Low-dimensional population evolving on the hypercube_lowd. More...

#include <ffpopsim_lowd.h>

Collaboration diagram for haploid_lowd:

Public Member Functions
	haploid_lowd (int L=1, int rng_seed=0)
	Default constructor. More...

virtual	~haploid_lowd ()
	Default destructor. More...

int	L ()

int	get_number_of_loci ()

double	N ()

double	get_population_size ()

double	get_generation ()

void	set_generation (double g)

double	get_mutation_rate (int locus, int direction)

int	get_recombination_model ()

double	get_recombination_rate (int locus)
	Get the recombination rate between a locus and the next one. More...

int	set_allele_frequencies (double *frequencies, unsigned long N)
	Initialize population in linkage equilibrium. More...

int	set_genotypes (vector< index_value_pair_t > gt)
	Initialize the population with genotype counts. More...

int	set_wildtype (unsigned long N)
	Initialize a wildtype population (00...0) More...

int	set_recombination_model (int rec_model)
	Set a new recombination model. More...

int	set_recombination_rates (double *rec_rates, int rec_model=-1)
	calculate recombination patterns More...

int	set_mutation_rates (double m)
	Set a uniform mutation rate for all loci and both directions. More...

int	set_mutation_rates (double m1, double m2)
	Set two mutation rates (forward / backward) for all loci. More...

int	set_mutation_rates (double *m)
	Set mutation rates (locus specific, both directions the same) More...

int	set_mutation_rates (double **m)
	Set mutation rates (locus and direction specific) More...

int	evolve (int gen=1)
	Evolve the population for some generations. More...

int	evolve_norec (int gen=1)
	Evolve the population for some generations, without recombination. More...

int	evolve_deterministic (int gen=1)
	Evolve the population for some generations, without resampling (deterministic) More...

double	get_genotype_frequency (int genotype)

double	get_allele_frequency (int locus)

double	get_pair_frequency (int locus1, int locus2)

double	get_chi (int locus)

double	get_chi2 (int locus1, int locus2)

double	get_LD (int locus1, int locus2)

double	get_moment (int locus1, int locus2)

double	genotype_entropy ()
	Get the genotype entropy. More...

double	allele_entropy ()
	Get the allele entropy. More...

double	get_fitness (int genotype)

stat_t	get_fitness_statistics ()
	Get fitness mean and variance in the population. More...

Public Attributes
hypercube_lowd	fitness

hypercube_lowd	population

double	carrying_capacity

double	outcrossing_rate

bool	circular

Protected Member Functions
int	get_random_seed ()
	Get a random seed from /dev/urandom. More...

int	select ()
	Selection step. More...

int	mutate ()
	Mutation step. More...

int	recombine ()
	Recombination step. More...

int	resample ()
	Resample the population according to the carrying capacity. More...

int	set_recombination_rates_general (double *rec_rates)
	Set the recombination rates for the general model. More...

int	set_recombination_patterns (vector< index_value_pair_t > iv)
	set recombination patterns with a list of index value pairs More...

int	marginalize_recombination_patterns ()
	Starting from a fully specified set of probabilities of recombination patterns, compute all sub patterns. More...

int	set_recombination_rates_single_crossover (double *rec_rates)
	Set the recombination rates for the single crossover model. More...

int	calculate_recombinants_free ()
	Calculate the recombinant distribution for the free recombination case. More...

int	calculate_recombinants_single ()
	Calculate the recombinant distribution for the single crossover case. More...

int	calculate_recombinants_general ()
	Calculate the recombinant distribution for the general case. More...

Protected Attributes
gsl_rng *	rng

int	seed

hypercube_lowd	recombinants

hypercube_lowd	mutants

double **	recombination_patterns

int	recombination_model

int	number_of_loci

double	population_size

int	generation

double	long_time_generation

double **	mutation_rates

Detailed Description

Low-dimensional population evolving on the hypercube_lowd.

This class enables simulation of short genomes ( \(L \lesssim 20\)) but potentially large populations. Random mutation, recombination and selection are supported. A number of properties of the population can be obtained using methods of this class, including:

genotype and allele frequencies;
statistics on fitness and phenotypic traits;
linkage disequilibrium.

Constructor & Destructor Documentation

haploid_lowd::haploid_lowd	(	int	L_in = `1`,
		int	rng_seed = `0`
	)

Default constructor.

Parameters

L_in	number of loci (at least 1)
rngseed	seed for the random number generator. If this is zero, time(NULL)+getpid() is used.

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haploid_lowd::~haploid_lowd ( )

virtual

Default destructor.

Release memory.

Member Function Documentation

double haploid_lowd::allele_entropy ( )

Get the allele entropy.

Returns: the allele entropy of the population

The allele entropy is defined as follows:

\[ S := - \sum_{i=1}^L \nu_i\log \nu_i + (1 - \nu_i)\log (1 - \nu_i), \]

where \(\nu_i\) is the frequency of the i-th allele.

