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simuPOP v1.1.8svn documentation
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Front Matter
Introduction
What is simuPOP?
An overview of simuPOP concepts
Features
License, Distribution and Installation
How to read this user’s guide
Other help sources
Loading and running simuPOP
Pythonic issues
from
simuPOP
import
* v.s.
import
simuPOP
References and the
clone()
member function
Zero-based indexes, absolute and relative indexes
Ranges and iterators
Empty,
ALL_AVAIL
and dynamic values for parameters
loci
,
reps
,
ancGen
and
subPops
User-defined functions and class
WithArgs
*
Exception handling *
Loading simuPOP modules
Short, long, binary, mutant and lineage modules and their optimized versions
Execution in multiple threads
Graphical user interface
Online help system
Debug-related functions and operators *
Random number generator *
Individuals and Populations
Genotypic structure
Haploid, diploid and haplodiploid populations
Autosomes, sex chromosomes, mitochondrial, and other types of chromosomes *
Information fields
Individual
Access individual genotype
individual sex, affection status and information fields
Population
Access and change individual genotype
Subpopulations
Virtual subpopulations and virtual splitters *
Advanced virtual subpopulation splitters **
Access individuals and their properties
Attach arbitrary auxillary information using information fields
Keep track of ancestral generations
Change genotypic structure of a population
Remove or extract individuals and subpopulations from a population
Store arbitrary population information as population variables
Save and load a population
Import and export datasets in unsupported formats *
simuPOP Operators
Introduction to operators
Apply operators to selected replicates and (virtual) subpopulations at selected generations
Applicable populations and (virtual) subpopulations
Dynamically determined loci (parameter
loci
) *
Write output of operators to one or more files
During-mating operators
Function form of an operator
Initialization
Initialize individual sex (operator
InitSex
)
Initialize genotype (operator
InitGenotype
)
Initialize information fields (operator
InitInfo
)
Expressions and statements
Output a Python string (operator
PyOutput
)
Execute Python statements (operator
PyExec
)
Evaluate and output Python expressions (operator
PyEval
)
Expression and statement involving individual information fields (operator
InfoEval
and
InfoExec
) *
Using functions in external modules in simuPOP expressions and statements
Demographic changes
Migration (operator
Migrator
)
Migration by probability
Migration by proportion and counts
Theoretical migration models
migrate from virtual subpopulations *
Arbitrary migration models **
Migration using backward migration matrix (operator
BackwardMigrator
)
Split subpopulations (operators
SplitSubPops
)
Merge subpopulations (operator
MergeSubPops
)
Resize subpopulations (operator
ResizeSubPops
)
Time-dependent migration rate
Genotype transmitters
Generic genotype transmitters (operators
GenoTransmitter
,
CloneGenoTransmitter
,
MendelianGenoTransmitter
,
SelfingGenoTransmitter
,
HaplodiploidGenoTransmitter
, and
MitochondrialGenoTransmitter
) *
Recombination (Operator
Recombinator
)
Gene conversion (Operator
Recombinator
) *
Tracking all recombination events **
Mutation
Mutation models specified by rate matrixes (
MatrixMutator
)
k-allele mutation model (
KAlleleMutator
)
Diallelic mutation models (
SNPMutator
)
Nucleotide mutation models (
AcgtMutator
)
Mutation model for microsatellite markers (
StepwiseMutator
)
Simulating arbitrary mutation models using a hybrid mutator (
PyMutator
)*
Mixed mutation models (
MixedMutator
) **
Context-dependent mutation models (
ContextMutator
)**
Manually-introduced mutations (
PointMutator
)
Apply mutation to (virtual) subpopulations *
Allele mapping **
Mutation rate and transition matrix of a
MatrixMutator
**
Infinite-sites model and other simulation techniques **
Recording and tracing individual mutants **
Penetrance
Map penetrance model (operator
MapPenetrance
)
Multi-allele penetrance model (operator
MaPenetrance
)
Multi-loci penetrance model (operator
MlPenetrance
)
Hybrid penetrance model (operator
PyPenetrance
)
Quantitative trait
A hybrid quantitative trait operator (operator
PyQuanTrait
)
Natural Selection
Natural selection through the selection of parents
Natural selection through the selection of offspring *
Are two selection scenarios equivalent? **
Map selector (operator
MapSelector
)
Multi-allele selector (operator
MaSelector
)
Multi-locus selection models (operator
MlSelector
)
A hybrid selector (operator
PySelector
)
Multi-locus random fitness effects (operator
PyMlSelector
)
Alternative implementations of natural selection
Frequency dependent or dynamic selection pressure *
Support for virtual subpopulations *
Natural selection in heterogeneous mating schemes **
Tagging operators
Inheritance tagger (operator
InheritTagger
)
Summarize parental informatin fields (operator
SummaryTagger)
Tracking parents (operator
ParentsTagger
)
