Index

_

__cmp__() (Individual method) (Population method) (Simulator method)

A

absIndIndex() (Population method) absLocusIndex() (GenoStruTrait method) acgtMutate() (built-in function) AcgtMutator (built-in class) AcgtMutator() (AcgtMutator method) add() (Simulator method) addChrom() (Population method) addChromFrom() (Population method) addIndFrom() (Population method) addInfoFields() (Population method) addLoci() (Population method) addLociFrom() (Population method) AdmixtureEvent (class in simuPOP.demography) AdmixtureEvent() (simuPOP.demography.AdmixtureEvent method) affected() (Individual method) AffectedSibpairSampler (class in simuPOP.sampling) AffectedSibpairSampler() (simuPOP.sampling.AffectedSibpairSampler method) AffectionSplitter (built-in class) AffectionSplitter() (AffectionSplitter method)

allele() (Individual method) alleleChar() (Individual method) alleleLineage() (Individual method) alleleName() (GenoStruTrait method) alleleNames() (GenoStruTrait method) allIndividuals() (Population method) ancestor() (Population method) ancestralGens() (Population method) apply() (BaseOperator method) (BasePenetrance method) (BaseQuanTrait method) (simuPOP.demography.AdmixtureEvent method) (simuPOP.demography.DemographicEvent method) (simuPOP.demography.ExpansionEvent method) (simuPOP.demography.MergeEvent method) (simuPOP.demography.ResizeEvent method) (simuPOP.demography.SplitEvent method) applyToIndividual() (BasePenetrance method) asPedigree() (Population method) asPopulation() (Pedigree method)

B

backwardMigrate() (built-in function) BackwardMigrator (built-in class) BackwardMigrator() (BackwardMigrator method) BaseMutator (built-in class) BaseMutator() (BaseMutator method) BaseOperator (built-in class) BaseOperator() (BaseOperator method) BasePenetrance (built-in class)

BasePenetrance() (BasePenetrance method) BaseQuanTrait (built-in class) BaseQuanTrait() (BaseQuanTrait method) BaseSampler (class in simuPOP.sampling) BaseSampler() (simuPOP.sampling.BaseSampler method) BaseSelector (built-in class) BaseSelector() (BaseSelector method) BaseVspSplitter (built-in class) BaseVspSplitter() (BaseVspSplitter method)

C

CaseControlSampler (class in simuPOP.sampling) CaseControlSampler() (simuPOP.sampling.CaseControlSampler method) chooseParents() (CombinedParentsChooser method) (PolyParentsChooser method) (PyParentsChooser method) (RandomParentChooser method) (RandomParentsChooser method) (SequentialParentChooser method) chromBegin() (GenoStruTrait method) chromByName() (GenoStruTrait method) chromEnd() (GenoStruTrait method) chromLocusPair() (GenoStruTrait method) chromName() (GenoStruTrait method) chromNames() (GenoStruTrait method) chromType() (GenoStruTrait method) chromTypes() (GenoStruTrait method) clearChromosome() (GenoTransmitter method) clone() (BaseOperator method) (BaseVspSplitter method) (Pedigree method) (Population method) (Simulator method) CloneGenoTransmitter (built-in class)

CloneGenoTransmitter() (CloneGenoTransmitter method) CloneMating (built-in class) CloneMating() (CloneMating method) closeOutput() (built-in function) CombinedParentsChooser (built-in class) CombinedParentsChooser() (CombinedParentsChooser method) CombinedSampler (class in simuPOP.sampling) CombinedSampler() (simuPOP.sampling.CombinedSampler method) CombinedSplitter (built-in class) CombinedSplitter() (CombinedSplitter method) ConditionalMating (built-in class) ConditionalMating() (ConditionalMating method) contextMutate() (built-in function) ContextMutator (built-in class) ContextMutator() (ContextMutator method) ControlledOffspringGenerator (built-in class) ControlledOffspringGenerator() (ControlledOffspringGenerator method) ControlledRandomMating (built-in class) ControlledRandomMating() (ControlledRandomMating method) copyChromosome() (GenoTransmitter method) copyChromosomes() (GenoTransmitter method) CosiModel (class in simuPOP.demography) CosiModel() (simuPOP.demography.CosiModel method)

