quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory > Class Template Reference

#include <quetzal/simulator/ForwardBackwardSpatiallyExplicit.hpp>

Detailed Description

template<typename Space, typename DispersalPolicy, typename CoalescencePolicy, typename Memory = quetzal::demography::memory_policy::on_RAM>
class quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >

Discrete-time coalescence simulator in a discrete spatially explicit landscape.

This simulator consists in a forward demographic simulation of population growth and migration, after what a backward coalescent simulation is performed that traces back the ancestry of a sample of gene copies sampled in one or more populations. Most Recent Common ancestor is not always fond in the time span of the spatial history, so if the chosen CoalescencePolicy implements the required behavior, ancestry can be simulated in the more distant past using another model like the DiscreteTimeWrightFisher model, to find the MRCA. Details concerning the mergers (binary mergers, simultaneous multiple mergers) can be controlled using the relevant Merger policy class when calling a coalescence function of the class interface.

Template Parameters

Space	deme identifiers (like the populations geographic coordinates)
Strategy	a template class argument (e.g. mass_based, individual_based) that indicates how dispersal should be defined in terms of demographic expansion algorithms. Strategy class implements the details (computing migrations probabilites as a function of the distance for example) whereas template specialization of the internal history_type class defines different migration algorithms.
CoalescencePolicy	a policy class for the demographic expansion.

Public Types
using	coord_type = Space
using	dispersal_policy_type = DispersalPolicy
using	N_value_type = typename DispersalPolicy::value_type
using	memory_policy = Memory
template<typename tree_type >
using	forest_type = quetzal::coalescence::container::Forest< coord_type, tree_type >

Public Member Functions
	ForwardBackwardSpatiallyExplicit (coord_type x_0, N_value_type N_0, unsigned int nb_generations)
	Constructor.
auto	distribution_area (unsigned int t) const
	Return demes with non-zero population size.
auto	get_functor_N () const noexcept
	Read-only access to the population size history.
template<typename Generator , typename Growth , typename Dispersal >
void	simulate_forward_demography (Growth growth, Dispersal kernel, Generator &gen)
	Simulate the forward-in-time demographic expansion.
template<typename Merger , typename Generator >
auto	make_forest_and_coalesce_along_spatial_history (std::map< coord_type, unsigned int > sample, Generator &gen)
	Initlize a forest based on sample counts then coalesce the forest along the spatial history, then stops and return an incomplete forest.
template<typename Merger , typename Generator >
auto	make_forest_using_sampling_time_and_coalesce_along_spatial_history (std::map< coord_type, unsigned int > sample, unsigned int sampling_time, Generator &gen)
	Initialize a forest based on sample counts, forwarding the sampling time to the forest contructor. Then coalesce the forest along the spatial history, then stops and return a possibly incomplete forest.
template<typename Merger , typename Generator , typename F , typename Tree , typename U >
auto	coalesce_along_spatial_history (forest_type< Tree > forest, F binary_op, Generator &gen, U make_tree)
	Coalesce a forest of nodes conditionally to the simulated demography.
template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator >
auto	coalesce_to_mrca (std::map< coord_type, unsigned int > sample, unsigned int sampling_time, Generator &gen)
	Create a forest from a sample and coalesce it conditionally to the simulated demography.
template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator >
auto	coalesce_to_mrca (std::map< coord_type, unsigned int > sample, Generator &gen)
	Create a forest from a sample and coalesce it conditionally to the simulated demography.
template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator , typename F >
auto	coalesce_to_mrca (std::map< coord_type, unsigned int > sample, unsigned int sampling_time, F leaf_name, Generator &gen)
	Create a forest from a sample giving name to tips, then coalesce them conditionally to the simulated demography.
template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename T , typename F1 , typename F2 , typename Generator >
auto	coalesce_to_mrca (std::vector< T > sample, unsigned int sampling_time, F1 get_location, F2 get_name, Generator &gen)
	Create a forest from a sample then coalesce them conditionally to the simulated demography.

Constructor & Destructor Documentation

ForwardBackwardSpatiallyExplicit()

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::ForwardBackwardSpatiallyExplicit ( coord_type  x_0, N_value_type  N_0, unsigned int  nb_generations  )

inline

Constructor.

Parameters

x_0	Initialization coordinate.
N_0	Population size at intialization
nb_generations	number of generations of the spatial process

Member Function Documentation

coalesce_to_mrca() [1/4]

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::coalesce_to_mrca ( std::map< coord_type, unsigned int >  sample, Generator &  gen  )

inline

Create a forest from a sample and coalesce it conditionally to the simulated demography.

Template Parameters

Merger	a coalescence merger to use
Generator	a random number Generator

Parameters

sample

the number of gene copies at each location @gen a random number generator

coalesce_to_mrca() [2/4]

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator , typename F >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::coalesce_to_mrca ( std::map< coord_type, unsigned int >  sample, unsigned int  sampling_time, F  leaf_name, Generator &  gen  )

inline

Create a forest from a sample giving name to tips, then coalesce them conditionally to the simulated demography.

Template Parameters

Generator	a random number Generator
F	a unary operation with signature equivalent to 'std::string fun(coord_type const& x, unsigned int t)'

Parameters

sample	the number of gene copies at each location
sampling_time	the time of sampling_time
leaf_name	a functor assigning a name to a tip as a function of its location and of sampling time. @gen a random number generator

coalesce_to_mrca() [3/4]

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename Generator >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::coalesce_to_mrca ( std::map< coord_type, unsigned int >  sample, unsigned int  sampling_time, Generator &  gen  )

inline

Create a forest from a sample and coalesce it conditionally to the simulated demography.

Template Parameters

Merger	a coalescence merger to use
Generator	a random number Generator

Parameters

sample	the number of gene copies at each location
sampling_time	the time of sampling_time to build the make_forest coalescence policy function @gen a random number generator

coalesce_to_mrca() [4/4]

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger = quetzal::coalescence::merger_policy::SimultaneousMultipleMerger< quetzal::coalescence::occupancy_spectrum::sampling_policy::on_the_fly>, typename T , typename F1 , typename F2 , typename Generator >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::coalesce_to_mrca ( std::vector< T >  sample, unsigned int  sampling_time, F1  get_location, F2  get_name, Generator &  gen  )

inline

Create a forest from a sample then coalesce them conditionally to the simulated demography.

Template Parameters

T	type of an individual
F1	a unary operation with signature equivalent to 'coord_type fun(const T& i)'
F2	a unary operation with signature equivalent to 'std::string fun(const T& i)'
Generator	a random number Generator

Parameters

sample	a collection of individuals (gene copies)
sampling_time	the time of sampling_time
get_location	a unary operation taking a sampled individual of type T as an argument and returning its geographic location
get_name	a functor taking a sampled individual of type T as an argument and returning an identifier @gen a random number generator

get_functor_N()

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::get_functor_N ( ) const

inlinenoexcept

Read-only access to the population size history.

Designed to be used for composing growth expression.

Returns

a functor with signature N_value_type fun(coord_type const& x, unsigned int t) giving the population size in deme \(x\) at time \(t\).

make_forest_and_coalesce_along_spatial_history()

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger , typename Generator >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::make_forest_and_coalesce_along_spatial_history ( std::map< coord_type, unsigned int >  sample, Generator &  gen  )

inline

Initlize a forest based on sample counts then coalesce the forest along the spatial history, then stops and return an incomplete forest.

Returns

A possibly incompletely coalesced forest.

make_forest_using_sampling_time_and_coalesce_along_spatial_history()

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Merger , typename Generator >

auto quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::make_forest_using_sampling_time_and_coalesce_along_spatial_history ( std::map< coord_type, unsigned int >  sample, unsigned int  sampling_time, Generator &  gen  )

inline

Initialize a forest based on sample counts, forwarding the sampling time to the forest contructor. Then coalesce the forest along the spatial history, then stops and return a possibly incomplete forest.

Returns

A possibly incompletely coalesced forest.

simulate_forward_demography()

template<typename Space , typename DispersalPolicy , typename CoalescencePolicy , typename Memory = quetzal::demography::memory_policy::on_RAM>

template<typename Generator , typename Growth , typename Dispersal >

void quetzal::simulator::ForwardBackwardSpatiallyExplicit< Space, DispersalPolicy, CoalescencePolicy, Memory >::simulate_forward_demography ( Growth  growth, Dispersal  kernel, Generator &  gen  )

inline

Simulate the forward-in-time demographic expansion.

Template Parameters

Growth	a growth functor, see param growth for details.
Dispersal	a dispersal kernel, see param kernel for details.

Parameters

growth	a functor simulating \(\tilde{N}_{x}^{t}\). The functor can possibly make use of get_functor_N. The signature of the function should be equivalent to the following: unsigned int sim_growth(V &gen, const coord_type &x, unsigned int t);
kernel	a functor representing the dispersal location kernel that simulates the coordinate of the next location conditionally to the current location \(x\). The signature should be equivalent to coord_type kernel(V &gen, const coord_type &x, unsigned int t);

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The documentation for this class was generated from the following file:

• /home/runner/work/quetzal-CoaTL/quetzal-CoaTL/src/include/quetzal/simulator/ForwardBackwardSpatiallyExplicit.hpp