quetzal::demography::HistoryBase< Space, DemographicPolicy, MemoryPolicy > Class Template Reference

#include <quetzal/demography/HistoryBase.hpp>

Detailed Description

template<typename Space, typename DemographicPolicy, typename MemoryPolicy>
class quetzal::demography::HistoryBase< Space, DemographicPolicy, MemoryPolicy >

Base class for simulating and recording spatial population history, encpasulating backward migration logic.

It makes use of the CRTP design pattern, meaning that this class has to be specialized to define History classes offering customized behaviors, like details of the demograhic algorithms (mass_based or individual_based) or storage aspects.

Template Parameters

Space	Demes identifiers.
DemographicPolicy	Policy Used for populations dynamics simulation algorithms, see demographic_policy
MemoryPolicy	Policy used for storage and access to demographic quantities, see memory_policy

Public Types
using	coord_type = Space
using	time_type = unsigned int
using	memory_policy = MemoryPolicy
using	demographic_policy = DemographicPolicy
using	value_type = typename demographic_policy::value_type
using	flow_type = typename memory_policy::template flow_type< coord_type, time_type, value_type >
using	pop_sizes_type = typename memory_policy::template pop_sizes_type< coord_type, time_type, value_type >
using	discrete_distribution_type = quetzal::utils::random::DiscreteDistribution< coord_type >

Public Member Functions
	HistoryBase (coord_type const &x, value_type N, unsigned int nb_generations)
	Constructor initializing the demographic database.
auto	distribution_area (time_type t) const
	Retrieve demes where N > 0 at time t.
auto &	pop_size (coord_type const &x, time_type const &t)
	Population size at deme x at time t.
auto	get_functor_N () const noexcept
	Read-only functor.
auto	get_pop_size (coord_type const &x, time_type const &t)
	Read-only.
void	set_pop_size (coord_type const &x, time_type const &t, value_type N)
	Used in derived class History to increment migrants.
unsigned int const &	nb_generations () const
	Last time recorded in the foward-in-time database history.
template<typename Generator >
coord_type	backward_kernel (coord_type const &x, time_type t, Generator &gen) const
	Samples a coordinate from the backward-in-time transition matrix.

Protected Attributes
std::unique_ptr< flow_type >	m_flows

Constructor & Destructor Documentation

HistoryBase()

template<typename Space , typename DemographicPolicy , typename MemoryPolicy >

quetzal::demography::HistoryBase< Space, DemographicPolicy, MemoryPolicy >::HistoryBase ( coord_type const &  x, value_type  N, unsigned int  nb_generations  )

inline

Constructor initializing the demographic database.

Parameters

x	the coordinate of introduction
N	the population size at coordinate x at time 0
nb_generations	the number of generations history is supposed to last

Member Function Documentation

backward_kernel()

template<typename Space , typename DemographicPolicy , typename MemoryPolicy >

template<typename Generator >

coord_type quetzal::demography::HistoryBase< Space, DemographicPolicy, MemoryPolicy >::backward_kernel ( coord_type const &  x, time_type  t, Generator &  gen  ) const

inline

Samples a coordinate from the backward-in-time transition matrix.

The transition matrix is computed from the demographic flows database. The returned coordinate object will basically answer the question: when an individual is found in \(x\) at time \(t\), where could it have been at time \(t-1\) ?

pop_size()

template<typename Space , typename DemographicPolicy , typename MemoryPolicy >

auto & quetzal::demography::HistoryBase< Space, DemographicPolicy, MemoryPolicy >::pop_size ( coord_type const &  x, time_type const &  t  )

inline

Population size at deme x at time t.

Returns

a reference to the value, initialized with value_type default constructor

Remarks

operator allows for more expressive mathematical style in client code

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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/demography/HistoryBase.hpp