Python Module Index

p


	p
	`pybrops`
	`pybrops.breed`
	`pybrops.breed.arch`
	`pybrops.breed.arch.BreedingEdge`
	`pybrops.breed.arch.BreedingGraph`
	`pybrops.breed.arch.BreedingNode`
	`pybrops.breed.arch.BreedingProgram`
	`pybrops.breed.arch.EmigrationOperator`
	`pybrops.breed.arch.GermplasmBank`
	`pybrops.breed.arch.ImmigrationOperator`
	`pybrops.breed.arch.RecurrentSelectionBreedingProgram`
	`pybrops.breed.op`
	`pybrops.breed.op.eval`
	`pybrops.breed.op.eval.EvaluationOperator`
	`pybrops.breed.op.init`
	`pybrops.breed.op.init.InitializationOperator`
	`pybrops.breed.op.log`
	`pybrops.breed.op.log.Logbook`
	`pybrops.breed.op.mate`
	`pybrops.breed.op.mate.MatingOperator`
	`pybrops.breed.op.psel`
	`pybrops.breed.op.psel.ParentSelectionOperator`
	`pybrops.breed.op.ssel`
	`pybrops.breed.op.ssel.SurvivorSelectionOperator`
	`pybrops.breed.prot`
	`pybrops.breed.prot.bv`
	`pybrops.breed.prot.bv.BreedingValueProtocol`
	`pybrops.breed.prot.bv.MeanPhenotypicBreedingValue`
	`pybrops.breed.prot.bv.TrueBreedingValue`
	`pybrops.breed.prot.gt`
	`pybrops.breed.prot.gt.DenseMaskedPhasedGenotyping`
	`pybrops.breed.prot.gt.DenseMaskedUnphasedGenotyping`
	`pybrops.breed.prot.gt.DenseUnphasedGenotyping`
	`pybrops.breed.prot.gt.GenotypingProtocol`
	`pybrops.breed.prot.mate`
	`pybrops.breed.prot.mate.FourWayCross`
	`pybrops.breed.prot.mate.FourWayDHCross`
	`pybrops.breed.prot.mate.MatingProtocol`
	`pybrops.breed.prot.mate.SelfCross`
	`pybrops.breed.prot.mate.ThreeWayCross`
	`pybrops.breed.prot.mate.ThreeWayDHCross`
	`pybrops.breed.prot.mate.TwoWayCross`
	`pybrops.breed.prot.mate.TwoWayDHCross`
	`pybrops.breed.prot.mate.util`
	`pybrops.breed.prot.pt`
	`pybrops.breed.prot.pt.G_E_Phenotyping`
	`pybrops.breed.prot.pt.PhenotypingProtocol`
	`pybrops.breed.prot.pt.TruePhenotyping`
	`pybrops.breed.prot.sel`
	`pybrops.breed.prot.sel.BinaryMateSelectionProtocol`
	`pybrops.breed.prot.sel.BinarySelectionProtocol`
	`pybrops.breed.prot.sel.cfg`
	`pybrops.breed.prot.sel.cfg.BinaryMateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.BinarySelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.IntegerMateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.IntegerSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.MateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.RealMateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.RealSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.SampledSelectionConfigurationMixin`
	`pybrops.breed.prot.sel.cfg.SelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.SimpleMateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.SimpleSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.SubsetMateSelectionConfiguration`
	`pybrops.breed.prot.sel.cfg.SubsetSelectionConfiguration`
	`pybrops.breed.prot.sel.EstimatedBreedingValueSelection`
	`pybrops.breed.prot.sel.ExpectedMaximumBreedingValueSelection`
	`pybrops.breed.prot.sel.FamilyEstimatedBreedingValueSelection`
	`pybrops.breed.prot.sel.GeneralizedWeightedGenomicEstimatedBreedingValueSelection`
	`pybrops.breed.prot.sel.GenomicEstimatedBreedingValueSelection`
	`pybrops.breed.prot.sel.GenotypeBuilderSelection`
	`pybrops.breed.prot.sel.IntegerMateSelectionProtocol`
	`pybrops.breed.prot.sel.IntegerSelectionProtocol`
	`pybrops.breed.prot.sel.L1NormGenomicSelection`
	`pybrops.breed.prot.sel.L2NormGenomicSelection`
