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Packages that use RateCategory | |
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Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Models | Provides classes for defing a phylogenetic model. |
Uses of RateCategory in Likelihood |
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Methods in Likelihood that return RateCategory | |
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RateCategory |
Likelihood.SiteLikelihood.getMostProbableRateCategory()
Gets the most probable rate category |
Methods in Likelihood that return types with arguments of type RateCategory | |
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java.util.Set<RateCategory> |
Probabilities.getRateCategory()
Gets the set of RateClasses that we have calculated probailities for |
Methods in Likelihood with parameters of type RateCategory | |
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double |
Probabilities.getFreq(RateCategory r,
java.lang.String state)
Gets the root frequency for a specified state under a specified RateClass |
Probabilities.RateProbabilities |
Probabilities.getP(RateCategory r)
Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass |
double |
Likelihood.SiteLikelihood.getRateCategoryProbability(RateCategory rc)
Gets the probability of being in a rate category |
Likelihood.RateLikelihood |
Likelihood.SiteLikelihood.getRateLikelihood(RateCategory rate)
Get the likelihood for a single rate class |
double |
Probabilities.getRateP(RateCategory r)
Gets the probability of a rate class |
Uses of RateCategory in Models |
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Methods in Models that return RateCategory | |
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static RateCategory |
RateCategory.fromFile(java.io.File mfile)
Creates an instance from the information in a file. |
Methods in Models that return types with arguments of type RateCategory | |
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java.util.Set<RateCategory> |
Model.getRates()
Gets a set of rate classes in the model |
java.util.Iterator<RateCategory> |
Model.iterator()
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Methods in Models with parameters of type RateCategory | |
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static Model |
Model.gammaRates(RateCategory r,
java.lang.String gamma,
int cats)
Creates a new model with multiple rate classes distributed by a gamma distribution (see Yang 1993) based on a single rate class |
double |
Model.getFreq(RateCategory r)
Gets the frquency of a rate class |
Constructors in Models with parameters of type RateCategory | |
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Model(RateCategory r)
Creates a new model with a single rate class |
Constructor parameters in Models with type arguments of type RateCategory | |
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Model(java.util.Map<RateCategory,java.lang.String> freq)
Creates a new model with multiple rate classes |
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