior>

`<speciesTreeStatistic>` element

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.

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

Element named <speciesTree> containing:
- Tree element (exactly one)
Element named <populationTree> containing:
- Tree element (exactly one)

Example:

<speciesTreeStatistic name="foo">
 <speciesTree>
   <argTreeModel idref="argTreeModel3"/>
 </speciesTree>
 <populationTree>
   <neighborJoiningTree idref="neighborJoiningTree2"/>
 </populationTree>
</speciesTreeStatistic>

`<statistic>` element

A statistic of a given name from the specified object.

The element takes following attributes:

Attribute name is String
The name of the statistic you wish to extract from the given object

The element has the following contents:

StatisticList element (exactly one)

Example:

<statistic name="foo">
  <expConstExp idref="expConstExp4"/>
</statistic>

`<STPopulationPrior>` element

The element takes following attributes:

Attribute (optional) log_root is Boolean

The element has the following contents:

SpeciesTreeModel element (exactly one)
Element named <tipsDistribution> containing:
- ParametricDistributionModel element (exactly one)
Element named <sigma> containing:
- Parameter element (exactly one)
Element named <STsigma> containing:
- Parameter element (exactly one)

Example:

<STPopulationPrior log_root="true">
  <speciesTree idref="speciesTree3"/>
 <tipsDistribution>
   <normalDistributionModel idref="normalDistributionModel2"/>
 </tipsDistribution>
 <STsigma>
   <duplicatedParameter idref="duplicatedParameter9"/>
 </STsigma>
</STPopulationPrior>

`<strictClockBranchRates>` element

This element provides a strict clock model. All branches have the same rate of molecular evolution.

The element has the following contents:

Element named <rate> containing:
- Parameter element (exactly one)
  
  The molecular evolutionary rate parameter

Example:

<strictClockBranchRates>
 <rate>
   <parameter idref="parameter2"/>
 </rate>
</strictClockBranchRates>

`<string>` element

returns a String. If a prompt attribute exists then the user is prompted for input, otherwise the character contents of the element are returned.

The element has the following contents:

One of:
- Attribute prompt is String
  A message displayed to the user when entering a value for this string
- String element (exactly one)

Example:

<string prompt="Enter the name of a dinosaur:"/>

`<subStatistic>` element

Allows you to choose specific dimensions of a given statistic

The element takes following attributes:

Attribute dimension is Integer;

The element has the following contents:

Statistic element (exactly one)

Example:

<subStatistic dimension="1 2 4 8">
  <lineageCountStatistic idref="lineageCountStatistic9"/>
</subStatistic>

`<substitutionEpochModel>` element

null

The element has the following contents:

Element named <models> containing:
- AbstractSubstitutionModel elements (one or more)
Parameter element (exactly one)

Example:

<substitutionEpochModel>
 <models>
   <CovarionHKYModel idref="CovarionHKYModel8"/>
   <covarionModel idref="covarionModel3"/>
   <TWOPHASEModel idref="TWOPHASEModel6"/>
   <msatAvgSubsetModel idref="msatAvgSubsetModel10"/>
 </models>
  <compoundParameter idref="compoundParameter9"/>
</substitutionEpochModel>

`<subtreeSlide>` element

An operator that slides a subtree.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) size is Double
Attribute (optional) targetAcceptance is Double
Attribute gaussian is Boolean
Attribute (optional) swapInRandomRate is Boolean
Attribute (optional) swapInRandomTrait is Boolean
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<subtreeSlide weight="1.0" size="1.0" targetAcceptance="1.0" gaussian="true" swapInRandomRate="true" swapInRandomTrait="true" autoOptimize="true">
  <treeModel idref="treeModel1"/>
</subtreeSlide>

`<sumStatistic>` element

This element returns a statistic that is the element-wise sum of the child statistics.

The element takes following attributes:

Attribute (optional) elementwise is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<sumStatistic elementwise="true">
  <lineageCountStatistic idref="lineageCountStatistic2"/>
</sumStatistic>

`<sumStatistic>` element

This element returns a statistic that is the element-wise sum of the child statistics.

The element takes following attributes:

Attribute (optional) elementwise is Boolean

The element has the following contents:

Statistic elements (one or more)

Example:

<sumStatistic elementwise="true">
  <popGraph idref="popGraph9"/>
  <notStatistic idref="notStatistic9"/>
  <differenceStatistic idref="differenceStatistic4"/>
  <varianceStatistic idref="varianceStatistic4"/>
</sumStatistic>

`<generalSubstitutionModel>` element

A general reversible model of sequence substitution for any data type.

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)

Example:

<generalSubstitutionModel>
  <extendedDataType idref="extendedDataType3"/>
 <frequencies>
   <frequencyModel idref="frequencyModel1"/>
 </frequencies>
 <rates>
   <compoundParameter idref="compoundParameter1"/>
 </rates>
</generalSubstitutionModel>

`<generalSubstitutionModel>` element

A general reversible model of sequence substitution for any data type.

The element has the following contents:

One of:
- Attribute dataType is String
  The type of sequence data
- DataType element (exactly one)

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
Element named <rateIndicator> containing:
- Parameter element (exactly one)

Example:

<generalSubstitutionModel>
  <hiddenNucleotides idref="hiddenNucleotides6"/>
 <frequencies>
   <frequencyModel idref="frequencyModel10"/>
 </frequencies>
 <rates>
   <diagonalMatrix idref="diagonalMatrix4"/>
 </rates>
</generalSubstitutionModel>

`<swapOperator>` element

This element represents an operator that swaps values in a multi-dimensional parameter.

The element takes following attributes:

Attribute weight is Double
Attribute size is Integer
Attribute autoOptimize is Boolean

The element has the following contents:

Parameter element (exactly one)

Example:

<swapOperator weight="1.0" size="1" autoOptimize="true">
  <matrixParameter idref="matrixParameter6"/>
</swapOperator>

`<taxa>` element

Defines a set of taxon objects.

The element has the following contents:

At least one of:**Taxa elements (one or more)
- Taxon elements (one or more)

Example:

<!-- A list of six taxa -->
<taxa id="greatApes">
	<taxon id="human"/>
	<taxon id="chimp"/>
	<taxon id="bonobo"/>
	<taxon id="gorilla"/>
	<taxon id="orangutan"/>
	<taxon id="siamang"/>
</taxa>

<!-- A list of three taxa by references to above taxon objects -->
<taxa id="humanAndChimps">
	<taxon idref="human"/>
	<taxon idref="chimp"/>
	<taxon idref="bonobo"/>
</taxa>

`<taxon>` element

The element takes following attributes:

Attribute id is String
A unique identifier for this taxon

The element has the following contents:

Attribute$Default element (zero or one)
Date element (zero or one)
Location element (zero or one)

Example:

<taxon id="foo"/>

`<teamOperator>` element

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.

The element takes following attributes:

Attribute weight is Double
Attribute size is Integer

The element has the following contents:

MCMCOperator elements (one or more)

Example:

<teamOperator weight="1.0" size="1">
  <treeBitRandomWalk idref="treeBitRandomWalk2"/>
  <generalizedSkylineGibbsOperator idref="generalizedSkylineGibbsOperator8"/>
</teamOperator>

`<test>` element

This element represents a boolean statistic that returns 1 if the conditions are met and 0 otherwise.

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic, for logging purposes

The element has the following contents:

Attribute element (exactly one)
One of:
- Element named <equals> containing:
  - Attribute element (exactly one)
- Element named <greaterThan> containing:
  - Attribute element (exactly one)
- Element named <lessThan> containing:
  - Attribute element (exactly one)
- Attribute equals is Double
- Attribute greaterThan is Double
- Attribute lessThan is Double
- Attribute inside is Double;
- Attribute outside is Double;

Example:

<test name="foo">
  <parameter idref="parameter7"/>
 <lessThan>
   <attr idref="attr10"/>
 </lessThan>
</test>

`<threadedCompoundLikelihood>` element

A likelihood function which is simply the product of its component likelihood functions.

The element takes following attributes:

Attribute (optional) robustWeight is Double

The element has the following contents:

Likelihood elements (one or more)

Example:

<threadedCompoundLikelihood robustWeight="1.0">
  <invgammaPrior idref="invgammaPrior5"/>
  <normalPrior idref="normalPrior3"/>
  <speciationLikelihood idref="speciationLikelihood10"/>
  <multivariateGammaPrior idref="multivariateGammaPrior2"/>
</threadedCompoundLikelihood>

`<tipHeightLikelihood>` element

Calculates the likelihood of the tipHeights given some parametric or empirical distribution.

The element has the following contents:

Element named <distribution> containing:
- ParametricDistributionModel element (exactly one)
Element named <tipHeights> containing:
- Parameter element (exactly one)

Example:

<tipHeightLikelihood>
 <distribution>
   <inverseGaussianDistributionModel idref="inverseGaussianDistributionModel1"/>
 </distribution>
 <tipHeights>
   <compoundParameter idref="compoundParameter1"/>
 </tipHeights>
</tipHeightLikelihood>

`<tipStateSwapOperator>` element

This element represents an operator to swap tip states between two random tips.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeLikelihood element (exactly one)

Example:

<tipStateSwapOperator weight="1.0">
  <ancestralTreeLikelihood idref="ancestralTreeLikelihood9"/>
</tipStateSwapOperator>

`<tipTraitSwapOperator>` element

This element represents an operator to swap tip traits between two random tips.