	`pybrops.breed.prot.sel.MateSelectionProtocol`
	`pybrops.breed.prot.sel.MeanExpectedHeterozygositySelection`
	`pybrops.breed.prot.sel.MeanGenomicRelationshipSelection`
	`pybrops.breed.prot.sel.MultiObjectiveGenomicSelection`
	`pybrops.breed.prot.sel.OptimalContributionSelection`
	`pybrops.breed.prot.sel.OptimalHaploidValueSelection`
	`pybrops.breed.prot.sel.OptimalPopulationValueSelection`
	`pybrops.breed.prot.sel.PopulationAlleleFrequencyDistanceSelection`
	`pybrops.breed.prot.sel.PopulationAlleleUnavailabilitySelection`
	`pybrops.breed.prot.sel.prob`
	`pybrops.breed.prot.sel.prob.BinaryMateSelectionProblem`
	`pybrops.breed.prot.sel.prob.BinarySelectionProblem`
	`pybrops.breed.prot.sel.prob.EstimatedBreedingValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.ExpectedMaximumBreedingValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.FamilyEstimatedBreedingValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.GeneralizedWeightedGenomicEstimatedBreedingValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.GenomicEstimatedBreedingValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.GenotypeBuilderSelectionProblem`
	`pybrops.breed.prot.sel.prob.IntegerMateSelectionProblem`
	`pybrops.breed.prot.sel.prob.IntegerSelectionProblem`
	`pybrops.breed.prot.sel.prob.L1NormGenomicSelectionProblem`
	`pybrops.breed.prot.sel.prob.L2NormGenomicSelectionProblem`
	`pybrops.breed.prot.sel.prob.MateSelectionProblem`
	`pybrops.breed.prot.sel.prob.MeanExpectedHeterozygositySelectionProblem`
	`pybrops.breed.prot.sel.prob.MeanGenomicRelationshipSelectionProblem`
	`pybrops.breed.prot.sel.prob.MultiObjectiveGenomicMatingProblem`
	`pybrops.breed.prot.sel.prob.MultiObjectiveGenomicSelectionProblem`
	`pybrops.breed.prot.sel.prob.OptimalContributionSelectionProblem`
	`pybrops.breed.prot.sel.prob.OptimalHaploidValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.OptimalPopulationValueSelectionProblem`
	`pybrops.breed.prot.sel.prob.PopulationAlleleFrequencyDistanceSelectionProblem`
	`pybrops.breed.prot.sel.prob.PopulationAlleleUnavailabilitySelectionProblem`
	`pybrops.breed.prot.sel.prob.RandomSelectionProblem`
	`pybrops.breed.prot.sel.prob.RealLookAheadGeneralizedWeightedGenomicSelectionProblem`
	`pybrops.breed.prot.sel.prob.RealMateSelectionProblem`
	`pybrops.breed.prot.sel.prob.RealSelectionProblem`
	`pybrops.breed.prot.sel.prob.SelectionProblem`
	`pybrops.breed.prot.sel.prob.SubsetMateSelectionProblem`
	`pybrops.breed.prot.sel.prob.SubsetSelectionProblem`
	`pybrops.breed.prot.sel.prob.trans`
	`pybrops.breed.prot.sel.prob.UsefulnessCriterionSelectionProblem`
	`pybrops.breed.prot.sel.prob.WeightedGenomicSelectionProblem`
	`pybrops.breed.prot.sel.RandomSelection`
	`pybrops.breed.prot.sel.RealMateSelectionProtocol`
	`pybrops.breed.prot.sel.RealSelectionProtocol`
	`pybrops.breed.prot.sel.SelectionProtocol`
	`pybrops.breed.prot.sel.soln`
	`pybrops.breed.prot.sel.soln.BinaryMateSelectionSolution`
	`pybrops.breed.prot.sel.soln.BinarySelectionSolution`
	`pybrops.breed.prot.sel.soln.IntegerMateSelectionSolution`
	`pybrops.breed.prot.sel.soln.IntegerSelectionSolution`
	`pybrops.breed.prot.sel.soln.MateSelectionSolution`
	`pybrops.breed.prot.sel.soln.RealMateSelectionSolution`
	`pybrops.breed.prot.sel.soln.RealSelectionSolution`
	`pybrops.breed.prot.sel.soln.SelectionSolution`
