Uses of Interface
pal.mep.DeltaModel
Packages that use DeltaModel
Package
Description
Classes for the analysis of "measurably evolving populations" (mep).
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Uses of DeltaModel in pal.mep
Methods in pal.mep that return DeltaModelModifier and TypeMethodDescriptionstatic final DeltaModelDeltaModel.Utils.getDisjointBased(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD) static final DeltaModelDeltaModel.Utils.getMutationRateModelBased(MutationRateModel.Factory mepFactory) For interfacing with time based mutation rate modelsstatic final DeltaModelDeltaModel.Utils.getUntimedBased()For serial sampled analysis when no time information is available.static final DeltaModelDeltaModel.Utils.getUntimedBased(double[] initalDeltas) For serial sampled analysis when no time information is available.Methods in pal.mep with parameters of type DeltaModelModifier and TypeMethodDescriptionstatic final DeltaModelDeltaModel.Utils.getDisjointBased(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD) -
Uses of DeltaModel in pal.supgma
Constructors in pal.supgma with parameters of type DeltaModelModifierConstructorDescriptionSUPGMADistanceMatrix(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel) Uses date/time information and a constant rate to correct distance matrices.SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm) constructor SUPGMA tree