hypercube_highd Class Reference

Hypercube class for high-dimensional simulations. More...

#include <ffpopsim_highd.h>

Public Member Functions
	hypercube_highd ()
	hypercube_highd (int dim_in, int s=0)
virtual	~hypercube_highd ()
int	set_up (int dim_in, int s=0)
unsigned int	get_dim ()
unsigned int	get_seed ()
double	get_func (boost::dynamic_bitset<> &genotype)
	Get single value on the hypercube. More...
double	get_additive_coefficient (int locus)
	: get the trait coefficient of a locus. More...
double	get_func_diff (boost::dynamic_bitset<> &genotype1, boost::dynamic_bitset<> &genotype2, vector< int > &diffpos)
	Calculate difference between two hypercube points efficiently. More...
void	reset ()
	Reset the hypercube. More...
void	reset_additive ()
	Reset the additive part of the hypercube. More...
int	set_additive_coefficient (double value, int locus, int expected_locus=-1)
	reset the value of an additive coefficient More...
int	add_coefficient (double value, vector< int > loci)
	assign single- or multi-locus trait coefficients. More...
int	set_random_epistasis_strength (double sigma)
	set the standard deviation of random epistatic fitness More...

Public Attributes
int	rng_offset
int	dim
double	hypercube_mean
double	epistatic_std
vector< coeff_single_locus_t >	coefficients_single_locus
vector< coeff_t >	coefficients_epistasis

Detailed Description

Hypercube class for high-dimensional simulations.

This class is used for representing properties of genotypes. Unlike the low-dimensional sister class, no attempt is made to monitor the whole hypercube, because the dimension the space of genotypes of length L is \(2^L\). As a consequence, no Fourier transformations are implemented.

The main use of this class is either for pointwise assigment of values (for instance, we assign fitness only for the actually observed genotypes) or for low-order Fourier coefficients, like like main fitness effects and two-site epistasis, which scale like L and \(L^2\), respectively.

Constructor & Destructor Documentation

hypercube_highd::hypercube_highd

(

)

hypercube_highd::hypercube_highd	(	int	dim_in,
		int	s = 0
	)

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hypercube_highd::~hypercube_highd ( )

virtual

Member Function Documentation

int hypercube_highd::add_coefficient	(	double	value,
		vector< int >	loci
	)

assign single- or multi-locus trait coefficients.

It takes a double and assigns it to a trait coefficients with index set specified in vector loci.

double hypercube_highd::get_additive_coefficient

(

int

locus

)

: get the trait coefficient of a locus.

Loop over the additive coefficients and return the value once the locus is found.

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unsigned int hypercube_highd::get_dim ( )

inline

double hypercube_highd::get_func

(

boost::dynamic_bitset<> &

genotype

)

Get single value on the hypercube.

Parameters

genotype

Point of the hypercube

Returns

the value corresponding to that point

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double hypercube_highd::get_func_diff	(	boost::dynamic_bitset<> &	genotype1,
		boost::dynamic_bitset<> &	genotype2,
		vector< int > &	diffpos
	)

Calculate difference between two hypercube points efficiently.

Parameters

genotype1	first point on the hypercube
genotype2	second point on the hypercube
diffpos	vector of positions at which they differ

Returns

the difference between the values, f(gt1) - f(gt2)

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unsigned int hypercube_highd::get_seed ( )

inline

void hypercube_highd::reset

(

)

Reset the hypercube.

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void hypercube_highd::reset_additive

(

)

Reset the additive part of the hypercube.

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int hypercube_highd::set_additive_coefficient	(	double	value,
		int	lindex,
		int	expected_locus = -1
	)

reset the value of an additive coefficient

Note: it requires the index of the coefficient and the locus it is supposed to refer to.

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int hypercube_highd::set_random_epistasis_strength

(

double

sigma

)

set the standard deviation of random epistatic fitness

int hypercube_highd::set_up	(	int	dim_in,
		int	s = 0
	)

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Member Data Documentation

vector<coeff_t> hypercube_highd::coefficients_epistasis

vector<coeff_single_locus_t> hypercube_highd::coefficients_single_locus

int hypercube_highd::dim

double hypercube_highd::epistatic_std

double hypercube_highd::hypercube_mean

int hypercube_highd::rng_offset

---

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

• src/ffpopsim_highd.h
• src/hypercube_highd.cpp