D

DemographicEvent (class in simuPOP.demography) DemographicEvent() (simuPOP.demography.DemographicEvent method) describeEvolProcess() (built-in function) DiscardIf (built-in class) discardIf() (built-in function) DiscardIf() (DiscardIf method) done() (simuPOP.utils.ProgressBar method) draw() (WeightedSampler method) drawAffectedSibpairSample() (in module simuPOP.sampling) drawAffectedSibpairSamples() (in module simuPOP.sampling) drawCaseControlSample() (in module simuPOP.sampling) drawCaseControlSamples() (in module simuPOP.sampling) drawCombinedSample() (in module simuPOP.sampling) drawCombinedSamples() (in module simuPOP.sampling) drawNuclearFamilySample() (in module simuPOP.sampling) drawNuclearFamilySamples() (in module simuPOP.sampling) drawRandomSample() (in module simuPOP.sampling) drawRandomSamples() (in module simuPOP.sampling) drawSample() (simuPOP.sampling.AffectedSibpairSampler method) (simuPOP.sampling.BaseSampler method) (simuPOP.sampling.CaseControlSampler method) (simuPOP.sampling.CombinedSampler method) (simuPOP.sampling.NuclearFamilySampler method) (simuPOP.sampling.PedigreeSampler method) (simuPOP.sampling.RandomSampler method) (simuPOP.sampling.ThreeGenFamilySampler method)

drawSamples() (simuPOP.sampling.AffectedSibpairSampler method) (WeightedSampler method) (simuPOP.sampling.BaseSampler method) (simuPOP.sampling.CaseControlSampler method) (simuPOP.sampling.CombinedSampler method) (simuPOP.sampling.NuclearFamilySampler method) (simuPOP.sampling.PedigreeSampler method) (simuPOP.sampling.RandomSampler method) (simuPOP.sampling.ThreeGenFamilySampler method) drawThreeGenFamilySample() (in module simuPOP.sampling) drawThreeGenFamilySamples() (in module simuPOP.sampling) dump() (built-in function) Dumper (built-in class) Dumper() (Dumper method) dvars() (Population method) (Simulator method)

E

EventBasedModel (class in simuPOP.demography) EventBasedModel() (simuPOP.demography.EventBasedModel method) evolve() (Population method) (Simulator method) ExpansionEvent (class in simuPOP.demography) ExpansionEvent() (simuPOP.demography.ExpansionEvent method) ExponentialGrowthModel (class in simuPOP.demography)

ExponentialGrowthModel() (simuPOP.demography.ExponentialGrowthModel method) export() (in module simuPOP.utils) Exporter (class in simuPOP.utils) Exporter() (simuPOP.utils.Exporter method) extract() (Simulator method) extractIndividuals() (Population method) extractSubPops() (Population method)

F

family() (simuPOP.sampling.AffectedSibpairSampler method) (simuPOP.sampling.NuclearFamilySampler method) (simuPOP.sampling.PedigreeSampler method) (simuPOP.sampling.ThreeGenFamilySampler method)

freq() (simuPOP.utils.Trajectory method) func() (simuPOP.utils.Trajectory method) function loadPopulation

G

GenoStruTrait chromName chromType infoField infoFields locusPos numChrom numLoci ploidy ploidyName

GenoStruTrait (built-in class) GenoStruTrait() (GenoStruTrait method) GenoTransmitter (built-in class) GenoTransmitter() (GenoTransmitter method) genotype() (Individual method) (Population method) GenotypeSplitter (built-in class) GenotypeSplitter() (GenotypeSplitter method) genotypic structure getRNG() (built-in function)

H

HaplodiploidGenoTransmitter (built-in class) HaplodiploidGenoTransmitter() (HaplodiploidGenoTransmitter method) HaplodiploidMating (built-in class) HaplodiploidMating() (HaplodiploidMating method) HermaphroditicMating (built-in class)

HermaphroditicMating() (HermaphroditicMating method) HeteroMating (built-in class) HeteroMating() (HeteroMating method) HomoMating (built-in class) HomoMating() (HomoMating method)

I

identifyAncestors() (Pedigree method) identifyFamilies() (Pedigree method) identifyOffspring() (Pedigree method) IdTagger (built-in class) IdTagger() (IdTagger method) IfElse (built-in class) IfElse() (IfElse method) importPopulation() (in module simuPOP.utils) indByID() (Pedigree method) (Population method) index absolute, [1] relative, [1] indexesOfLoci() (GenoStruTrait method) indInfo() (Population method) Individual (built-in class) Individual() (Individual method) individual() (Population method) individuals() (Population method) individualsWithRelatives() (Pedigree method) info() (Individual method) InfoEval (built-in class) infoEval() (built-in function) InfoEval() (InfoEval method) InfoExec (built-in class) infoExec() (built-in function)

InfoExec() (InfoExec method) infoField() (GenoStruTrait method) infoFields() (GenoStruTrait method) infoIdx() (GenoStruTrait method) InfoSplitter (built-in class) InfoSplitter() (InfoSplitter method) InheritTagger (built-in class) InheritTagger() (InheritTagger method) InitGenotype (built-in class) initGenotype() (built-in function) InitGenotype() (InitGenotype method) initialize() (CombinedParentsChooser method) (PolyParentsChooser method) (PyParentsChooser method) (RandomParentChooser method) (RandomParentsChooser method) (SequentialParentChooser method) initializer InitInfo (built-in class) initInfo() (built-in function) InitInfo() (InitInfo method) InitLineage (built-in class) InitLineage() (InitLineage method) InitSex (built-in class) initSex() (built-in function) InitSex() (InitSex method) InstantChangeModel (class in simuPOP.demography) InstantChangeModel() (simuPOP.demography.InstantChangeModel method)

K

kAlleleMutate() (built-in function)

KAlleleMutator (built-in class) KAlleleMutator() (KAlleleMutator method)

L

lineage() (Individual method) (Population method) LinearGrowthModel (class in simuPOP.demography) LinearGrowthModel() (simuPOP.demography.LinearGrowthModel method) loadPedigree() (built-in function) loadPopulation() (built-in function) locateRelatives() (Pedigree method)

lociByNames() (GenoStruTrait method) lociDist() (GenoStruTrait method) lociNames() (GenoStruTrait method) lociPos() (GenoStruTrait method) locusByName() (GenoStruTrait method) locusName() (GenoStruTrait method) locusPos() (GenoStruTrait method)

M

MaPenetrance (built-in class) maPenetrance() (built-in function) MaPenetrance() (MaPenetrance method) MapPenetrance (built-in class) mapPenetrance() (built-in function) MapPenetrance() (MapPenetrance method) MapSelector (built-in class) MapSelector() (MapSelector method) MaSelector (built-in class) MaSelector() (MaSelector method) mating scheme, [1] MatingScheme (built-in class) MatingScheme() (MatingScheme method) matrixMutate() (built-in function) MatrixMutator (built-in class) MatrixMutator() (MatrixMutator method) MendelianGenoTransmitter (built-in class) MendelianGenoTransmitter() (MendelianGenoTransmitter method) MergeEvent (class in simuPOP.demography) MergeEvent() (simuPOP.demography.MergeEvent method) MergeSubPops (built-in class) mergeSubPops() (built-in function) MergeSubPops() (MergeSubPops method) mergeSubPops() (Population method) migr2DSteppingStoneRates() (in module simuPOP.demography) migrate() (built-in function)

Migrator (built-in class) Migrator() (Migrator method) migrHierarchicalIslandRates() (in module simuPOP.demography) migrIslandRates() (in module simuPOP.demography) migrSteppingStoneRates() (in module simuPOP.demography) MitochondrialGenoTransmitter (built-in class) MitochondrialGenoTransmitter() (MitochondrialGenoTransmitter method) mixedMutate() (built-in function) MixedMutator (built-in class) MixedMutator() (MixedMutator method) MlPenetrance (built-in class) mlPenetrance() (built-in function) MlPenetrance() (MlPenetrance method) MlSelector (built-in class) MlSelector() (MlSelector method) moduleInfo moduleInfo() (built-in function) MonogamousMating (built-in class) MonogamousMating() (MonogamousMating method) MultiStageModel (class in simuPOP.demography) MultiStageModel() (simuPOP.demography.MultiStageModel method) mutants() (Individual method) (Population method) (simuPOP.utils.Trajectory method) Mutation mutators() (simuPOP.utils.Trajectory method)

N

name() (AffectionSplitter method) (BaseVspSplitter method) (CombinedSplitter method) (GenotypeSplitter method) (InfoSplitter method) (ProductSplitter method) (ProportionSplitter method) (RNG method) (RangeSplitter method) (SexSplitter method) NoneOp (built-in class) NoneOp() (NoneOp method) NuclearFamilySampler (class in simuPOP.sampling) NuclearFamilySampler() (simuPOP.sampling.NuclearFamilySampler method)

numChrom() (GenoStruTrait method) numLoci() (GenoStruTrait method), [1] numRep() (Simulator method) numSubPop() (Population method) numVirtualSubPop() (AffectionSplitter method) (BaseVspSplitter method) (CombinedSplitter method) (GenotypeSplitter method) (InfoSplitter method) (Population method) (ProductSplitter method) (ProportionSplitter method) (RangeSplitter method) (SexSplitter method)

O

OffspringGenerator (built-in class) OffspringGenerator() (OffspringGenerator method) OffspringTagger (built-in class) OffspringTagger() (OffspringTagger method)

operator Stat OutOfAfricaModel (class in simuPOP.demography) OutOfAfricaModel() (simuPOP.demography.OutOfAfricaModel method)

P

parallelizable() (PedigreeMating method) ParentsTagger (built-in class) ParentsTagger() (ParentsTagger method) Pause (built-in class) Pause() (Pause method) Pedigree (built-in class) Pedigree() (Pedigree method) PedigreeMating (built-in class) PedigreeMating() (PedigreeMating method) PedigreeSampler (class in simuPOP.sampling) PedigreeSampler() (simuPOP.sampling.PedigreeSampler method) PedigreeTagger (built-in class) PedigreeTagger() (PedigreeTagger method) penetrance ploidy() (GenoStruTrait method) ploidyName() (GenoStruTrait method) plot() (simuPOP.demography.CosiModel method) (simuPOP.demography.EventBasedModel method) (simuPOP.demography.ExponentialGrowthModel method) (simuPOP.demography.InstantChangeModel method) (simuPOP.demography.LinearGrowthModel method) (simuPOP.demography.MultiStageModel method) (simuPOP.demography.OutOfAfricaModel method) (simuPOP.demography.SettlementOfNewWorldModel method) pointMutate() (built-in function) PointMutator (built-in class) PointMutator() (PointMutator method) PolygamousMating (built-in class) PolygamousMating() (PolygamousMating method) PolyParentsChooser (built-in class) PolyParentsChooser() (PolyParentsChooser method) popSize() (Population method) Population, [1] Population save vars Population (built-in class) Population() (Population method) population() (Simulator method) populations() (Simulator method) prepareSample() (simuPOP.sampling.AffectedSibpairSampler method) (simuPOP.sampling.BaseSampler method) (simuPOP.sampling.CaseControlSampler method) (simuPOP.sampling.CombinedSampler method) (simuPOP.sampling.NuclearFamilySampler method) (simuPOP.sampling.PedigreeSampler method) (simuPOP.sampling.RandomSampler method) (simuPOP.sampling.ThreeGenFamilySampler method)

ProductSplitter (built-in class) ProductSplitter() (ProductSplitter method) ProgressBar (class in simuPOP.utils) ProgressBar() (simuPOP.utils.ProgressBar method) ProportionSplitter (built-in class) ProportionSplitter() (ProportionSplitter method) push() (Population method) PyEval (built-in class) pyEval() (built-in function) PyEval() (PyEval method) PyExec (built-in class) pyExec() (built-in function) PyExec() (PyExec method) PyMlPenetrance (built-in class) pyMlPenetrance() (built-in function) PyMlPenetrance() (PyMlPenetrance method) PyMlSelector (built-in class) PyMlSelector() (PyMlSelector method) pyMutate() (built-in function) PyMutator (built-in class) PyMutator() (PyMutator method) PyOperator (built-in class) PyOperator() (PyOperator method) PyOutput (built-in class) PyOutput() (PyOutput method) PyParentsChooser (built-in class) PyParentsChooser() (PyParentsChooser method) PyPenetrance (built-in class) pyPenetrance() (built-in function) PyPenetrance() (PyPenetrance method) PyQuanTrait (built-in class) pyQuanTrait() (built-in function) PyQuanTrait() (PyQuanTrait method) PySelector (built-in class) PySelector() (PySelector method) PyTagger (built-in class) PyTagger() (PyTagger method)

Q

quantitative trait

R

r randBinomial() (RNG method) randChisq() (RNG method) randExponential() (RNG method) randGamma() (RNG method) randGeometric() (RNG method) randInt() (RNG method) randMultinomial() (RNG method) randNormal() (RNG method) RandomMating (built-in class) RandomMating() (RandomMating method) RandomParentChooser (built-in class) RandomParentChooser() (RandomParentChooser method) RandomParentsChooser (built-in class) RandomParentsChooser() (RandomParentsChooser method) RandomSampler (class in simuPOP.sampling) RandomSampler() (simuPOP.sampling.RandomSampler method) RandomSelection (built-in class) RandomSelection() (RandomSelection method) randPoisson() (RNG method)

randTruncatedBinomial() (RNG method) randTruncatedPoisson() (RNG method) randUniform() (RNG method) RangeSplitter (built-in class) RangeSplitter() (RangeSplitter method) recodeAlleles() (Population method) Recombinator (built-in class) Recombinator() (Recombinator method) removeIndividuals() (Population method) removeInfoFields() (Population method) removeLoci() (Population method) removeSubPops() (Population method) reset() (IdTagger method) resize() (Population method) ResizeEvent (class in simuPOP.demography) ResizeEvent() (simuPOP.demography.ResizeEvent method) ResizeSubPops (built-in class) resizeSubPops() (built-in function) ResizeSubPops() (ResizeSubPops method) RNG (built-in class) RNG() (RNG method)