The element takes following attributes:

Attribute trait is String
Attribute weight is Double

The element has the following contents:

IntegratedMultivariateTraitLikelihood element (exactly one)

Example:

<tipTraitSwapOperator trait="foo" weight="1.0">
  ERROR!
</tipTraitSwapOperator>

`<tkf91Likelihood>` element

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.

The element has the following contents:

TreeModel element (exactly one)
Alignment element (exactly one)
GammaSiteModel element (exactly one)
TKF91Model element (exactly one)

Example:

<tkf91Likelihood>
  <treeModel idref="treeModel10"/>
  <hypermutantAlignment idref="hypermutantAlignment8"/>
  <siteModel idref="siteModel9"/>
  <tkf91Model idref="tkf91Model2"/>
</tkf91Likelihood>

`<tkf91Model>` element

The TKF91 (Thorne, Kishino & Felsenstein 1991) model of insertion-deletion.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <lengthDistribution> containing:
- Parameter element (exactly one)
Element named <deathRate> containing:
- Parameter element (exactly one)

Example:

<tkf91Model units="substitutions">
 <lengthDistribution>
   <matrixParameter idref="matrixParameter4"/>
 </lengthDistribution>
 <deathRate>
   <compoundParameter idref="compoundParameter7"/>
 </deathRate>
</tkf91Model>

`<tmrcaStatistic>` element

A statistic that has as its value the height of the most recent common ancestor of a set of taxa in a given tree

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging
Attribute (optional) rate is Boolean

The element has the following contents:

Tree element (exactly one)
Element named <mrca> containing:
- Taxa element (exactly one)
At least one of:**Attribute (optional) forParent is Boolean
- Attribute (optional) includeStem is Boolean

Example:

<tmrcaStatistic name="foo" rate="true" forParent="true">
  <upgmaTree idref="upgmaTree3"/>
 <mrca>
   <taxa idref="taxa4"/>
 </mrca>
</tmrcaStatistic>

`<TN93Model>` element

This element represents an instance of the TN93 (Tamura and Nei 1993) model of nucleotide evolution.

The element has the following contents:

Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <kappa1> containing:
- Variable element (exactly one)
Element named <kappa2> containing:
- Variable element (exactly one)

Example:

<TN93Model>
 <frequencies>
   <frequencyModel idref="frequencyModel10"/>
 </frequencies>
 <kappa1>
   <diagonalMatrix idref="diagonalMatrix6"/>
 </kappa1>
 <kappa2>
   <maskedParameter idref="maskedParameter8"/>
 </kappa2>
</TN93Model>

`<argPartitionOperator>` element

An operator that picks a new partitioning uniformly at random.

The element takes following attributes:

Attribute weight is Integer
Attribute (optional) tossSize is Integer
Attribute (optional) tossAll is Boolean

The element has the following contents:

ARGModel element (exactly one)

Example:

<argPartitionOperator weight="1" tossSize="1" tossAll="true">
  <argTreeModel idref="argTreeModel2"/>
</argPartitionOperator>

`<traceAnalysis>` element

Performs a trace analysis. Estimates the mean of the various statistics in the given log file.

The element takes following attributes:

Attribute fileName is String
The name of a BEAST log file (can not include trees, which should be logged separately
Attribute (optional) burnIn is Integer
Attribute (optional) stdError is Boolean
Attribute (optional) computeMSE is Boolean

The element has the following contents:

Element named <expectation> containing:
- Attribute name is String
- Attribute value is String

Example:

<traceAnalysis fileName="foo" burnIn="1" stdError="true" computeMSE="true">
 <expectation name="foo" value="foo"/>
 <expectation name="foo" value="foo"/>
 <expectation name="foo" value="foo"/>
</traceAnalysis>

`<traitGibbsOperator>` element

This element returns a multivariate Gibbs operator on traits for possible all nodes.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) onlyInternalNodes is Boolean
Attribute (optional) onlyTipsWithPriors is Boolean

The element has the following contents:

SampledMultivariateTraitLikelihood element (exactly one)
MultivariateDistributionLikelihood elements (zero or more)
Element named <rootPrior> containing:
- MultivariateDistributionLikelihood element (exactly one)
GeoSpatialCollectionModel element (zero or one)

Example:

<traitGibbsOperator weight="1.0" onlyInternalNodes="true" onlyTipsWithPriors="true">
  ERROR!
  <multivariateNormalPrior idref="multivariateNormalPrior2"/>
</traitGibbsOperator>

`<traitRateGibbsOperator>` element

This element returns a multivariate Gibbs operator on traits for possible all nodes.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

AbstractMultivariateTraitLikelihood element (exactly one)
ArbitraryBranchRates element (exactly one)
DistributionLikelihood element (exactly one)

Example:

<traitRateGibbsOperator weight="1.0">
  <inhibitionLikelihood idref="inhibitionLikelihood3"/>
  <arbitraryBranchRates idref="arbitraryBranchRates9"/>
  <modelSpecificPseudoPrior idref="modelSpecificPseudoPrior1"/>
</traitRateGibbsOperator>

`<tree>` element

This element represents a rooted binary tree and associated attributes.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

SimpleNode element (exactly one)

Example:

<tree units="substitutions">
  <node idref="node9"/>
</tree>

`<treeBitMoveOperator>` element

This element returns a bit-move operator on a given parameter.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) indicatorTrait is String
Attribute (optional) trait2 is String

The element has the following contents:

TreeModel element (exactly one)

Example:

<treeBitMoveOperator weight="1.0" indicatorTrait="foo" trait2="foo">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel1"/>
</treeBitMoveOperator>

`<treeBitRandomWalk>` element

This element returns a bit-random walk operator on a random indicator/variable pair in the tree.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) indicatorTrait is String
Attribute (optional) trait2 is String
Attribute (optional) swapTrait2 is Boolean
Attribute (optional) k is Integer

The element has the following contents:

TreeModel element (exactly one)

Example:

<treeBitRandomWalk weight="1.0" indicatorTrait="foo" trait2="foo" swapTrait2="true" k="1">
  <treeModel idref="treeModel1"/>
</treeBitRandomWalk>

`<diffusionRateStatistic>` element

A statistic that returns the average of the branch rates

The element takes following attributes:

Attribute (optional) name is String
Attribute (optional) greatCircleDistance is Boolean

The element has the following contents:

AbstractMultivariateTraitLikelihood elements (one or more)

Example:

<diffusionRateStatistic name="foo" greatCircleDistance="true">
  <inhibitionLikelihood idref="inhibitionLikelihood7"/>
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood6"/>
  <multivariateTraitLikelihood idref="multivariateTraitLikelihood7"/>
</diffusionRateStatistic>

`<treeLengthStatistic>` element

A statistic that returns the average of the branch rates

The element takes following attributes:

Attribute (optional) name is String

The element has the following contents:

TreeModel element (exactly one)

Example:

<treeLengthStatistic name="foo">
  <treeModel idref="treeModel8"/>
</treeLengthStatistic>

`<treeLikelihood>` element

This element represents the likelihood of a patternlist on a tree given the site model.

The element takes following attributes:

Attribute (optional) useAmbiguities is Boolean
Attribute (optional) allowMissingTaxa is Boolean
Attribute (optional) storePartials is Boolean
Attribute (optional) forceJavaCore is Boolean
Attribute (optional) forceRescaling is Boolean

The element has the following contents:

PatternList element (exactly one)
TreeModel element (exactly one)
SiteModel element (exactly one)
BranchRateModel element (zero or one)
TipPartialsModel element (zero or one)

Example:

<treeLikelihood useAmbiguities="true" allowMissingTaxa="true" storePartials="true" forceJavaCore="true" forceRescaling="true">
  <mergePatterns idref="mergePatterns2"/>
  <treeModel idref="treeModel2"/>
  <siteModel idref="siteModel8"/>
</treeLikelihood>

`<treeMetricStatistic>` element

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.

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging
Attribute (optional) method is String
comparision method (TOPOLOGY,BILLERA,ROBINSONSFOULD,CLADEHEIGHTM,BRANCHSCORE,CLADEMETRIC)

The element has the following contents:

Element named <target> containing:
- Tree element (exactly one)
Element named <reference> containing:
- Tree element (exactly one)

Example:

<treeMetricStatistic name="foo" method="foo">
 <target>
   <newick idref="newick8"/>
 </target>
 <reference>
   <argTreeModel idref="argTreeModel8"/>
 </reference>
</treeMetricStatistic>

`<treeModel>` element

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.