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int haploid_lowd::calculate_recombinants_free ( )

protected

Calculate the recombinant distribution for the free recombination case.

Returns: zero if successful, nonzero otherwise

Almost the same as for the more general case below, but kept separate for performance reasons - this is the most expensive part (3^L).

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int haploid_lowd::calculate_recombinants_general ( )

protected

Calculate the recombinant distribution for the general case.

Returns: zero if successful, nonzero otherwise

Calculate the distribution after recombination assumed in random mating with pairs sampled with replacement.

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int haploid_lowd::calculate_recombinants_single ( )

protected

Calculate the recombinant distribution for the single crossover case.

Returns: zero if successful, nonzero otherwise

Calculate the distribution after recombination assumed in random mating with pairs sampled with replacement.

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int haploid_lowd::evolve ( int gen = 1 )

Evolve the population for some generations.

Parameters

gen	number of generations

Returns: zero if successful, error code in the faulty step otherwise

Note: the order of selection, mutation, recombination, and resampling could be changed according to needs and beliefs. Note that only recombination calculates the inverse fourier transform of the population. It does so BEFORE the recombination step. To evaluate all allele frequencies and linkage disequilibria, call population.fft_func_to_coeff()

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int haploid_lowd::evolve_deterministic ( int gen = 1 )

Evolve the population for some generations, without resampling (deterministic)

Parameters

gen	number of generations

Returns: zero if successful, error code in the faulty step otherwise

Note: the order of selection, mutation, and recombination could be changed according to needs and beliefs. Note that only recombination calculates the inverse fourier transform of the population. It does so BEFORE the recombination step. To evaluate all allele frequencies and linkage disequilibria, call population.fft_func_to_coeff()

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int haploid_lowd::evolve_norec ( int gen = 1 )

Evolve the population for some generations, without recombination.

Parameters

gen	number of generations

Returns: zero if successful, error code in the faulty step otherwise

Note: the order of selection, mutation, and resampling could be changed according to needs and beliefs.

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double haploid_lowd::genotype_entropy ( )

Get the genotype entropy.

Returns: the genotype entropy of the population

The genotype entropy is defined as follows:

\[ S := - \sum_{g} \nu_g \cdot \log \nu_g, \]

where \(g\) runs over all possible genomes, and \(\nu_g\) is the frequency of that genome in the population.

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double haploid_lowd::get_allele_frequency ( int locus )

inline

double haploid_lowd::get_chi ( int locus )

inline

double haploid_lowd::get_chi2	(	int	locus1,
		int	locus2
	)

inline

double haploid_lowd::get_fitness ( int genotype )

inline

stat_t haploid_lowd::get_fitness_statistics ( )

Get fitness mean and variance in the population.

Returns: stat_t with the requested statistics

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double haploid_lowd::get_generation ( )

inline

double haploid_lowd::get_genotype_frequency ( int genotype )

inline

double haploid_lowd::get_LD	(	int	locus1,
		int	locus2
	)

inline

double haploid_lowd::get_moment	(	int	locus1,
		int	locus2
	)

inline

double haploid_lowd::get_mutation_rate	(	int	locus,
		int	direction
	)

inline

int haploid_lowd::get_number_of_loci ( )

inline

double haploid_lowd::get_pair_frequency	(	int	locus1,
		int	locus2
	)

inline

double haploid_lowd::get_population_size ( )

inline

int haploid_lowd::get_random_seed ( )

protected

Get a random seed from /dev/urandom.

Returns: non-deterministic, random seed

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int haploid_lowd::get_recombination_model ( )

inline

double haploid_lowd::get_recombination_rate ( int locus )

Get the recombination rate between a locus and the next one.

Parameters

locus the locus AFTER which the recombination rate is seeked

Returns: the recombination rate, -1 for FREE_RECOMBINATION

Note: for SINGLE_CROSSOVER, the recombination rate after the last locus is the rate of no recombination at all.

int haploid_lowd::L ( )

inline

int haploid_lowd::marginalize_recombination_patterns ( )

protected

Starting from a fully specified set of probabilities of recombination patterns, compute all sub patterns.

Parameters

@returns zero if successful, error codes otherwise

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int haploid_lowd::mutate ( )

protected

Mutation step.

Returns: zero if successful, nonzero otherwise

Calculate the distribution of mutants and update the population distribution

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double haploid_lowd::N ( )

inline

int haploid_lowd::recombine ( )

protected

Recombination step.

Returns: zero if successful, error codes otherwise

Calculate the distribution of recombinants and update the population, a fraction (outcrossing_rate) of the population is replaced by the recombinant distribution, calculated differently depending on whether free recombination or general recombination is used

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int haploid_lowd::resample ( )

protected

Resample the population according to the carrying capacity.

Returns: zero if successful, error codes otherwise

Note: genotypes with few individuals are sampled using the Poisson distribution, allowing for strict zero; genotypes with many individuals are resampled using a Gaussian distribution, for performance reasons.