	`pybrops.breed.prot.sel.soln.SubsetMateSelectionSolution`
	`pybrops.breed.prot.sel.soln.SubsetSelectionSolution`
	`pybrops.breed.prot.sel.SubsetMateSelectionProtocol`
	`pybrops.breed.prot.sel.SubsetSelectionProtocol`
	`pybrops.breed.prot.sel.targetfn`
	`pybrops.breed.prot.sel.transfn`
	`pybrops.breed.prot.sel.UnconstrainedGeneralized1NormGenomicSelection`
	`pybrops.breed.prot.sel.UnconstrainedMultiObjectiveGenomicMating`
	`pybrops.breed.prot.sel.UnconstrainedSelectionProtocol`
	`pybrops.breed.prot.sel.UsefulnessCriterionSelection`
	`pybrops.breed.prot.sel.WeightedGenomicSelection`
	`pybrops.breed.prot.sel.weightfn`
	`pybrops.core`
	`pybrops.core.error`
	`pybrops.core.error.error_attr_python`
	`pybrops.core.error.error_generic_numpy`
	`pybrops.core.error.error_generic_python`
	`pybrops.core.error.error_io_python`
	`pybrops.core.error.error_type_h5py`
	`pybrops.core.error.error_type_numpy`
	`pybrops.core.error.error_type_pandas`
	`pybrops.core.error.error_type_python`
	`pybrops.core.error.error_value_h5py`
	`pybrops.core.error.error_value_numpy`
	`pybrops.core.error.error_value_pandas`
	`pybrops.core.error.error_value_python`
	`pybrops.core.io`
	`pybrops.core.io.Copyable`
	`pybrops.core.io.CSVDictInputOutput`
	`pybrops.core.io.CSVInputOutput`
	`pybrops.core.io.DictInputOutput`
	`pybrops.core.io.HDF5InputOutput`
	`pybrops.core.io.NPYInputOutput`
	`pybrops.core.io.NPZInputOutput`
	`pybrops.core.io.NumPyInputOutput`
	`pybrops.core.io.PandasDictInputOutput`
	`pybrops.core.io.PandasInputOutput`
	`pybrops.core.mat`
	`pybrops.core.mat.DenseMatrix`
	`pybrops.core.mat.DenseMutableMatrix`
	`pybrops.core.mat.DensePhasedMatrix`
	`pybrops.core.mat.DensePhasedTaxaVariantMatrix`
	`pybrops.core.mat.DenseScaledMatrix`
	`pybrops.core.mat.DenseScaledSquareTaxaTraitMatrix`
	`pybrops.core.mat.DenseSquare2TaxaTraitMatrix`
	`pybrops.core.mat.DenseSquareMatrix`
	`pybrops.core.mat.DenseSquareTaxaMatrix`
	`pybrops.core.mat.DenseSquareTaxaSquareTraitMatrix`
	`pybrops.core.mat.DenseSquareTaxaTraitMatrix`
	`pybrops.core.mat.DenseSquareTraitMatrix`
	`pybrops.core.mat.DenseTaxaMatrix`
	`pybrops.core.mat.DenseTaxaTraitMatrix`
	`pybrops.core.mat.DenseTaxaVariantMatrix`
	`pybrops.core.mat.DenseTraitMatrix`
	`pybrops.core.mat.DenseVariantMatrix`
	`pybrops.core.mat.GroupableMatrix`
	`pybrops.core.mat.Matrix`
	`pybrops.core.mat.MutableMatrix`
	`pybrops.core.mat.PhasedMatrix`
	`pybrops.core.mat.PhasedTaxaVariantMatrix`
	`pybrops.core.mat.PrunableMatrix`
	`pybrops.core.mat.ScaledMatrix`
	`pybrops.core.mat.ScaledSquareTaxaTraitMatrix`
	`pybrops.core.mat.SortableMatrix`
	`pybrops.core.mat.SquareMatrix`
	`pybrops.core.mat.SquareTaxaMatrix`
	`pybrops.core.mat.SquareTaxaSquareTraitMatrix`
	`pybrops.core.mat.SquareTaxaTraitMatrix`
	`pybrops.core.mat.SquareTraitMatrix`
	`pybrops.core.mat.TaxaMatrix`
	`pybrops.core.mat.TaxaTraitMatrix`
	`pybrops.core.mat.TaxaVariantMatrix`
	`pybrops.core.mat.TraitMatrix`
	`pybrops.core.mat.VariantMatrix`
	`pybrops.core.random`
	`pybrops.core.random.prng`
	`pybrops.core.random.sampling`
	`pybrops.core.util`
	`pybrops.core.util.array`
	`pybrops.core.util.h5py`
	`pybrops.core.util.haplo`
	`pybrops.core.util.iterator`
	`pybrops.core.util.mate`
	`pybrops.core.util.pareto`
	`pybrops.core.util.subroutines`
	`pybrops.core.util.trans`
	`pybrops.model`
	`pybrops.model.embvmat`
	`pybrops.model.embvmat.DenseExpectedMaximumBreedingValueMatrix`