The element has the following contents:

Tree element (exactly one)
Element named <rootHeight> containing:
- Parameter element (exactly one)
  
  A parameter definition with id only (cannot be a reference!)
Element named <nodeHeights> containing:
- Attribute (optional) rootNode is Boolean
  If true the root height is included in the parameter
- Attribute (optional) internalNodes is Boolean
  If true the internal node heights (minus the root) are included in the parameter
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)
Element named <leafHeight> containing:
- Attribute taxon is String
  The name of the taxon for the leaf
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)
Element named <nodeTraits> containing:
- Attribute name is String
  The name of the trait attribute in the taxa
- Attribute (optional) rootNode is Boolean
  If true the root trait is included in the parameter
- Attribute (optional) internalNodes is Boolean
  If true the internal node traits (minus the root) are included in the parameter
- Attribute (optional) leafNodes is Boolean
  If true the leaf node traits are included in the parameter
- Attribute (optional) traitDimension is Integer
  The number of dimensions (if multivariate)
- Attribute (optional) initialValue is Double
  The initial value(s)
- Attribute (optional) fireTreeEvents is Boolean
  Whether to fire tree events if the traits change
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)
Element named <nodeRates> containing:
- Attribute (optional) rootNode is Boolean
  If true the root rate is included in the parameter
- Attribute (optional) internalNodes is Boolean
  If true the internal node rate (minus the root) are included in the parameter
- Attribute (optional) leafNodes is Boolean
  If true the leaf node rate are included in the parameter
- Attribute (optional) initialValue is Double
  The initial value(s)
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)
Element named <leafTrait> containing:
- Attribute taxon is String
  The name of the taxon for the leaf
- Attribute name is String
  The name of the trait attribute in the taxa
- Parameter element (exactly one)
  A parameter definition with id only (cannot be a reference!)

Example:

<!-- the tree model as special sockets for attaching parameters to various aspects of the tree     -->
<!-- The treeModel below shows the standard setup with a parameter associated with the root height -->
<!-- a parameter associated with the internal node heights (minus the root height) and             -->
<!-- a parameter associates with all the internal node heights                                     -->
<!-- Notice that these parameters are overlapping                                                  -->
<!-- The parameters are subsequently used in operators to propose changes to the tree node heights -->
<treeModel id="treeModel1">
	<tree idref="startingTree"/>
	<rootHeight>
		<parameter id="treeModel1.rootHeight"/>
	</rootHeight>
	<nodeHeights internalNodes="true" rootNode="false">
		<parameter id="treeModel1.internalNodeHeights"/>
	</nodeHeights>
	<nodeHeights internalNodes="true" rootNode="true">
		<parameter id="treeModel1.allInternalNodeHeights"/>
	</nodeHeights>
</treeModel>

`<treeShapeStatistics>` element

A statistic that reports a handful of tree shape statistics on the given target tree.

The element takes following attributes:

Attribute (optional) name is String
A name for this statistic primarily for the purposes of logging

The element has the following contents:

Element named <target> containing:
- TreeModel element (exactly one)

Example:

<treeShapeStatistics name="foo">
 <target>
   <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel7"/>
 </target>
</treeShapeStatistics>

`<treeTraceAnalysis>` element

Analyses and reports on a trace consisting of trees.

The element takes following attributes:

Attribute fileName is String
name of a tree log file
Attribute (optional) burnIn is Integer
Attribute (optional) minCladeProbability is Double
Attribute (optional) credSetProbability is Double
Attribute (optional) shortReport is Boolean
Attribute (optional) referenceTree is String

Example:

<treeTraceAnalysis fileName="trees.log" burnIn="1" minCladeProbability="1.0" credSetProbability="1.0" shortReport="true" referenceTree="foo"/>

`<treeUniform>` element

Simultanouesly change height of two nodes.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) count is Integer

The element has the following contents:

TreeModel element (exactly one)

Example:

<treeUniform weight="1.0" count="1">
  <treeModel idref="treeModel5"/>
</treeUniform>

`<twoEpoch>` element

A demographic model of two epochs.

The element takes following attributes:

Attribute units is String
the units

The element has the following contents:

Element named <modernEpoch> containing:
- DemographicModel element (exactly one)
  
  The demographic model for the recent epoch.
Element named <ancientEpoch> containing:
- DemographicModel element (exactly one)
  
  The demographic model for the ancient epoch.
Element named <transitionTime> containing:
- Parameter element (exactly one)
  
  The time that splits the two epochs.

Example:

<twoEpoch units="substitutions">
 <modernEpoch>
   <constantExponential idref="constantExponential3"/>
 </modernEpoch>
 <ancientEpoch>
   <constantExponential idref="constantExponential6"/>
 </ancientEpoch>
 <transitionTime>
   <designMatrix idref="designMatrix5"/>
 </transitionTime>
</twoEpoch>

`<twoPartDistribution>` element

Calculates the likelihood of some data given some parametric or empirical distribution.

Example:

<twoPartDistribution/>

`<TWOPHASEModel>` element

This element represents an instance of the Two Phase Model of microsatellite evolution.

The element takes following attributes:

Attribute (optional) estimateSubmodelParameters is String
whether or not to esitmate the parameters of the submodel

The element has the following contents:

Microsatellite element (exactly one)
Element named <frequencies> containing:
- FrequencyModel element (exactly one)
Element named <Submodel> containing:
- OnePhaseModel element (exactly one)
Element named <OnePhasePrParam> containing:
- Parameter element (exactly one)
Element named <GeoParam> containing:
- Parameter element (exactly one)
Element named <TransformParam> containing:
- Parameter element (exactly one)

Example:

<TWOPHASEModel estimateSubmodelParameters="foo">
  <microsatellite idref="microsatellite8"/>
 <Submodel>
   <LINEARBIASModel idref="LINEARBIASModel7"/>
 </Submodel>
 <OnePhasePrParam>
   <matrixParameter idref="matrixParameter6"/>
 </OnePhasePrParam>
 <GeoParam>
   <maskedParameter idref="maskedParameter5"/>
 </GeoParam>
</TWOPHASEModel>

`<UCLikelihood>` element

This element returns an object that can calculate the likelihood of rates in a tree under the assumption of (log)normally distributed rates.

The element takes following attributes:

Attribute (optional) logspace is Boolean
true if model considers the log of the rates.

The element has the following contents:

TreeModel element (exactly one)
Element named <rates> containing:
- Parameter element (exactly one)
  
  The branch rates parameter
Element named <rootRate> containing:
- Parameter element (exactly one)
  
  The root rate parameter
Element named <variance> containing:
- Parameter element (exactly one)
  
  The standard deviation of the (log)normal distribution

Example:

<UCLikelihood logspace="true">
  <treeModel idref="treeModel1"/>
 <rates>
   <matrixParameter idref="matrixParameter3"/>
 </rates>
 <rootRate>
   <diagonalMatrix idref="diagonalMatrix2"/>
 </rootRate>
 <variance>
   <compoundSymmetricMatrix idref="compoundSymmetricMatrix5"/>
 </variance>
</UCLikelihood>

`<uniformDistributionModel>` element

Describes a uniform distribution with a given lower and upper bounds

The element has the following contents:

Element named <lower> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

Element named <upper> containing:
- One of:
  - Parameter element (exactly one)
  - Double element (exactly one)

Example:

<uniformDistributionModel>
 <lower>
   1.0
 </lower>
 <upper>
   1.0
 </upper>
</uniformDistributionModel>

`<uniformIntegerOperator>` element

An operator that picks new parameter values uniformly at random.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) upper is Double
Attribute (optional) lower is Double
Attribute (optional) count is Double

The element has the following contents:

Parameter element (exactly one)

Example:

<uniformIntegerOperator weight="1.0" upper="1.0" lower="1.0" count="1.0">
  <duplicatedParameter idref="duplicatedParameter8"/>
</uniformIntegerOperator>

`<uniformNodeHeightPrior>` element

This element represents the likelihood of the tree given the demographic function.

The element takes following attributes:

Attribute (optional) analytic is Boolean
Attribute (optional) maxRootHeight is Double
Attribute (optional) mcSampleSize is Integer
Attribute (optional) marginal is Boolean
Attribute (optional) approximate is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<uniformNodeHeightPrior analytic="true" maxRootHeight="1.0" mcSampleSize="1" marginal="true" approximate="true">
  <treeModel idref="treeModel9"/>
</uniformNodeHeightPrior>

`<uniformOperator>` element

An operator that picks new parameter values uniformly at random.

The element takes following attributes:

Attribute weight is Double
Attribute (optional) lower is Double
Attribute (optional) upper is Double

The element has the following contents:

Parameter element (exactly one)

Example:

<uniformOperator weight="1.0" lower="1.0" upper="1.0">
  <duplicatedParameter idref="duplicatedParameter8"/>
</uniformOperator>

`<uniformPartitionLikelihood>` element

null

The element has the following contents:

ARGModel element (exactly one)

Example:

<uniformPartitionLikelihood>
  <argTreeModel idref="argTreeModel8"/>
</uniformPartitionLikelihood>

`<uniformPrior>` element

Calculates the prior probability of some data under a given uniform distribution.

