Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W

_

__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)
addOption() (simuOpt.Params 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)

applyToIndividual() (BasePenetrance method)

asDict() (simuOpt.Params method)

asList() (simuOpt.Params method)

asPedigree() (Population method)

asPopulation() (Pedigree method)

B

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)
BoxPlotter (class in simuPOP.plotter)
BoxPlotter() (simuPOP.plotter.BoxPlotter method)

C

CaseControlSampler (class in simuPOP.sampling)

CaseControlSampler() (simuPOP.sampling.CaseControlSampler 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)
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)

D

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

evolve() (Population method)

(Simulator 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

H

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

HistPlotter (class in simuPOP.plotter)
HistPlotter() (simuPOP.plotter.HistPlotter 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]

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)
InfoPlotter (class in simuPOP.plotter)
InfoPlotter() (simuPOP.plotter.InfoPlotter 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)
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)

K

kAlleleMutate() (built-in function)
KAlleleMutator (built-in class)

KAlleleMutator() (KAlleleMutator method)

L

lineage() (Individual method)

(Population method)

loadConfig() (simuOpt.Params 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], [2]

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)

MergeSubPops (built-in class)

mergeSubPops() (built-in function)

MergeSubPops() (MergeSubPops method)

mergeSubPops() (Population method)

migrate() (built-in function)

Migrator

(built-in class)

Migrator() (Migrator method)

migrHierarchicalIslandRates() (in module simuPOP.utils)

migrIslandRates() (in module simuPOP.utils)

migrSteppingStoneRates() (in module simuPOP.utils)

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)

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)

newDevice() (in module simuPOP.plotter)

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

P

parallelizable() (PedigreeMating method)

param() (in module simuOpt)

Params (class in simuOpt)

Params() (simuOpt.Params 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.utils.Trajectory method)

plotPedigree() (in module simuPOP.sampling)

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)

processArgs() (simuOpt.Params 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

QQPlotter (class in simuPOP.plotter)
QQPlotter() (simuPOP.plotter.QQPlotter method)

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)
ResizeSubPops (built-in class)
resizeSubPops() (built-in function)
ResizeSubPops() (ResizeSubPops method)
RevertFixedSites (built-in class)
RevertFixedSites() (RevertFixedSites method)
RNG (built-in class)
RNG() (RNG method)

S

save() (Pedigree method)

(Population method)

saveConfig() (simuOpt.Params method)

saveCSV() (in module simuPOP.utils)

saveFigure() (in module simuPOP.plotter)

SavePopulation (built-in class)

SavePopulation() (SavePopulation method)

ScatterPlotter (class in simuPOP.plotter)

ScatterPlotter() (simuPOP.plotter.ScatterPlotter 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)

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.gsl (module)

simuPOP.plotter (module)

simuPOP.sampling (module)

simuPOP.utils (module)

snpMutate() (built-in function)

SNPMutator (built-in class)

SNPMutator() (SNPMutator method)

sortIndividuals() (Population 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)
termGetParam() (simuOpt.Params method)
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)
usage() (simuOpt.Params method)

useAncestralGen() (Population method)

V

valueAnd() (in module simuOpt)
valueBetween() (in module simuOpt)
valueEqual() (in module simuOpt)
valueGE() (in module simuOpt)
valueGT() (in module simuOpt)
valueIsInteger() (in module simuOpt)
valueIsList() (in module simuOpt)
valueIsNum() (in module simuOpt)
valueLE() (in module simuOpt)
valueListOf() (in module simuOpt)
valueLT() (in module simuOpt)
valueNot() (in module simuOpt)
valueNotEqual() (in module simuOpt)
valueOneOf() (in module simuOpt)

valueOr() (in module simuOpt)

valueSumTo() (in module simuOpt)

valueTrueFalse() (in module simuOpt)

valueValidDir() (in module simuOpt)

valueValidFile() (in module simuOpt)

VarPlotter (class in simuPOP.plotter)

VarPlotter() (simuPOP.plotter.VarPlotter method)

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)

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