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simuPOP v1.1.8svn documentation
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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
class RevertFixedSites
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 RevertIf
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
class Params
Function param
Function valueNot
Function valueOr
Function valueAnd
Function valueOneOf
Function valueTrueFalse
Function valueBetween
Function valueGT
Function valueGE
Function valueLT
Function valueLE
Function valueEqual
Function valueNotEqual
Function valueIsNum
Function valueIsInteger
Function valueIsList
Function valueListOf
Function valueSumTo
Function valueValidDir
Function valueValidFile
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.plotter
class VarPlotter
class ScatterPlotter
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
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