Tracking index of offspring within families (operator
OffspringTagger
)
Assign unique IDs to individuals (operator
IdTagger
)
Tracking Pedigrees (operator
PedigreeTagger
)
A hybrid tagger (operator
PyTagger
)
Tagging that involves other parental information
Statistics calculation (operator
Stat
)
How statistics calculation works
defdict
datatype
Support for virtual subpopulations
Counting individuals by sex and affection status
Number of segregating and fixed sites
Allele count and frequency
Genotype count and frequency
Homozygote and heterozygote count and frequency
Haplotype count and frequency
Summary statistics of information fields
Linkage disequilibrium
Genetic association
population structure
Hardy-Weinberg equilibrium test
Measure of Inbreeding
Effective population size
Other statistics
Support for sex and customized chromosome types
Conditional operators
Conditional operator (operator
IfElse
) *
Conditionally terminate an evolutionary process (operator
TerminateIf
)
Conditionally revert an evolutionary process to a saved state (operator
RevertIf
)
Conditional during mating operator (operator
DiscardIf
)
Miscellaneous operators
An operator that does nothing (operator
NoneOp
)
dump the content of a population (operator
Dumper
)
Save a population during evolution (operator
SavePopulation
)
Pause and resume an evolutionary process (operator
Pause
) *
Measuring execution time of operators (operator
TicToc
) *
Hybrid and Python operators
Hybrid operators
Python operator
PyOperator
*
During-mating Python operator *
Define your own operators *
Evolving populations
Mating Schemes
Control the size of the offspring generation
Advanced use of demographic functions *
Determine the number of offspring during mating
Dynamic population size determined by number of offspring *
Determine sex of offspring
Monogamous mating
Polygamous mating
Asexual random mating
Mating in haplodiploid populations
Self-fertilization
Heterogeneous mating schemes *
Conditional mating schemes
Simulator
Add, access and remove populations from a simulator
Number of generations to evolve
Evolve populations in a simulator
Non-random and customized mating schemes *
The structure of a homogeneous mating scheme *
Offspring generators *
Genotype transmitters *
A Python parent chooser *
Using C++ to implement a parent chooser **
Age structured populations with overlapping generations **
Tracing allelic lineage *
Pedigrees
Create a pedigree object
Locate close and remote relatives of each individual
Identify pedigrees (related individuals)
Save and load pedigrees
Evolve a population following a specified pedigree structure **
Simulation of mitochondrial DNAs (mtDNAs) *
Utility Modules
Module
simuOpt
(function
simuOpt.setOptions
)
Class
simuOpt.Params
(deprecated)
Define a parameter specification list.
Get parameters (function
getParam
)
Access, manipulate and extract parameters
Module
simuPOP.utils
Trajectory simulation (classes
Trajectory
and
TrajectorySimulator
)
Forward-time trajectory simulations (function
simulateForwardTrajectory
)
Backward-time trajectory simulations (function
simulateBackwardTrajectory
).
Graphical or text-based progress bar (class
ProgressBar
)
Display population variables (function
viewVars
)
Import simuPOP population from files in
GENEPOP,
PHYLIP
and
FSTAT
formats (function
importPopulation
)
Export simuPOP population to files in
STRUCTURE,
GENEPOP
,
FSTAT,
Phylip,
PED,
MAP,
MS,
and
CSV
formats (function
export
and operator
Exporter
)
Export simuPOP population in csv format (function
saveCSV
, deprecated)
Module
simuPOP.demography
Predefined migration models
Uniform interface of demographic models
Demographic models defined by outcomes
Demographic models defined by population changes (events)
Predefined demographic models for human populations
Demographic model without predefined generations to evolve *
Module
simuPOP.plotter
Derived keyword arguments *
Plot of expressions and their histories (operator
plotter.VarPlotter
)
Scatter plots (operator
plotter.ScatterPlotter
)
Module
simuPOP.sampling
Introduction
Sampling individuals randomly (class
RandomSampler
, functions
drawRandomSample
and
drawRandomSamples
)
Sampling cases and controls (class
CaseControlSampler
, functions
CaseControlSample
and
CaseControlSamples
)
Sampling Pedigrees (functions
indexToID
and
plotPedigree
)
Sampling affected sibpairs (class
AffectedSibpairSampler
, functions
drawAffectedSibpairSample(s)
)
Sampling nuclear families (class
NuclearFamilySampler
, functions
drawNuclearFamilySample
and
drawNuclearFamilySample
s)
Sampling three-generation families (class
ThreeGenFamilySampler
, functions
drawThreeGenFamilySample
and
drawThreeGenFamilySamples
)
Sampling different types of samples (class
CombinedSampler
, functions
drawCombinedSample
and
drawCombinedSamples
)
Sampling from subpopulations and virtual subpopulations *
Module
simuPOP.gsl
Module
simuPOP.sandbox
A real world example
Simulation scenario
Demographic model
Mutation and selection models
Output statistics
Initialize and evolve the population
Option handling
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