Uses of Interface
pal.math.LMSSolver
Packages that use LMSSolver
Package
Description
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
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Uses of LMSSolver in pal.math
Modifier and TypeMethodDescriptionstatic final LMSSolver
LMSSolver.Utils.getSimpleSolver()
Obtain a simple LMSSolver that uses the "traditional" method for LMS stuff (IE, using row reduction to find the inverse, with poor numerical accuracy) -
Uses of LMSSolver in pal.supgma
Methods in pal.supgma with parameters of type LMSSolverModifier and TypeMethodDescriptionSUPGMABase.generateAlignmentBootstrappedSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.generateSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.inferCI
(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver) SUPGMABase.process
(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.process
(AlgorithmCallback callback, LMSSolver solver) Tree[]
SUPGMABase.PopulationParameters.simulateTrees
(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.solve
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)