Egglib 2.1.11
C++ library reference manual
Classes
coalesce

Coalescent simulator. More...

Classes

class  Arg
 Ancestral recombination graph. More...
 
class  Change
 Pure virtual base class for parameter changes. More...
 
class  SingleParamChange
 Pure virtual base class for single parameter changes. More...
 
class  PopulationParamChange
 Single parameter changes applied to a single population. More...
 
class  Bottleneck
 Bottleneck event. More...
 
class  PopulationBottleneck
 Population-specific bottleneck event. More...
 
class  AllPopulationSizeChange
 Change of the size of all populations. More...
 
class  SinglePopulationSizeChange
 Change of a single population size. More...
 
class  GrowthRateChange
 Change of the growth rate of all populations. More...
 
class  PopulationGrowthRateChange
 Change of a single population's growth rate. More...
 
class  SelfingRateChange
 Change of the selfing rate. More...
 
class  PopulationFusion
 Fusion of two populations. More...
 
class  PopulationSplit
 Split of a population. More...
 
class  AllMigrationRateChange
 Change of the migration rate of all population pairs. More...
 
class  SingleMigrationRateChange
 Change of a single migration rate. More...
 
class  Controller
 Controls a coalescent simulation. More...
 
class  Current
 Represents the current set of populations. More...
 
class  Edge
 Edge of the ancestral recombination graph. More...
 
class  EdgePool
 Pool of Edge objects. More...
 
class  Mutation
 Very simple container of some information relative to a mutation. More...
 
class  Mutator
 Implements mutation models. More...
 
class  ParamSet
 Set of parameters. More...
 
class  Population
 Handles a single population. More...
 

Detailed Description

Coalescent simulator.

The set of classes implements a three-scale coalescent simulator with recombination, and a flexible mutation model. The main classes are Controller (the starting point for generating genealogies), ParamSet (that centralizes parameter specification), the Change hierarchy (that implements demographic change specifications), Arg (ancestral recombination graph; the result of generation a genealogy) and Mutator (that generates genotype data from an ARG).


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