• Front Matter
• simuPOP Components
  • Individual, Population, pedigree and Simulator
    • class GenoStruTrait
    • class Individual
    • class Population
    • class Pedigree
    • class Simulator
  • Virtual splitters
    • class BaseVspSplitter
    • class SexSplitter
    • class AffectionSplitter
    • class InfoSplitter
    • class ProportionSplitter
    • class RangeSplitter
    • class GenotypeSplitter
    • class CombinedSplitter
    • class ProductSplitter
  • Mating Schemes
    • class MatingScheme
    • class HomoMating
    • class HeteroMating
    • class ConditionalMating
    • class PedigreeMating
    • class SequentialParentChooser
    • class SequentialParentsChooser
    • class RandomParentChooser
    • class RandomParentsChooser
    • class PolyParentsChooser
    • class CombinedParentsChooser
    • class PyParentsChooser
    • class OffspringGenerator
    • class ControlledOffspringGenerator
  • Pre-defined mating schemes
    • class CloneMating
    • class RandomSelection
    • class RandomMating
    • class MonogamousMating
    • class PolygamousMating
    • class HaplodiploidMating
    • class SelfMating
    • class HermaphroditicMating
    • class ControlledRandomMating
  • Utility Classes
    • class WithArgs
    • class WithMode
    • class RNG
    • class WeightedSampler
  • Global functions
    • Function closeOutput
    • Function describeEvolProcess
    • Function loadPopulation
    • Function loadPedigree
    • Function moduleInfo
    • Function getRNG
    • Function setRNG
    • Function setOptions
    • Function turnOnDebug
    • Function turnOffDebug
• Operator References
  • Base class for all operators
    • class BaseOperator
  • Initialization
    • class InitSex
    • class InitInfo
    • class InitGenotype
    • class InitLineage
  • Expression and Statements
    • class PyOutput
    • class PyEval
    • class PyExec
    • class InfoEval
    • class InfoExec
  • Demographic models
    • class Migrator
    • class BackwardMigrator
    • class SplitSubPops
    • class MergeSubPops
    • class ResizeSubPops
  • Genotype transmitters
    • class GenoTransmitter
    • class CloneGenoTransmitter
    • class MendelianGenoTransmitter
    • class SelfingGenoTransmitter
    • class HaplodiploidGenoTransmitter
    • class MitochondrialGenoTransmitter
    • class Recombinator
  • Mutation
    • class BaseMutator
    • class MatrixMutator
    • class KAlleleMutator
    • class StepwiseMutator
    • class PyMutator
    • class MixedMutator
    • class ContextMutator
    • class PointMutator
    • class SNPMutator
    • class AcgtMutator
  • Penetrance
    • class BasePenetrance
    • class MapPenetrance
    • class MaPenetrance
    • class MlPenetrance
    • class PyPenetrance
    • class PyMlPenetrance
  • Quantitative Trait
    • class BaseQuanTrait
    • class PyQuanTrait
  • Natural selection
    • class BaseSelector
    • class MapSelector
    • class MaSelector
    • class MlSelector
    • class PySelector
    • class PyMlSelector
  • Tagging operators
    • class IdTagger
    • class InheritTagger
    • class SummaryTagger
    • class ParentsTagger
    • class OffspringTagger
    • class PedigreeTagger
    • class PyTagger
  • Statistics Calculation
    • class Stat
  • Conditional operators
    • class IfElse
    • class TerminateIf
    • class DiscardIf
  • The Python operator
    • class PyOperator
  • Miscellaneous operators
    • class NoneOp
    • class Dumper
    • class SavePopulation
    • class Pause
    • class TicToc
  • Function form of operators
    • Function acgtMutate
    • Function contextMutate
    • Function discardIf
    • Function dump
    • Function infoEval
    • Function infoExec
    • Function initGenotype
    • Function initInfo
    • Function initSex
    • Function kAlleleMutate
    • Function maPenetrance
    • Function mapPenetrance
    • Function matrixMutate
    • Function mergeSubPops
    • Function migrate
    • Function backwardMigrate
    • Function mixedMutate
    • Function mlPenetrance
    • Function pointMutate
    • Function pyEval
    • Function pyExec
    • Function pyMutate
    • Function pyPenetrance
    • Function pyMlPenetrance
    • Function pyQuanTrait
    • Function resizeSubPops
    • Function snpMutate
    • Function splitSubPops
    • Function stat
    • Function stepwiseMutate
    • Function tagID
• Utility Modules
  • Module simuOpt
    • Function setOptions
  • Module simuPOP.utils
    • class Trajectory
    • class TrajectorySimulator
    • Function simulateForwardTrajectory
    • Function simulateBackwardTrajectory
    • class ProgressBar
    • Function viewVars
    • Function saveCSV
    • class Exporter
    • Function importPopulation
    • Function export
  • Module simuPOP.demography
    • Function migrIslandRates
    • Function migrHierarchicalIslandRates
    • Function migrSteppingStoneRates
    • Function migrtwoDSteppingStoneRates
    • class EventBasedModel
    • class DemographicEvent
    • class ExpansionEvent
    • class ResizeEvent
    • class SplitEvent
    • class MergeEvent
    • class AdmixtureEvent
    • class InstantChangeModel
    • class ExponentialGrowthModel
    • class LinearGrowthModel
    • class MultiStageModel
    • class OutOfAfricaModel
    • class SettlementOfNewWorldModel
    • class CosiModel
  • Module simuPOP.sampling
    • class BaseSampler
    • class RandomSampler
    • Function drawRandomSample
    • Function drawRandomSamples
    • class CaseControlSampler
    • Function drawCaseControlSample
    • Function drawCaseControlSamples
    • class PedigreeSampler
    • class AffectedSibpairSampler
    • Function drawAffectedSibpairSample
    • Function drawAffectedSibpairSamples
    • class NuclearFamilySampler
    • Function drawNuclearFamilySample
    • Function drawNuclearFamilySamples
    • class ThreeGenFamilySampler
    • Function drawThreeGenFamilySample
    • Function drawThreeGenFamilySamples
    • class CombinedSampler
    • Function drawCombinedSample
    • Function drawCombinedSamples
  • Module simuPOP.gsl