S

save() (Pedigree method) (Population method) saveCSV() (in module simuPOP.utils) SavePopulation (built-in class) SavePopulation() (SavePopulation method) seed() (RNG method) selection SelfingGenoTransmitter (built-in class) SelfingGenoTransmitter() (SelfingGenoTransmitter method) SelfMating (built-in class) SelfMating() (SelfMating method) SequentialParentChooser (built-in class) SequentialParentChooser() (SequentialParentChooser method) SequentialParentsChooser (built-in class) SequentialParentsChooser() (SequentialParentsChooser method) set() (RNG method) setAffected() (Individual method) setAllele() (Individual method) setAlleleLineage() (Individual method) setAncestralDepth() (Population method) setGenotype() (Individual method) (Population method) setIndInfo() (Population method) setInfo() (Individual method) setInfoFields() (Population method) setLineage() (Individual method) (Population method) setOptions() (built-in function) (in module simuOpt) setRNG setRNG() (built-in function) setSex() (Individual method) setSubPopByIndInfo() (Population method) setSubPopName() (Population method) SettlementOfNewWorldModel (class in simuPOP.demography) SettlementOfNewWorldModel() (simuPOP.demography.SettlementOfNewWorldModel method) setVirtualSplitter() (Population method) sex() (Individual method) SexSplitter (built-in class) SexSplitter() (SexSplitter method)

simuBackward() (simuPOP.utils.TrajectorySimulator method) simuForward() (simuPOP.utils.TrajectorySimulator method) simulateBackwardTrajectory() (in module simuPOP.utils) simulateForwardTrajectory() (in module simuPOP.utils) Simulator (built-in class) Simulator() (Simulator method) simuOpt (module) simuPOP.demography (module) simuPOP.gsl (module) simuPOP.sampling (module) simuPOP.utils (module) snpMutate() (built-in function) SNPMutator (built-in class) SNPMutator() (SNPMutator method) sortIndividuals() (Population method) SplitEvent (class in simuPOP.demography) SplitEvent() (simuPOP.demography.SplitEvent method) splitSubPop() (Population method) SplitSubPops (built-in class) splitSubPops() (built-in function) SplitSubPops() (SplitSubPops method) Stat (built-in class) stat() (built-in function) Stat() (Stat method) stepwiseMutate() (built-in function) StepwiseMutator (built-in class) StepwiseMutator() (StepwiseMutator method) subPopBegin() (Population method) subPopByName() (Population method) subPopEnd() (Population method) subPopIndPair() (Population method) subPopName() (Population method) subPopNames() (Population method) subPopSize() (Population method) subPopSizes() (Population method) SummaryTagger (built-in class) SummaryTagger() (SummaryTagger method) swap() (Population method)

T

tagID() (built-in function) TerminateIf (built-in class) TerminateIf() (TerminateIf method) ThreeGenFamilySampler (class in simuPOP.sampling) ThreeGenFamilySampler() (simuPOP.sampling.ThreeGenFamilySampler method) TicToc (built-in class) TicToc() (TicToc method) totNumLoci() (GenoStruTrait method)

traceRelatives() (Pedigree method) Trajectory (class in simuPOP.utils) Trajectory() (simuPOP.utils.Trajectory method) TrajectorySimulator (class in simuPOP.utils) TrajectorySimulator() (simuPOP.utils.TrajectorySimulator method) transmitGenotype() (MendelianGenoTransmitter method) (Recombinator method) turnOffDebug() (built-in function) turnOnDebug() (built-in function)

U

update() (simuPOP.utils.ProgressBar method)

updateInfoFieldsFrom() (Population method) useAncestralGen() (Population method)

V

vars() (Population method) (Simulator method)

viewVars() (in module simuPOP.utils) virtualSplitter() (Population method) vspByName() (BaseVspSplitter method)

W

WeightedSampler (built-in class) WeightedSampler() (WeightedSampler method) WithArgs (built-in class)

WithArgs() (WithArgs method) WithMode (built-in class) WithMode() (WithMode method)