Uses of Interface
pal.mep.DeltaModel
Packages that use DeltaModel
Package
Description
Classes for the analysis of "measurably evolving populations" (mep).
-
Uses of DeltaModel in pal.mep
Methods in pal.mep that return DeltaModelModifier and TypeMethodDescriptionstatic final DeltaModel
DeltaModel.Utils.getDisjointBased
(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD) static final DeltaModel
DeltaModel.Utils.getMutationRateModelBased
(MutationRateModel.Factory mepFactory) For interfacing with time based mutation rate modelsstatic final DeltaModel
DeltaModel.Utils.getUntimedBased()
For serial sampled analysis when no time information is available.static final DeltaModel
DeltaModel.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 DeltaModel
DeltaModel.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