Uses of Class
pal.misc.TimeOrderCharacterData
Packages that use TimeOrderCharacterData
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for the analysis of "measurably evolving populations" (mep).
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Uses of TimeOrderCharacterData in pal.coalescent
Methods in pal.coalescent with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionSerialCoalescentSimulator.simulateIntervals
(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree) Simulates a set of CoalescentIntervals from a genealogy.Constructors in pal.coalescent with parameters of type TimeOrderCharacterDataModifierConstructorDescriptionSerialCoalescentGenerator
(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate) Results will not contain alignmentsSerialCoalescentGenerator
(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher) Results will not contain alignmentsSerialCoalescentGenerator
(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory) SerialCoalescentGenerator
(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory) -
Uses of TimeOrderCharacterData in pal.eval
Methods in pal.eval with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic final Tree
LikelihoodTool.optimiseMRDT
(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore) Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.static final Tree
LikelihoodTool.optimiseMRDT
(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore) Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.static final Tree
LikelihoodTool.optimiseSRDT
(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore) Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter. -
Uses of TimeOrderCharacterData in pal.gui
Methods in pal.gui that return TimeOrderCharacterDataModifier and TypeMethodDescriptionfinal TimeOrderCharacterData
TreePainter.getTimeOrderCharacterData()
Methods in pal.gui with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionfinal void
TreePainter.setTimeOrderCharacterData
(TimeOrderCharacterData tocd) Constructors in pal.gui with parameters of type TimeOrderCharacterDataModifierConstructorDescriptionTreeComponent
(Tree tree, TimeOrderCharacterData tocd, boolean usingSymbols) -
Uses of TimeOrderCharacterData in pal.mep
Methods in pal.mep that return TimeOrderCharacterDataMethods in pal.mep with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionDeltaModel.generateInstance
(TimeOrderCharacterData tocd) static final DeltaModel
DeltaModel.Utils.getDisjointBased
(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD) static final MutationRateModel.Factory
SteppedMutationRate.getFactory
(double[] muChanges, TimeOrderCharacterData tocd) Generate a MutationRateModel.Factory class for a SteppedMutationRateMutationRateModel.scale
(TimeOrderCharacterData toScale) Constructors in pal.mep with parameters of type TimeOrderCharacterDataModifierConstructorDescriptionSteppedMutationRate
(double[] rates, TimeOrderCharacterData timeInfo) Construct mutation rate model of a give rate in given units.SteppedMutationRate
(double[] rates, TimeOrderCharacterData timeInfo, boolean fixed) Construct mutation rate model of a give rate in given units. -
Uses of TimeOrderCharacterData in pal.misc
Methods in pal.misc that return TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic TimeOrderCharacterData
TimeOrderCharacterData.clone
(TimeOrderCharacterData tocd) Returns a clone of the specified TimeOrderCharacterDatafinal TimeOrderCharacterData
TimeOrderCharacterData.createSubgroup
(int subgroupNumber) Creates a TimeOrderCharacterData which is a subset of this sub group.TimeOrderCharacterData.generateDummyTimedTOCD
(double[] sampleRates) TimeOrderCharacterData.generateExpectedSubsitutionsTimedTOCD
(double[] sampleRates) Given an array of rates between samples (matching exactly the samples in order) then produces a TimeOrderCharacterData object that is timed by Expected Substitutions.TimeOrderCharacterData.getReordered
(IdGroup base) Creates a new TimeOrderCharacterData object with the same properites as this one but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)TimeOrderCharacterData.scale
(double rate, int newUnits) Extracts a subset of a TimeOrderCharacterData.Methods in pal.misc with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic TimeOrderCharacterData
TimeOrderCharacterData.clone
(TimeOrderCharacterData tocd) Returns a clone of the specified TimeOrderCharacterDatavoid
TimeOrderCharacterData.setOrdinals
(TimeOrderCharacterData tocd) Set time ordinals from another TimeOrderCharacterData.void
TimeOrderCharacterData.setOrdinals
(TimeOrderCharacterData tocd, IdGroup standard, boolean doTimes) Set time ordinals from another TimeOrderCharacterData.void
TimeOrderCharacterData.setTimesAndOrdinals
(TimeOrderCharacterData tocd) Constructors in pal.misc with parameters of type TimeOrderCharacterData -
Uses of TimeOrderCharacterData in pal.substmodel
Methods in pal.substmodel with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic final TemporalModelChange
TemporalModelChange.Utils.getSpecificTime
(double time, TimeOrderCharacterData tocd) -
Uses of TimeOrderCharacterData in pal.supgma
Methods in pal.supgma with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionvoid
RateHandler.adjustDistances
(double[][] matrix, TimeOrderCharacterData tocd) void
ThetaHandler.adjustDistances
(double[][] matrix, TimeOrderCharacterData tocd) ThetaHandler.generateDemographicModel
(double[] deltas, double[] thetas, TimeOrderCharacterData tocd) May return null if not possible to infer demographic modelRateHandler.generateRateModelFactory
(double[] deltas, TimeOrderCharacterData tocd) int
RateHandler.getNumberOfParameters
(TimeOrderCharacterData tocd) int
ThetaHandler.getNumberOfParameters
(TimeOrderCharacterData tocd) Constructors in pal.supgma with parameters of type TimeOrderCharacterDataModifierConstructorDescriptionSUPGMABase
(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd) SUPGMADistanceMatrix
(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel) Uses date/time information and a constant rate to correct distance matrices.SUPGMATree
(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm) constructor SUPGMA treeSUPGMATree
(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm) constructor SUPGMA tree -
Uses of TimeOrderCharacterData in pal.tree
Methods in pal.tree that return TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic TimeOrderCharacterData
TreeUtils.extractTimeOrderCharacterData
(Tree tree, int units) Extracts a time order character data from a tree.Methods in pal.tree with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic final ParameterizedTree.Factory
MutationRateModelTree.getParameterizedTreeFactory
(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd) Obtain a ParameterizedTree.Factory for generating Unconstrained treesConstructors in pal.tree with parameters of type TimeOrderCharacterDataModifierConstructorDescriptionMutationRateModelTree
(Tree t, TimeOrderCharacterData tocd, MutationRateModel model) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).MutationRateModelTree
(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). -
Uses of TimeOrderCharacterData in pal.xml
Methods in pal.xml that return TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic TimeOrderCharacterData
ElementParser.parseTimeDataElement
(Element e) Methods in pal.xml with parameters of type TimeOrderCharacterDataModifier and TypeMethodDescriptionstatic Element
ElementFactory.createTimeDataElement
(TimeOrderCharacterData tocd, Document document)