The element takes following attributes:

Attribute lower is Double
Attribute upper is Double

The element has the following contents:

Statistic elements (one or more)

Example:

<uniformPrior lower="1.0" upper="1.0">
  <speciesTreeStatistic idref="speciesTreeStatistic3"/>
  <logarithmStatistic idref="logarithmStatistic4"/>
</uniformPrior>

`<uniformNodeHeightPrior>` element

This element represents the likelihood of the tree given the demographic function.

The element takes following attributes:

Attribute (optional) analytic is Boolean
Attribute (optional) maxRootHeight is Double
Attribute (optional) mcSampleSize is Integer
Attribute (optional) marginal is Boolean
Attribute (optional) approximate is Boolean

The element has the following contents:

TreeModel element (exactly one)

Example:

<uniformNodeHeightPrior analytic="true" maxRootHeight="1.0" mcSampleSize="1" marginal="true" approximate="true">
  <empiricalTreeDistributionModel idref="empiricalTreeDistributionModel10"/>
</uniformNodeHeightPrior>

`<upDownOperator>` element

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.

The element takes following attributes:

Attribute scaleFactor is Double
Attribute weight is Double
Attribute (optional) autoOptimize is Boolean

The element has the following contents:

Element named <up> containing:
- Scalable element (zero or one)
- Parameter element (zero or one)
- Element named <scale> containing:
  - Attribute (optional) count is Integer
  - Attribute (optional) df is Integer
  - Scalable element (exactly one)
Element named <down> containing:
- Scalable element (zero or one)
- Parameter element (zero or one)
- Element named <scale> containing:
  - Attribute (optional) count is Integer
  - Attribute (optional) df is Integer
  - Scalable element (exactly one)

Example:

<upDownOperator scaleFactor="1.0" weight="1.0" autoOptimize="true">
 <up/>
 <up/>
 <down/>
 <down/>
</upDownOperator>

`<upgmaTree>` element

This element returns a UPGMA tree generated from the given distances.

The element takes following attributes:

Attribute (optional) usingDates is Boolean
Attribute (optional) rootHeight is Double

The element has the following contents:

DistanceMatrix element (exactly one)

Example:

<upgmaTree usingDates="true" rootHeight="1.0">
  <distanceMatrix idref="distanceMatrix9"/>
</upgmaTree>

`<variableDemographic>` element

This element represents the likelihood of the tree given the population size vector.

The element takes following attributes:

Attribute (optional) type is String
Attribute (optional) logUnits is Boolean
Attribute (optional) useMidpoints is Boolean

The element has the following contents:

Element named <populationSizes> containing:
- Parameter element (exactly one)
Element named <indicators> containing:
- Parameter element (exactly one)
Element named <trees> containing:
- Element named <ptree> containing:
  - Attribute (optional) ploidy is Double
  - TreeModel element (exactly one)

Example:

<variableDemographic type="foo" logUnits="true" useMidpoints="true">
 <populationSizes>
   <designMatrix idref="designMatrix4"/>
 </populationSizes>
 <indicators>
   <diagonalMatrix idref="diagonalMatrix4"/>
 </indicators>
 <trees>
  <ptree ploidy="1.0">
    <treeModel idref="treeModel10"/>
  </ptree>
  <ptree ploidy="1.0">
    <treeModel idref="treeModel2"/>
  </ptree>
  <ptree ploidy="1.0">
    <treeModel idref="treeModel8"/>
  </ptree>
 </trees>
</variableDemographic>

`<varianceStatistic>` element

This element returns a statistic that is the variance of the child statistics.

The element has the following contents:

Statistic elements (one or more)

Example:

<varianceStatistic>
  <gmrfPopSizeStatistic idref="gmrfPopSizeStatistic7"/>
  <gmrfPopSizeStatistic idref="gmrfPopSizeStatistic9"/>
  <externalLengthStatistic idref="externalLengthStatistic9"/>
</varianceStatistic>

`<VDAnalysis>` element

reconstruct population graph from EBSP run.

The element takes following attributes:

Attribute (optional) burnIn is Double
The number of states (not sampled states, but actual states) that are discarded from the beginning of the trace and are excluded from the analysis
Attribute (optional) Confidencelevels is Double;
Attribute (optional) useQuantiles is Boolean
Attribute (optional) logUnits is Boolean
Attribute (optional) useMidpoints is Boolean
Attribute (optional) nBins is Integer
Attribute (optional) nChanges is Integer

The element has the following contents:

Element named <logFileName> containing:
- String element (exactly one)
  
  The name of a BEAST log file
Element named <treeFileNames> containing:
- Element named <treeOfLoci> containing:
  - String element (exactly one)
    
    The name of a BEAST trees log file
Element named <populationModelType> containing:
- String element (exactly one)
  
  population model type (stepwise, linear ...
Element named <populationFirstColumn> containing:
- String element (exactly one)
  
  Name of first column of population size
Element named <indicatorsFirstColumn> containing:
- String element (exactly one)
  
  Name of first column of population indicators
Element named <rootheightColumn> containing:
- String element (exactly one)
  
  Name of trace column of root height
Element named <allDemographicsFileName> containing:
- String element (exactly one)
  
  Name of file to output all demographic functions

Example:

<VDAnalysis burnIn="1.0" Confidencelevels="0.5 1.0" useQuantiles="true" logUnits="true" useMidpoints="true" nBins="1" nChanges="1">
 <logFileName>
   foo
 </logFileName>
 <treeFileNames>
  <treeOfLoci>
    foo
  </treeOfLoci>
  <treeOfLoci>
    foo
  </treeOfLoci>
 </treeFileNames>
 <populationModelType>
   foo
 </populationModelType>
 <populationFirstColumn>
   foo
 </populationFirstColumn>
 <indicatorsFirstColumn>
   foo
 </indicatorsFirstColumn>
</VDAnalysis>

`<wideExchange>` element

This element represents a wide exchange operator. This operator swaps two random subtrees.

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeModel element (exactly one)

Example:

<wideExchange weight="1.0">
  <treeModel idref="treeModel10"/>
</wideExchange>

`<wilsonBalding>` element

An operator which performs the Wilson-Balding move on a tree

The element takes following attributes:

Attribute weight is Double

The element has the following contents:

TreeModel element (exactly one)

Example:

<wilsonBalding weight="1.0">
  <treeModel idref="treeModel2"/>
</wilsonBalding>

`<yangCodonModel>` element

This element represents the Yang model of codon evolution.

The element takes following attributes:

Attribute (optional) geneticCode is String
The genetic code to use

The element has the following contents:

Element named <omega> containing:
- Parameter element (exactly one)
Element named <kappa> containing:
- Parameter element (exactly one)
FrequencyModel element (exactly one)

Example:

<yangCodonModel geneticCode="flatwormMitochondrial">
 <omega>
   <parameter idref="parameter9"/>
 </omega>
 <kappa>
   <designMatrix idref="designMatrix7"/>
 </kappa>
  <frequencyModel idref="frequencyModel7"/>
</yangCodonModel>

`<yuleModel>` element

A speciation model of a simple constant rate Birth-death process.

The element takes following attributes:

Attribute (optional) conditionalOnRoot is Boolean
Attribute units is String
the units

The element has the following contents:

Element named <birthRate> containing:
- Parameter element (exactly one)

Example:

<yuleModel conditionalOnRoot="true" units="substitutions">
 <birthRate>
   <designMatrix idref="designMatrix7"/>
 </birthRate>
</yuleModel>

BEAST types

The following is a list of generic types that elements represent in a beast file.

ARGModel

Elements of this type include:

argTreeModel

ARGPartitionLikelihood

Elements of this type include:

hierarchicalPartitionLikelihood
poissonPartitionLikelihood
uniformPartitionLikelihood

ARGRatePrior

Elements of this type include:

argRatePrior

AbstractDistributionLikelihood

Elements of this type include:

cachedPrior
distributionLikelihood
modelSpecificPseudoPrior
multivariateGammaPrior
multivariateNormalPrior
twoPartDistribution

AbstractMultivariateTraitLikelihood

Elements of this type include:

inhibitionLikelihood
multivariateTraitLikelihood

AbstractSubstitutionModel

Elements of this type include:

ASYMQUADModel
CovarionHKYModel
HKYModel
LINEARBIASModel
MutationDeathModel
TN93Model
TWOPHASEModel
aminoAcidModel
binarySubstitutionModel
covarionModel
gtrCovarionModel
lewisMk
mkSubstitutionModel
msatAvgSubsetModel
substitutionEpochModel
yangCodonModel

Alignment

Elements of this type include:

alignment
convert
hypermutantAlignment
sequenceSimulator

ArbitraryBranchRates

Elements of this type include:

arbitraryBranchRates

Attribute

Elements of this type include:

RPNcalculator
argReassortmentNodeCount
argTimingStatistic
argTotalLengthStatistic
argTreeCount
attr
coalescentIntervalStatistic
compatibilityStatistic
compoundParameter
compoundSymmetricMatrix
correlation
date
designMatrix
diagonalMatrix
differenceStatistic
duplicatedParameter
exponentialStatistic
expressionStatistic
externalLengthStatistic
generalizedSkylinePopSizeStatistic
gmrfHeightsStatistic
gmrfPopSizeStatistic
lineageCountStatistic
logarithmStatistic
loggableStatistic
maskedParameter
matrixParameter
meanStatistic
monophylyStatistic
monotonicStatistic
mrcaTraitStatistic
multivariateOUModel
negativeStatistic
nodeHeightsStatistic
notStatistic
parameter
parsimonyStateStatistic
parsimonyStatistic
partitionStatistic
popGraph
productStatistic
rateCovarianceStatistic
rateStatistic
ratioStatistic
reciprocalStatistic
speciesTreeStatistic
statistic
subStatistic
sumStatistic
test
tmrcaStatistic
treeLengthStatistic
treeMetricStatistic
treeShapeStatistics
varianceStatistic

Attribute$Default

Elements of this type include:

BayesianSkylineLikelihood

Elements of this type include:

generalizedSkyLineLikelihood

BayesianStochasticSearchVariableSelection

Elements of this type include:

Boolean

Elements of this type include:

BooleanStatistic

Elements of this type include:

compatibilityStatistic
monophylyStatistic
monotonicStatistic
test

BranchRateModel

Elements of this type include:

ACLikelihood
UCLikelihood
arbitraryBranchRates
argDiscretizedBranchRates
argLocalClock
compoundBranchRateModel
continuousTraitRateModel
discreteTraitRateModel
discretizedBranchRates
localClockModel
mixtureModelBranchRates
randomDiscretizedBranchRates
randomLocalClockModel
rateEpochBranchRates
scaledTreeLengthModel
strictClockBranchRates

BranchRates

Elements of this type include:

ACLikelihood
UCLikelihood
arbitraryBranchRates
argDiscretizedBranchRates
argLocalClock
compoundBranchRateModel
continuousTraitRateModel
discreteTraitRateModel
discretizedBranchRates
localClockModel
mixtureModelBranchRates
randomDiscretizedBranchRates
randomLocalClockModel
rateEpochBranchRates
scaledTreeLengthModel
strictClockBranchRates

BranchingModel

Elements of this type include:

betaSplittingModel

ColourSamplerModel

Elements of this type include:

Columns

Elements of this type include:

column

CompoundParameter

Elements of this type include:

compoundParameter
compoundSymmetricMatrix
designMatrix
diagonalMatrix
matrixParameter

DataType

Elements of this type include:

extendedDataType
generalDataType
hiddenNucleotides
kStateType
microsatellite

Date

Elements of this type include:

date

DemographicModel

Elements of this type include:

cataclysm
constExpConst
constantExponential
constantLogistic
constantSize
empiricalPiecewise
expConstExp
expansion
exponentialGrowth
exponentialLogistic
exponentialSawtooth
logisticGrowth
piecewisePopulation
scaledPiecewisePopulation
twoEpoch
variableDemographic

DesignMatrix

Elements of this type include:

designMatrix

DistanceMatrix

Elements of this type include:

distanceMatrix

Distribution

Elements of this type include:

exponentialDistributionModel
gammaDistributionModel
inverseGaussianDistributionModel
logNormalDistributionModel
normalDistributionModel
onePGammaDistributionModel
uniformDistributionModel

DistributionLikelihood

Elements of this type include:

cachedPrior
distributionLikelihood
modelSpecificPseudoPrior
twoPartDistribution

Double

Elements of this type include:

double
multiLociDistance

Double;

Elements of this type include:

EmpiricalTreeDistributionModel

Elements of this type include:

empiricalTreeDistributionModel

FrequencyModel

Elements of this type include:

frequencyModel

GMRFSkyrideLikelihood

Elements of this type include:

gmrfSkyrideLikelihood
gmrfTestLikelihood

GammaSiteModel

Elements of this type include:

siteModel

GeneralizedLinearModel

Elements of this type include:

multivariateOUModel

GeoSpatialCollectionModel

Elements of this type include:

HypermutantAlignment

Elements of this type include:

Identifiable

Elements of this type include:

ACLikelihood
ASYMQUADModel
BrownianMotion
CovarionHKYModel
DirichletSiteModel
HKYModel
LINEARBIASModel
MutationDeathModel
Ornstein-Uhlenbeck
RPNcalculator
STPopulationPrior
TN93Model
TWOPHASEModel
UCLikelihood
alignment
alsTreeLikelihood
aminoAcidModel
ancestralTreeLikelihood
anyTipObservationProcess
arbitraryBranchRates
argCoalescentLikelihood
argDiscretizedBranchRates
argLocalClock
argRatePrior
argReassortmentNodeCount
argTimingStatistic
argTotalLengthStatistic
argTreeCount
argTreeLikelihood
argTreeModel
argUniformPrior
ascertainedPatterns
attributePatterns
avgPosteriorIBDReporter
benchmarker
betaSplittingModel
binaryCovarionModel
binarySubstitutionModel
binomialLikelihood
birthDeathModel
booleanLikelihood
branchingLikelihood
cachedPrior
cartogramDiffusionModel
cataclysm
categorySiteModel
coalescentIntervalStatistic
coalescentLikelihood
compatibilityStatistic
compoundBranchRateModel
compoundLikelihood
compoundParameter
compoundSymmetricMatrix
constExpConst
constantExponential
constantLogistic
constantSize
continuousTraitRateModel
convert
correlation
covarionModel
ctmcScalePrior
designMatrix
diagonalMatrix
differenceStatistic
dirichletPrior
discreteTraitRateModel
discretizedBranchRates
distanceMatrix
distributionLikelihood
dummyLikelihood
dummyModel
duplicatedParameter
empiricalDistributionLikelihood
empiricalPiecewise
empiricalTreeDistributionModel
expConstExp
expansion
exponentialBranchLengthsPrior
exponentialDistributionModel
exponentialGrowth
exponentialLogistic
exponentialMarkovLikelihood
exponentialPrior
exponentialSawtooth
exponentialStatistic
expressionStatistic
externalLengthStatistic
flatGeoSpatialPrior
frequencyModel
gammaDistributionModel
gammaPrior
generalizedSkyLineLikelihood
generalizedSkylinePopSizeStatistic
glmModel
glmSubstitutionModel
gmrfHeightsStatistic
gmrfPopSizeStatistic
gmrfSkyrideLikelihood
gmrfTestLikelihood
greatCircleDiffusionModel
gtrCovarionModel
gtrModel
hierarchicalPartitionLikelihood
hypermutantAlignment
hypermutantErrorModel
ibdReporter
inhibitionLikelihood
inverseGaussianDistributionModel
invgammaPrior
laplacePrior
lewisMk
lineageCountStatistic
localClockModel
location
logNormalDistributionModel
logNormalPrior
logarithmStatistic
loggableStatistic
logisticGrowth
maskedParameter
matrixParameter
mcmc
meanStatistic
mergePatterns
microsatellitePattern
microsatelliteSamplerTreeLikelihood
microsatelliteSamplerTreeModel
microsatelliteSimulator
mixedDistributionLikelihood
mixtureCartogramDiffusionModel
mixtureModel
mixtureModelBranchRates
mkSubstitutionModel
modelSpecificPseudoPrior
monophylyStatistic
monotonicStatistic
mrcaTraitStatistic
msatAvgSubsetModel
multivariateDiffusionModel
multivariateGammaPrior
multivariateInverseWishartPrior
multivariateNormalPrior
multivariateOUModel
multivariateTDiffusionModel
multivariateTraitLikelihood
multivariateWishartPrior
negativeStatistic
neighborJoiningTree
newick
nodeHeightsStatistic
nodePosteriorLikelihood
normalDistributionModel
normalPrior
notStatistic
oneOnXPrior
onePGammaDistributionModel
optimizer
ovariableSkyLineLikelihood
parameter
parsimonyStateStatistic
parsimonyStatistic
partitionStatistic
patternSubSet
patterns
piecewisePopulation
poissonPartitionLikelihood
poissonPrior
popGraph
positiveDefiniteSubstitutionModel
productStatistic
randomDiscretizedBranchRates
randomLocalClockModel
randomLocalYuleModel
randomWalk
rateCovarianceStatistic
rateEpochBranchRates
rateStatistic
ratioStatistic
reciprocalStatistic
sampleStateAndCategoryModel
sampleStateModel
scaledPiecewisePopulation
scaledTreeLengthModel
sequence
sequenceErrorModel
sequenceSimulator
singleTipObservationProcess
siteModel
sp
speciationLikelihood
species
speciesCoalescent
speciesTree
speciesTreePopulationPrior
speciesTreeStatistic
statistic
strictClockBranchRates
subStatistic
substitutionEpochModel
sumStatistic
taxa
taxon
test
threadedCompoundLikelihood
tipHeightLikelihood
tkf91Likelihood
tkf91Model
tmrcaStatistic
tree
treeLengthStatistic
treeLikelihood
treeMetricStatistic
treeModel
treeShapeStatistics
twoEpoch
twoPartDistribution
uniformDistributionModel
uniformNodeHeightPrior
uniformPartitionLikelihood
uniformPrior
upgmaTree
variableDemographic
varianceStatistic
yangCodonModel
yuleModel

Integer

Elements of this type include:

integer

Integer;

Elements of this type include:

IntegratedMultivariateTraitLikelihood

Elements of this type include:

KMLCoordinates

Elements of this type include:

coordinates

Likelihood

Elements of this type include:

ACLikelihood
ASYMQUADModel
BrownianMotion
LINEARBIASModel
Ornstein-Uhlenbeck
STPopulationPrior
TWOPHASEModel
UCLikelihood
alsTreeLikelihood
ancestralTreeLikelihood
arbitraryBranchRates
argCoalescentLikelihood
argDiscretizedBranchRates
argLocalClock
argRatePrior
argTreeLikelihood
argUniformPrior
avgPosteriorIBDReporter
benchmarker
binomialLikelihood
booleanLikelihood
branchingLikelihood
cachedPrior
coalescentLikelihood
compoundBranchRateModel
compoundLikelihood
continuousTraitRateModel
ctmcScalePrior
dirichletPrior
discreteTraitRateModel
discretizedBranchRates
distributionLikelihood
dummyLikelihood
dummyModel
empiricalDistributionLikelihood
exponentialBranchLengthsPrior
exponentialMarkovLikelihood
exponentialPrior
flatGeoSpatialPrior
gammaPrior
generalizedSkyLineLikelihood
glmModel
gmrfSkyrideLikelihood
gmrfTestLikelihood
hierarchicalPartitionLikelihood
ibdReporter
inhibitionLikelihood
invgammaPrior
laplacePrior
localClockModel
logNormalPrior
microsatelliteSamplerTreeLikelihood
mixedDistributionLikelihood
mixtureModelBranchRates
modelSpecificPseudoPrior
msatAvgSubsetModel
multivariateGammaPrior
multivariateInverseWishartPrior
multivariateNormalPrior
multivariateOUModel
multivariateTraitLikelihood
multivariateWishartPrior
nodePosteriorLikelihood
normalPrior
oneOnXPrior
ovariableSkyLineLikelihood
poissonPartitionLikelihood
poissonPrior
randomDiscretizedBranchRates
randomLocalClockModel
randomWalk
rateEpochBranchRates
scaledTreeLengthModel
speciationLikelihood
speciesCoalescent
speciesTreePopulationPrior
strictClockBranchRates
threadedCompoundLikelihood
tipHeightLikelihood
tkf91Likelihood
treeLikelihood
twoPartDistribution
uniformNodeHeightPrior
uniformPartitionLikelihood
uniformPrior

LinearRegression

Elements of this type include:

Location

Elements of this type include:

location

Loggable

Elements of this type include:

ACLikelihood
ASYMQUADModel
BrownianMotion
LINEARBIASModel
Ornstein-Uhlenbeck
RPNcalculator
STPopulationPrior
TWOPHASEModel
UCLikelihood
alsTreeLikelihood
ancestralTrait
ancestralTreeLikelihood
arbitraryBranchRates
argCoalescentLikelihood
argDiscretizedBranchRates
argLocalClock
argRatePrior
argReassortmentNodeCount
argTimingStatistic
argTotalLengthStatistic
argTreeCount
argTreeLikelihood
argTreeModel
argUniformPrior
avgPosteriorIBDReporter
benchmarker
binomialLikelihood
booleanLikelihood
branchingLikelihood
cachedPrior
coalescentIntervalStatistic
coalescentLikelihood
compatibilityStatistic
compoundBranchRateModel
compoundLikelihood
compoundParameter
compoundSymmetricMatrix
continuousTraitRateModel
correlation
ctmcScalePrior
designMatrix
diagonalMatrix
differenceStatistic
dirichletPrior
discreteTraitRateModel
discretizedBranchRates
distributionLikelihood
dummyLikelihood
dummyModel
duplicatedParameter
empiricalDistributionLikelihood
exponentialBranchLengthsPrior
exponentialMarkovLikelihood
exponentialPrior
exponentialStatistic
expressionStatistic
externalLengthStatistic
flatGeoSpatialPrior
gammaPrior
generalizedSkyLineLikelihood
generalizedSkylinePopSizeStatistic
glmModel
gmrfHeightsStatistic
gmrfPopSizeStatistic
gmrfSkyrideLikelihood
gmrfTestLikelihood
hierarchicalPartitionLikelihood
ibdReporter
inhibitionLikelihood
invgammaPrior
laplacePrior
lineageCountStatistic
localClockModel
logNormalPrior
logarithmStatistic
loggableStatistic
maskedParameter
matrixParameter
meanStatistic
microsatelliteSamplerTreeLikelihood
mixedDistributionLikelihood
mixtureModelBranchRates
modelSpecificPseudoPrior
monophylyStatistic
monotonicStatistic
mrcaTraitStatistic
msatAvgSubsetModel
multivariateGammaPrior
multivariateInverseWishartPrior
multivariateNormalPrior
multivariateOUModel
multivariateTraitLikelihood
multivariateWishartPrior
negativeStatistic
nodeHeightsStatistic
nodePosteriorLikelihood
normalPrior
notStatistic
oneOnXPrior
operators
ovariableSkyLineLikelihood
parameter
parsimonyStateStatistic
parsimonyStatistic
partitionStatistic
poissonPartitionLikelihood
poissonPrior
popGraph
positiveDefiniteSubstitutionModel
productStatistic
randomDiscretizedBranchRates
randomLocalClockModel
randomWalk
rateCovarianceStatistic
rateEpochBranchRates
rateStatistic
ratioStatistic
reciprocalStatistic
scaledTreeLengthModel
speciationLikelihood
speciesCoalescent
speciesTreePopulationPrior
speciesTreeStatistic
statistic
strictClockBranchRates
subStatistic
sumStatistic
test
threadedCompoundLikelihood
tipHeightLikelihood
tkf91Likelihood
tmrcaStatistic
treeLengthStatistic
treeLikelihood
treeMetricStatistic
treeShapeStatistics
twoPartDistribution
uniformNodeHeightPrior
uniformPartitionLikelihood
uniformPrior
varianceStatistic

Logger

Elements of this type include:

log
logArg
logArgTree
logML
logTree
randomLocalLogger

MCMCOperator

Elements of this type include:

ARGEventOperator
FixedNodeheightSubtreePruneRegraft
GibbsPruneAndRegraft
GibbsSubtreeSwap
ImportanceNarrowExchange
ImportancePruneAndRegraft
ImportanceSubtreeSwap
NearestNeighborInterchange
addremoveARGEvent
alignmentChunkOperator
argNarrowExchange
argPartitionOperator
argSubtreeSlide
argSwapOperator
argWideExchange
bitFlipInSubstitutionModelOperator
bitFlipOperator
bitMoveOperator
bitSwapOperator
centeredScale
deltaExchange
dirtyLikelihood
discretizedLocationOperator
empiricalTreeDistributionOperator
generalizedSkylineGibbsOperator
gmrfBlockUpdateOperator
gmrfFixedEffectsGibbsOperator
jointOperator
logRandomWalkOperator
microsatUpDownOperator
msatModelSelectOperator
msatModelSwitchOperator
mvouOperator
narrowExchange
newARGEvent
nodeReHeight
normalGammaPrecisionGibbsOperator
normalNormalMeanGibbsOperator
poolSwapOperator
precisionGibbsOperator
randomWalkIntegerNodeHeightWeightedOperator
randomWalkIntegerOperator
randomWalkIntegerSetSizeWeightedOperator
randomWalkOnMapOperator
randomWalkOperator
rateBitExchangeOperator
rateExchange
rateSampleOperator
rateScaleOperator
rateVarianceScaleOperator
regressionGibbsEffectOperator
regressionGibbsPrecisionOperator
regressionMetropolizedIndicatorOperator
sampleNonActiveOperator
scaleOperator
selectorOperator
setOperator
slidingPatternsOperator
subtreeSlide
swapOperator
teamOperator
tipStateSwapOperator
tipTraitSwapOperator
traitGibbsOperator
traitRateGibbsOperator
treeBitMoveOperator
treeBitRandomWalk
treeUniform
uniformIntegerOperator
uniformOperator
upDownOperator
wideExchange
wilsonBalding

MapDiffusionModel

Elements of this type include:

MatrixParameter

Elements of this type include:

compoundSymmetricMatrix
designMatrix
diagonalMatrix
matrixParameter

Microsatellite

Elements of this type include:

microsatellite

MicrosatelliteModel

Elements of this type include:

ASYMQUADModel
LINEARBIASModel
TWOPHASEModel
msatAvgSubsetModel

MicrosatelliteSamplerTreeModel

Elements of this type include:

microsatelliteSamplerTreeModel

Model

Elements of this type include:

ACLikelihood
ASYMQUADModel
BrownianMotion
CovarionHKYModel
DirichletSiteModel
HKYModel
LINEARBIASModel
MutationDeathModel
Ornstein-Uhlenbeck
TN93Model
TWOPHASEModel
UCLikelihood
alsTreeLikelihood
aminoAcidModel
ancestralTreeLikelihood
anyTipObservationProcess
arbitraryBranchRates
argCoalescentLikelihood
argDiscretizedBranchRates
argLocalClock
argRatePrior
argTreeModel
argUniformPrior
betaSplittingModel
binaryCovarionModel
binarySubstitutionModel
birthDeathModel
branchingLikelihood
cartogramDiffusionModel
cataclysm
categorySiteModel
coalescentLikelihood
compoundBranchRateModel
constExpConst
constantExponential
constantLogistic
constantSize
continuousTraitRateModel
covarionModel
ctmcScalePrior
discreteTraitRateModel
discretizedBranchRates
dummyModel
empiricalPiecewise
empiricalTreeDistributionModel
expConstExp
expansion
exponentialBranchLengthsPrior
exponentialDistributionModel
exponentialGrowth
exponentialLogistic
exponentialMarkovLikelihood
exponentialSawtooth
frequencyModel
gammaDistributionModel
generalizedSkyLineLikelihood
glmSubstitutionModel
gmrfSkyrideLikelihood
gmrfTestLikelihood
greatCircleDiffusionModel
gtrCovarionModel
gtrModel
hierarchicalPartitionLikelihood
hypermutantErrorModel
inhibitionLikelihood
inverseGaussianDistributionModel
lewisMk
localClockModel
logNormalDistributionModel
logisticGrowth
microsatelliteSamplerTreeLikelihood
microsatelliteSamplerTreeModel
mixtureCartogramDiffusionModel
mixtureModel
mixtureModelBranchRates
mkSubstitutionModel
msatAvgSubsetModel
multivariateDiffusionModel
multivariateOUModel
multivariateTDiffusionModel
multivariateTraitLikelihood
normalDistributionModel
onePGammaDistributionModel
ovariableSkyLineLikelihood
piecewisePopulation
poissonPartitionLikelihood
positiveDefiniteSubstitutionModel
randomDiscretizedBranchRates
randomLocalClockModel
randomLocalYuleModel
randomWalk
rateEpochBranchRates
sampleStateAndCategoryModel
sampleStateModel
scaledPiecewisePopulation
scaledTreeLengthModel
sequenceErrorModel
singleTipObservationProcess
siteModel
speciationLikelihood
species
speciesTree
strictClockBranchRates
substitutionEpochModel
tkf91Likelihood
tkf91Model
treeLikelihood
treeModel
twoEpoch
uniformDistributionModel
uniformNodeHeightPrior
uniformPartitionLikelihood
variableDemographic
yangCodonModel
yuleModel

MultivariateDiffusionModel

Elements of this type include:

cartogramDiffusionModel
greatCircleDiffusionModel
mixtureCartogramDiffusionModel
multivariateDiffusionModel
multivariateTDiffusionModel

MultivariateDistributionLikelihood

Elements of this type include:

multivariateGammaPrior
multivariateNormalPrior

MutationDeathType

Elements of this type include:

extendedDataType

NodePosteriorTreeLikelihood

Elements of this type include:

OldAbstractCoalescentLikelihood

Elements of this type include:

generalizedSkyLineLikelihood
gmrfSkyrideLikelihood
gmrfTestLikelihood
ovariableSkyLineLikelihood

OnePhaseModel

Elements of this type include:

ASYMQUADModel
LINEARBIASModel

OperatorSchedule

Elements of this type include:

operators

Parameter

Elements of this type include:

compoundParameter
compoundSymmetricMatrix
designMatrix
diagonalMatrix
duplicatedParameter
maskedParameter
matrixParameter
parameter

ParametricDistributionModel

Elements of this type include:

exponentialDistributionModel
gammaDistributionModel
inverseGaussianDistributionModel
logNormalDistributionModel
normalDistributionModel
onePGammaDistributionModel
uniformDistributionModel

PatternList

Elements of this type include:

alignment
ascertainedPatterns
attributePatterns
convert
hypermutantAlignment
mergePatterns
microsatellitePattern
microsatelliteSimulator
patternSubSet
patterns
sequenceSimulator

Patterns

Elements of this type include:

microsatellitePattern
microsatelliteSimulator

Polygon2D

Elements of this type include:

circle
polygon

RandomLocalTreeVariable

Elements of this type include:

randomLocalClockModel
randomLocalYuleModel

RateEvolutionLikelihood

Elements of this type include:

ACLikelihood
UCLikelihood

SampledMultivariateTraitLikelihood

Elements of this type include:

Scalable

Elements of this type include:

speciesTree

Sequence

Elements of this type include:

sequence

SimpleMCMCOperator

Elements of this type include:

ARGEventOperator
FixedNodeheightSubtreePruneRegraft
ImportanceNarrowExchange
ImportancePruneAndRegraft
ImportanceSubtreeSwap
NearestNeighborInterchange
addremoveARGEvent
alignmentChunkOperator
argNarrowExchange
argPartitionOperator
argSubtreeSlide
argSwapOperator
argWideExchange
bitFlipOperator
bitMoveOperator
bitSwapOperator
centeredScale
dirtyLikelihood
empiricalTreeDistributionOperator
generalizedSkylineGibbsOperator
gmrfFixedEffectsGibbsOperator
jointOperator
logRandomWalkOperator
microsatUpDownOperator
mvouOperator
narrowExchange
newARGEvent
nodeReHeight
poolSwapOperator
randomWalkIntegerNodeHeightWeightedOperator
randomWalkIntegerOperator
randomWalkIntegerSetSizeWeightedOperator
rateExchange
rateSampleOperator
rateScaleOperator
rateVarianceScaleOperator
sampleNonActiveOperator
scaleOperator
selectorOperator
setOperator
subtreeSlide
swapOperator
teamOperator
tipStateSwapOperator
tipTraitSwapOperator
treeUniform
uniformIntegerOperator
uniformOperator
upDownOperator
wideExchange
wilsonBalding

SimpleNode

Elements of this type include:

node

SiteList

Elements of this type include:

alignment
convert
hypermutantAlignment
sequenceSimulator

SiteModel

Elements of this type include:

DirichletSiteModel
categorySiteModel
sampleStateAndCategoryModel
sampleStateModel
siteModel

SitePatterns

Elements of this type include:

SpeciationModel

Elements of this type include:

birthDeathModel
randomLocalYuleModel
yuleModel

SpeciesBindings

Elements of this type include:

species

SpeciesBindings$SPinfo

Elements of this type include:

sp

SpeciesTreeModel

Elements of this type include:

speciesTree

Statistic

Elements of this type include:

RPNcalculator
argReassortmentNodeCount
argTimingStatistic
argTotalLengthStatistic
argTreeCount
coalescentIntervalStatistic
compatibilityStatistic
compoundParameter
compoundSymmetricMatrix
correlation
designMatrix
diagonalMatrix
differenceStatistic
duplicatedParameter
exponentialStatistic
expressionStatistic
externalLengthStatistic
generalizedSkylinePopSizeStatistic
gmrfHeightsStatistic
gmrfPopSizeStatistic
lineageCountStatistic
logarithmStatistic
loggableStatistic
maskedParameter
matrixParameter
meanStatistic
monophylyStatistic
monotonicStatistic
mrcaTraitStatistic
multivariateOUModel
negativeStatistic
nodeHeightsStatistic
notStatistic
parameter
parsimonyStateStatistic
parsimonyStatistic
partitionStatistic
popGraph
productStatistic
rateCovarianceStatistic
rateStatistic
ratioStatistic
reciprocalStatistic
speciesTreeStatistic
statistic
subStatistic
sumStatistic
test
tmrcaStatistic
treeLengthStatistic
treeMetricStatistic
treeShapeStatistics
varianceStatistic

StatisticList

Elements of this type include:

ACLikelihood
ASYMQUADModel
BrownianMotion
CovarionHKYModel
DirichletSiteModel
HKYModel
LINEARBIASModel
MutationDeathModel
Ornstein-Uhlenbeck
TN93Model
TWOPHASEModel
UCLikelihood
alsTreeLikelihood
aminoAcidModel
ancestralTreeLikelihood
anyTipObservationProcess
arbitraryBranchRates
argCoalescentLikelihood
argDiscretizedBranchRates
argLocalClock
argRatePrior
argTreeModel
argUniformPrior
betaSplittingModel
binaryCovarionModel
binarySubstitutionModel
birthDeathModel
branchingLikelihood
cartogramDiffusionModel
cataclysm
categorySiteModel
coalescentLikelihood
compoundBranchRateModel
constExpConst
constantExponential
constantLogistic
constantSize
continuousTraitRateModel
covarionModel
ctmcScalePrior
discreteTraitRateModel
discretizedBranchRates
dummyModel
empiricalPiecewise
empiricalTreeDistributionModel
expConstExp
expansion
exponentialBranchLengthsPrior
exponentialDistributionModel
exponentialGrowth
exponentialLogistic
exponentialMarkovLikelihood
exponentialSawtooth
frequencyModel
gammaDistributionModel
generalizedSkyLineLikelihood
gmrfSkyrideLikelihood
gmrfTestLikelihood
greatCircleDiffusionModel
gtrCovarionModel
hierarchicalPartitionLikelihood
hypermutantErrorModel
inhibitionLikelihood
inverseGaussianDistributionModel
lewisMk
localClockModel
logNormalDistributionModel
logisticGrowth
microsatelliteSamplerTreeLikelihood
microsatelliteSamplerTreeModel
mixtureCartogramDiffusionModel
mixtureModelBranchRates
mkSubstitutionModel
msatAvgSubsetModel
multivariateDiffusionModel
multivariateOUModel
multivariateTDiffusionModel
multivariateTraitLikelihood
normalDistributionModel
onePGammaDistributionModel
ovariableSkyLineLikelihood
piecewisePopulation
poissonPartitionLikelihood
positiveDefiniteSubstitutionModel
randomDiscretizedBranchRates
randomLocalClockModel
randomLocalYuleModel
randomWalk
rateEpochBranchRates
sampleStateAndCategoryModel
sampleStateModel
scaledPiecewisePopulation
scaledTreeLengthModel
sequenceErrorModel
singleTipObservationProcess
siteModel
speciationLikelihood
species
speciesTree
strictClockBranchRates
substitutionEpochModel
tkf91Likelihood
tkf91Model
treeLikelihood
treeModel
twoEpoch
uniformDistributionModel
uniformNodeHeightPrior
uniformPartitionLikelihood
variableDemographic
yangCodonModel
yuleModel

String

Elements of this type include:

string

String;

Elements of this type include:

SubstitutionModel

Elements of this type include:

ASYMQUADModel
CovarionHKYModel
HKYModel
LINEARBIASModel
MutationDeathModel
TN93Model
TWOPHASEModel
aminoAcidModel
binaryCovarionModel
binarySubstitutionModel
covarionModel
glmSubstitutionModel
gtrCovarionModel
gtrModel
lewisMk
mkSubstitutionModel
msatAvgSubsetModel
positiveDefiniteSubstitutionModel
substitutionEpochModel
yangCodonModel

TKF91Likelihood

Elements of this type include:

tkf91Likelihood

TKF91Model

Elements of this type include:

tkf91Model

TabularData

Elements of this type include:

VDAnalysis
logFileTrace

Taxa

Elements of this type include:

taxa

Taxon

Elements of this type include:

sp
taxon

TaxonList

Elements of this type include:

alignment
argTreeModel
ascertainedPatterns
attributePatterns
convert
distanceMatrix
empiricalTreeDistributionModel
hypermutantAlignment
mergePatterns
microsatellitePattern
microsatelliteSimulator
neighborJoiningTree
newick
patternSubSet
patterns
sequenceSimulator
speciesTree
taxa
tree
treeModel
upgmaTree

TipPartialsModel

Elements of this type include:

hypermutantErrorModel
sequenceErrorModel

Tree

Elements of this type include:

argTreeModel
empiricalTreeDistributionModel
neighborJoiningTree
newick
speciesTree
tree
treeModel
upgmaTree

TreeAttributeProvider

Elements of this type include:

cartogramDiffusionModel
greatCircleDiffusionModel
mixtureCartogramDiffusionModel
multivariateDiffusionModel
multivariateTDiffusionModel

TreeColouringProvider

Elements of this type include:

TreeLikelihood

Elements of this type include:

alsTreeLikelihood
ancestralTreeLikelihood
treeLikelihood

TreeLogger$LogUpon

Elements of this type include:

ImportanceNarrowExchange
speciesTree

TreeModel

Elements of this type include:

empiricalTreeDistributionModel
treeModel

TreeTraitProvider

Elements of this type include:

ancestralTreeLikelihood
inhibitionLikelihood
logAllTraits
multivariateTraitLikelihood
randomLocalYuleModel
speciesTree

ValuesPool

Elements of this type include:

Variable

Elements of this type include:

compoundParameter
compoundSymmetricMatrix
designMatrix
diagonalMatrix
duplicatedParameter
maskedParameter
matrixParameter
parameter

VariableDemographicModel

Elements of this type include:

variableDemographic

BEAST v1.6.x XML Reference

From BEAST Software

Contents

BEAST v1.6.0 Parser Library (2002-2010)

<ACLikelihood> element

<addremoveARGEvent> element

<alignment> element

<alignmentChunkOperator> element

<alsTreeLikelihood> element

<aminoAcidModel> element

<ancestralTrait> element

<ancestralTrait> element

<ancestralTreeLikelihood> element

<anyTipObservationProcess> element

<arbitraryBranchRates> element

<argCoalescentLikelihood> element

<argDiscretizedBranchRates> element

<ARGEventOperator> element

<argLocalClock> element

<argTreeModel> element

<argNarrowExchange> element

<argPartitionOperator> element

<argRatePrior> element

<argReassortmentNodeCount> element

<argSubtreeSlide> element

<argSwapOperator> element

<argTimingStatistic> element

<argTotalLengthStatistic> element

<argTraceAnalysis> element

<argTreeCount> element

<argTreeLikelihood> element

<argTreeModel> element

<argUniformPrior> element

<argWideExchange> element

<array> element

<ascertainedPatterns> element

<ASYMQUADModel> element

<attr> element

<attributePatterns> element

<attributes> element

<avgPosteriorIBDReporter> element

<ancestralTreeLikelihood> element

<complexSubstitutionModel> element

<DirichletSiteModel> element

<frequencyModel> element

<siteModel> element

<benchmarker> element

<betaSplittingModel> element

<binaryCovarionModel> element

<binarySubstitutionModel> element

<binomialLikelihood> element

<birthDeathModel> element

<bitFlipInSubstitutionModelOperator> element

<bitFlipOperator> element

<bitMoveOperator> element

<bitSwapOperator> element

<booleanLikelihood> element

<branchDirections> element

<branchingLikelihood> element

<branchMagnitudes> element

<BrownianMotion> element

<cachedPrior> element

<cartogramDiffusionModel> element

<cataclysm> element

<categorySiteModel> element

<centeredScale> element

<circle> element

<coalescentIntervalStatistic> element

<coalescentLikelihood> element

<coalescentTree> element

<column> element

<compatibilityStatistic> element

<complexSubstitutionModel> element

<compoundBranchRateModel> element

<compoundLikelihood> element

<compoundParameter> element

<compoundSymmetricMatrix> element

<constantExponential> element

<constantLogistic> element

<constantSize> element

`<ACLikelihood>` element

`<addremoveARGEvent>` element

`<alignment>` element

`<alignmentChunkOperator>` element

`<alsTreeLikelihood>` element

`<aminoAcidModel>` element

`<ancestralTrait>` element

`<ancestralTrait>` element

`<ancestralTreeLikelihood>` element

`<anyTipObservationProcess>` element

`<arbitraryBranchRates>` element

`<argCoalescentLikelihood>` element

`<argDiscretizedBranchRates>` element

`<ARGEventOperator>` element

`<argLocalClock>` element

`<argTreeModel>` element

`<argNarrowExchange>` element

`<argPartitionOperator>` element

`<argRatePrior>` element

`<argReassortmentNodeCount>` element

`<argSubtreeSlide>` element

`<argSwapOperator>` element

`<argTimingStatistic>` element

`<argTotalLengthStatistic>` element

`<argTraceAnalysis>` element

`<argTreeCount>` element

`<argTreeLikelihood>` element

`<argTreeModel>` element

`<argUniformPrior>` element

`<argWideExchange>` element

`<array>` element

`<ascertainedPatterns>` element

`<ASYMQUADModel>` element

`<attr>` element

`<attributePatterns>` element

`<attributes>` element

`<avgPosteriorIBDReporter>` element

`<ancestralTreeLikelihood>` element

`<complexSubstitutionModel>` element

`<DirichletSiteModel>` element

`<frequencyModel>` element

`<siteModel>` element

`<benchmarker>` element

`<betaSplittingModel>` element

`<binaryCovarionModel>` element

`<binarySubstitutionModel>` element

`<binomialLikelihood>` element

`<birthDeathModel>` element

`<bitFlipInSubstitutionModelOperator>` element

`<bitFlipOperator>` element

`<bitMoveOperator>` element

`<bitSwapOperator>` element

`<booleanLikelihood>` element

`<branchDirections>` element

`<branchingLikelihood>` element

`<branchMagnitudes>` element

`<BrownianMotion>` element

`<cachedPrior>` element

`<cartogramDiffusionModel>` element

`<cataclysm>` element

`<categorySiteModel>` element

`<centeredScale>` element

`<circle>` element

`<coalescentIntervalStatistic>` element

`<coalescentLikelihood>` element

`<coalescentTree>` element

`<column>` element

`<compatibilityStatistic>` element

`<complexSubstitutionModel>` element

`<compoundBranchRateModel>` element

`<compoundLikelihood>` element

`<compoundParameter>` element

`<compoundSymmetricMatrix>` element

`<constantExponential>` element

`<constantLogistic>` element

`<constantSize>` element

`<constExpConst>` element

`<continuousTraitRateModel>` element

`<convert>` element

`<coordinates>` element