	`pybrops.model.embvmat.ExpectedMaximumBreedingValueMatrix`
	`pybrops.model.gmod`
	`pybrops.model.gmod.AdditiveDominanceEpistaticLinearGenomicModel`
	`pybrops.model.gmod.AdditiveDominanceLinearGenomicModel`
	`pybrops.model.gmod.AdditiveLinearGenomicModel`
	`pybrops.model.gmod.CoancestryLinearGenomicModel`
	`pybrops.model.gmod.DenseAdditiveDominanceLinearGenomicModel`
	`pybrops.model.gmod.DenseAdditiveLinearGenomicModel`
	`pybrops.model.gmod.DenseLinearGenomicModel`
	`pybrops.model.gmod.GenomicModel`
	`pybrops.model.gmod.LinearGenomicModel`
	`pybrops.model.gmod.NonlinearGenomicModel`
	`pybrops.model.gmod.rrBLUPModel0`
	`pybrops.model.pcvmat`
	`pybrops.model.pcvmat.AdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.AdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseAdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseAdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseDihybridDHAdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseDihybridDHAdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseFourWayDHAdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseFourWayDHAdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseThreeWayDHAdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseThreeWayDHAdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.DenseTwoWayDHAdditiveProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.DenseTwoWayDHAdditiveProgenyGenicCovarianceMatrix`
	`pybrops.model.pcvmat.ProgenyGeneticCovarianceMatrix`
	`pybrops.model.pcvmat.ProgenyGenicCovarianceMatrix`
	`pybrops.model.vmat`
	`pybrops.model.vmat.AdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.AdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.DenseAdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseAdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.DenseDihybridDHAdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseDihybridDHAdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.DenseFourWayDHAdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseFourWayDHAdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.DenseGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseGenicVarianceMatrix`
	`pybrops.model.vmat.DenseThreeWayDHAdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseThreeWayDHAdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.DenseTwoWayDHAdditiveGeneticVarianceMatrix`
	`pybrops.model.vmat.DenseTwoWayDHAdditiveGenicVarianceMatrix`
	`pybrops.model.vmat.fcty`
	`pybrops.model.vmat.fcty.AdditiveGeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.AdditiveGenicVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.DenseDihybridDHAdditiveGeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.DenseFourWayDHAdditiveGeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.DenseThreeWayDHAdditiveGeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.DenseTwoWayDHAdditiveGeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.DenseTwoWayDHAdditiveGenicVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.GeneticVarianceMatrixFactory`
	`pybrops.model.vmat.fcty.GenicVarianceMatrixFactory`
	`pybrops.model.vmat.GeneticVarianceMatrix`
	`pybrops.model.vmat.GenicVarianceMatrix`
	`pybrops.model.vmat.util`
	`pybrops.model.wgebvmat`
	`pybrops.model.wgebvmat.DenseWeightedGenomicEstimatedBreedingValueMatrix`
	`pybrops.model.wgebvmat.WeightedGenomicEstimatedBreedingValueMatrix`
	`pybrops.opt`
	`pybrops.opt.algo`
	`pybrops.opt.algo.BinaryGeneticAlgorithm`
	`pybrops.opt.algo.BinaryOptimizationAlgorithm`
	`pybrops.opt.algo.IntegerGeneticAlgorithm`
	`pybrops.opt.algo.IntegerOptimizationAlgorithm`
	`pybrops.opt.algo.NSGA2BinaryGeneticAlgorithm`
	`pybrops.opt.algo.NSGA2IntegerGeneticAlgorithm`
	`pybrops.opt.algo.NSGA2MemeticSubsetGeneticAlgorithm`
	`pybrops.opt.algo.NSGA2RealGeneticAlgorithm`
	`pybrops.opt.algo.NSGA2SubsetGeneticAlgorithm`
	`pybrops.opt.algo.NSGA3SubsetGeneticAlgorithm`
	`pybrops.opt.algo.OptimizationAlgorithm`
	`pybrops.opt.algo.pymoo_addon`
	`pybrops.opt.algo.RealGeneticAlgorithm`
	`pybrops.opt.algo.RealOptimizationAlgorithm`
	`pybrops.opt.algo.SortingSteepestDescentSubsetHillClimber`
	`pybrops.opt.algo.SortingSubsetOptimizationAlgorithm`
	`pybrops.opt.algo.SteepestDescentSubsetHillClimber`
	`pybrops.opt.algo.SubsetGeneticAlgorithm`
	`pybrops.opt.algo.SubsetOptimizationAlgorithm`
	`pybrops.opt.algo.UnconstrainedNSGA2SetGeneticAlgorithm`
	`pybrops.opt.algo.UnconstrainedOptimizationAlgorithm`
	`pybrops.opt.algo.UnconstrainedSetGeneticAlgorithm`
	`pybrops.opt.algo.UnconstrainedSteepestAscentSetHillClimber`
	`pybrops.opt.prob`
	`pybrops.opt.prob.BinaryProblem`
	`pybrops.opt.prob.FunctionWeight`
	`pybrops.opt.prob.IntegerProblem`
	`pybrops.opt.prob.Problem`
	`pybrops.opt.prob.RealProblem`
	`pybrops.opt.prob.SubsetProblem`
	`pybrops.opt.soln`
	`pybrops.opt.soln.BinarySolution`
	`pybrops.opt.soln.IntegerSolution`
	`pybrops.opt.soln.RealSolution`
	`pybrops.opt.soln.Solution`
	`pybrops.opt.soln.SubsetSolution`
	`pybrops.popgen`
	`pybrops.popgen.bvmat`
	`pybrops.popgen.bvmat.BreedingValueMatrix`
	`pybrops.popgen.bvmat.DenseBreedingValueMatrix`
	`pybrops.popgen.bvmat.DenseEstimatedBreedingValueMatrix`
	`pybrops.popgen.bvmat.DenseGenomicEstimatedBreedingValueMatrix`
	`pybrops.popgen.cmat`
	`pybrops.popgen.cmat.CoancestryMatrix`
	`pybrops.popgen.cmat.DenseCoancestryMatrix`
	`pybrops.popgen.cmat.DenseGeneralizedWeightedCoancestryMatrix`
	`pybrops.popgen.cmat.DenseMolecularCoancestryMatrix`
	`pybrops.popgen.cmat.DenseVanRadenCoancestryMatrix`
	`pybrops.popgen.cmat.DenseYangCoancestryMatrix`
	`pybrops.popgen.cmat.fcty`
	`pybrops.popgen.cmat.fcty.CoancestryMatrixFactory`
	`pybrops.popgen.cmat.fcty.DenseCoancestryMatrixFactory`
	`pybrops.popgen.cmat.fcty.DenseGeneralizedWeightedCoancestryMatrixFactory`
	`pybrops.popgen.cmat.fcty.DenseMolecularCoancestryMatrixFactory`
	`pybrops.popgen.cmat.fcty.DenseVanRadenCoancestryMatrixFactory`
	`pybrops.popgen.cmat.fcty.DenseYangCoancestryMatrixFactory`
	`pybrops.popgen.gmap`
	`pybrops.popgen.gmap.DenseGeneticMappableMatrix`
	`pybrops.popgen.gmap.ExtendedGeneticMap`
	`pybrops.popgen.gmap.GeneticMap`
	`pybrops.popgen.gmap.GeneticMapFunction`
	`pybrops.popgen.gmap.GeneticMappableMatrix`
	`pybrops.popgen.gmap.HaldaneMapFunction`
	`pybrops.popgen.gmap.KosambiMapFunction`
	`pybrops.popgen.gmap.StandardGeneticMap`
	`pybrops.popgen.gmap.util`
	`pybrops.popgen.gmat`
	`pybrops.popgen.gmat.DenseGenotypeMatrix`
	`pybrops.popgen.gmat.DensePhasedGenotypeMatrix`
	`pybrops.popgen.gmat.GenotypeMatrix`
	`pybrops.popgen.gmat.HaplotypeMatrix`
	`pybrops.popgen.gmat.PhasedGenotypeMatrix`
	`pybrops.popgen.gmat.PhasedHaplotypeMatrix`
	`pybrops.test`
	`pybrops.test.assert_python`