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int haploid_lowd::select ( )

protected

Selection step.

Returns: zero if successful, nonzero otherwise

Note: Population distribution is reweighted with exp(fitness) and renormalized.

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int haploid_lowd::set_allele_frequencies	(	double *	freq,
		unsigned long	N_in
	)

Initialize population in linkage equilibrium.

Parameters

freq	allele frequencies
N_in	population size

Returns: zero if successful, error codes otherwise

Note: when this function is used to initialize the population, it is likely that the fitness distribution has a very large width. In turn, this can result in an immediate and dramatic drop in diversity within the first few generations. Please check fitness statistics before starting the evolution if this worries you.

Note: the population size will be set. If not set yet, the carrying capacity will be set to the same number.

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void haploid_lowd::set_generation ( double g )

inline

int haploid_lowd::set_genotypes ( vector< index_value_pair_t > gt )

Initialize the population with genotype counts.

Parameters

gt	vector of index_value_pair_t type with indices and counts

Returns: zero if successful, error codes otherwise

Note: the population size will be set as the total sum of counts of all genotypes. If not set yet, the carrying capacity will be set to the same number.

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int haploid_lowd::set_mutation_rates ( double m )

Set a uniform mutation rate for all loci and both directions.

Parameters

m	mutation rate

Returns: zero if successful, error codes otherwise

int haploid_lowd::set_mutation_rates	(	double	mforward,
		double	mbackward
	)

Set two mutation rates (forward / backward) for all loci.

Parameters

mforward	forward mutation rate
mbackward	backward mutation rate

Returns: zero if successful, error codes otherwise

int haploid_lowd::set_mutation_rates ( double * m )

Set mutation rates (locus specific, both directions the same)

Parameters

m	array of mutation rates

Returns: zero if successful, error codes otherwise

int haploid_lowd::set_mutation_rates ( double ** m )

Set mutation rates (locus and direction specific)

Parameters

m	array of mutation rates

Returns: zero if successful, error codes otherwise

int haploid_lowd::set_recombination_model ( int rec_model )

Set a new recombination model.

Parameters

rec_model the new recombination model

Returns: zero if successful, error codes otherwise

The allowed models are FREE_RECOMBINATION, SINGLE_CROSSOVER, and CROSSOVERS.

Note: this function call involves memory release and allocation.

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int haploid_lowd::set_recombination_patterns ( vector< index_value_pair_t > iv )

protected

set recombination patterns with a list of index value pairs

Parameters

vector of index_value_pair_t structures

Returns: zero if successful, error code otherwise

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int haploid_lowd::set_recombination_rates	(	double *	rec_rates,
		int	rec_model = `-1`
	)

calculate recombination patterns

Parameters

rec_rates	a vector of recombination rates.
rec_model	an int with the model of recombination to use

Note: rec_rates must have length L-1 for linear chromosomes, length L for circular ones. Note: rec_model must be either CROSSOVERS or, for linear genomes, SINGLE_CROSSOVER

Returns: zero if successful, error codes otherwise (e.g. out of memory)

A routine the calculates the probability of all possible recombination patterns and subpatterns thereof from a vector of recombination rates (rec_rates) passed as argument. It allocated the memory ( \(3^L\) or \(L \: 2^L\)) and calculates the entire distribution.

Note: the default value for rec_model is the current recombination model or, if that is FREE_RECOMBINATION, then it's CROSSOVERS.

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int haploid_lowd::set_recombination_rates_general ( double * rec_rates )

protected

Set the recombination rates for the general model.

Parameters

rec_rates array with the recombination rates

Returns: zero if successful, error codes otherwise

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int haploid_lowd::set_recombination_rates_single_crossover ( double * rec_rates )

protected

Set the recombination rates for the single crossover model.

Parameters

rec_rates array with the recombination rates

Returns: zero if successful, error codes otherwise

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int haploid_lowd::set_wildtype ( unsigned long N_in )

Initialize a wildtype population (00...0)

Parameters

N_in	number of individuals

Returns: 0 if successful, nonzero otherwise.

Note: the population size will be set. If not set yet, the carrying capacity will be set to the same number.

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Member Data Documentation

double haploid_lowd::carrying_capacity

bool haploid_lowd::circular

hypercube_lowd haploid_lowd::fitness

int haploid_lowd::generation

protected

double haploid_lowd::long_time_generation

protected

hypercube_lowd haploid_lowd::mutants

protected

double** haploid_lowd::mutation_rates

protected

int haploid_lowd::number_of_loci

protected

double haploid_lowd::outcrossing_rate

hypercube_lowd haploid_lowd::population

double haploid_lowd::population_size

protected

hypercube_lowd haploid_lowd::recombinants

protected

int haploid_lowd::recombination_model

protected

double** haploid_lowd::recombination_patterns

protected

gsl_rng* haploid_lowd::rng

protected

int haploid_lowd::seed

protected

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

src/ffpopsim_lowd.h
src/haploid_lowd.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation