HIV population with facultative drug treatment. More...

#include <hivpopulation.h>

Inheritance diagram for hivpopulation:

Collaboration diagram for hivpopulation:

Public Member Functions
	hivpopulation (int N=0, int rng_seed=0, double mutation_rate=3e-5, double coinfection_rate=1e-2, double crossover_rate=1e-3)
	Construct a HIV population with certain parameters. More...

virtual	~hivpopulation ()
	Destructor. More...

void	set_treatment (double t)

double	get_treatment ()

int	read_replication_coefficients (istream &model)

int	read_resistance_coefficients (istream &model)

int	write_genotypes (ostream &out_genotypes, int sample_size, string gt_label="", int start=0, int length=0)

Public Member Functions inherited from haploid_highd
	haploid_highd (int L=0, int rng_seed=0, int number_of_traits=1, bool all_polymorphic=false)
	Default constructor. More...

virtual	~haploid_highd ()
	Destructor. More...

double	get_mutation_rate ()

void	set_mutation_rate (double m)

bool	is_all_polymorphic ()

vector< poly_t >	get_polymorphisms ()

vector< poly_t >	get_fixed_mutations ()

vector< int >	get_number_of_mutations ()

int	L ()

int	get_number_of_loci ()

int	N ()

int	get_population_size ()

int	get_generation ()

void	set_generation (int g)

int	get_number_of_clones ()

int	get_number_of_traits ()

double	get_participation_ratio ()

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

int	set_genotypes (vector< genotype_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	track_locus_genealogy (vector< int > loci)
	Designates as set of loci to have their genealogy tracked. More...

void	add_genotype (boost::dynamic_bitset<> genotype, int n=1)
	Add the genotype specified by a bitset to the current population in in n copies. More...

int	add_trait_coefficient (double value, vector< int > loci, int t=0)

void	clear_trait (int t=0)

void	clear_traits ()

void	set_random_trait_epistasis (double epistasis_std, int traitnumber=0)

int	add_fitness_coefficient (double value, vector< int > loci)

void	clear_fitness ()

void	set_random_epistasis (double epistasis_std)

int	evolve (int gen=1)
	Evolve for some generations under the specified conditions. More...

int	bottleneck (int size_of_bottleneck)
	Cause a bottleneck in the population size. More...

unsigned int	flip_single_locus (int locus)
	Flip a spin at a specific locus in random individual. More...

void	calc_stat ()
	Calculate trait and fitness statistics and allele frequences. More...

void	unique_clones ()
	Remove duplicate clones. More...

vector< int >	get_nonempty_clones ()
	Obtain a list of the good clones. More...

int	random_clone ()
	Get a random clone from the population. More...

int	random_clones (unsigned int n_o_individuals, vector< int > *sample)
	Sample random individuals from the population. More...

string	get_genotype_string (unsigned int i)

int	distance_Hamming (unsigned int clone1, unsigned int clone2, vector< unsigned int * > *chunks=NULL, unsigned int every=1)

int	distance_Hamming (boost::dynamic_bitset<> gt1, boost::dynamic_bitset<> gt2, vector< unsigned int * > *chunks=NULL, unsigned int every=1)
	Calculate Hamming distance between two sequences. More...

stat_t	get_diversity_statistics (unsigned int n_sample=1000)
	Calculate diversity in the current population (Hamming distance between pairs of sequences) More...

stat_t	get_divergence_statistics (unsigned int n_sample=1000)
	Calculate mean and variance of the divergence from the [00...0] bitset. More...

double	get_allele_frequency (int l)

double	get_derived_allele_frequency (int l)

double	get_pair_frequency (int locus1, int locus2)
	Get the joint frequency of two alleles. More...

vector< double >	get_pair_frequencies (vector< vector< int > > *loci)
	Get the joint frequency of two alleles, for a vector of allele pairs. More...

double	get_chi (int l)

double	get_derived_chi (int l)

double	get_chi2 (int locus1, int locus2)

double	get_LD (int locus1, int locus2)

double	get_moment (int locus1, int locus2)

void	set_trait_weights (double *weights)

double	get_trait_weight (int t)

double	get_fitness (int n)

int	get_clone_size (int n)

double	get_trait (int n, int t=0)

vector< coeff_t >	get_trait_epistasis (int t=0)

stat_t	get_fitness_statistics ()

stat_t	get_trait_statistics (int t=0)

double	get_trait_covariance (int t1, int t2)

double	get_max_fitness ()

void	update_traits ()
	For each clone, recalculate its traits. More...

void	update_fitness ()
	For each clone, update fitness assuming traits are already up to date. More...

int	get_divergence_histogram (gsl_histogram *hist, unsigned int bins=10, vector< unsigned int > *chunks=NULL, unsigned int every=1, unsigned int n_sample=1000)
	Get histogram of divergence from the [00...0] bitset. More...

int	get_diversity_histogram (gsl_histogram *hist, unsigned int bins=10, vector< unsigned int > *chunks=NULL, unsigned int every=1, unsigned int n_sample=1000)
	Get histogram of diversity in the population (mutual Hamming distance) More...

int	get_fitness_histogram (gsl_histogram **hist, unsigned int bins=10, unsigned int n_sample=1000)
	Calculate histogram of fitness from traits. More...

int	print_allele_frequencies (ostream &out)
	Print all allele frequencies into a stream provided. More...

int	read_ms_sample (istream &gts, int skip_locus, int multiplicity)
	Read the output of Hudson's ms and use it to initialize the genotype distribution. More...

int	read_ms_sample_sparse (istream &gts, int skip_locus, int multiplicity, int distance)
	Read the output of Hudson's ms and use it to initialize the genotype distribution. More...

Public Attributes
hivgene	env

Public Attributes inherited from haploid_highd
hypercube_highd *	trait

vector< clone_t >	population

int	carrying_capacity

double	outcrossing_rate

double	crossover_rate

int	recombination_model

bool	circular

double	growth_rate

multi_locus_genealogy	genealogy

Protected Member Functions
virtual void	calc_individual_fitness_from_traits (clone_t *tempgt)
	Set the fitness from replication and resistance for a single clone. More...

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

void	produce_random_sample (int size=1000)
	Produce and store a random sample of the population for stochastic processes. More...

int	mutate ()
	Mutate random clones at random loci (all loci) More...

int	select_gametes ()
	Generate offspring according to fitness (selection) and segregate some for sexual mating. More...

double	relaxation_value ()
	Get the log of the exp-average fitness plus relaxation term. More...

double	get_logmean_expfitness ()
	Get the population exp-average of fitness, used for keeping the population size fixed. More...

unsigned int	flip_single_locus (unsigned int clonenum, int locus)
	Flip a spin (locus) in individual. More...

void	shuffle_genotypes ()

int	new_generation ()

int	partition_cumulative (vector< unsigned int > &partition_cum)
	Calculate the cumulative partition of sequences into clones. More...

int	provide_at_least (int n)
	: allocates memory for a sufficient number of clones More...

void	calc_allele_freqs ()
	calculate and store allele frequencies More...

void	reassortment_pattern ()
	Produce a random reassortement pattern. More...

void	crossover_pattern ()
	Choose a number of crossover points and produce a crossover pattern. More...

int	add_recombinants ()
	Pair and mate sexual gametes. More...

int	recombine (int parent1, int parent2)
	Recombine two genotypes parent1 and parent2 to produce two new genotypes. More...

int	recombine_crossover (int parent1, int parent2, int ng)

void	calc_fitness_stat ()
	Calculate and store fitness population statistics. More...

void	calc_trait_stat ()
	Calculate and store trait population statistics and covariances. More...

void	calc_individual_traits (clone_t &tempgt)
	Calculate traits of the chosen clone. More...

void	calc_individual_fitness (clone_t &tempgt)
	Calculate fitness of a particular clone. More...

void	calc_individual_traits (int clonenum)

void	calc_individual_fitness (int clonenum)

void	check_individual_maximal_fitness (clone_t &tempgt)

double	get_trait_difference (clone_t &tempgt1, clone_t &tempgt2, vector< int > &diffpos, int traitnum)
	Calculate trait difference between two clones. More...

virtual void	calc_individual_fitness_from_traits (clone_t &tempgt)
	Calculate fitness from traits of the chosen clone. More...

virtual void	calc_individual_fitness_from_traits (int clonenum)

void	add_clone_to_genealogy (int locus, int dest, int parent, int left, int right, int cs, int n)

Additional Inherited Members
Protected Attributes inherited from haploid_highd
gsl_rng *	evo_generator

gsl_rng *	label_generator

int	seed

vector< int >	random_sample

int	number_of_loci

int	population_size

int	number_of_traits

int	generation

int	number_of_clones

double	mutation_rate

double	participation_ratio

int	last_clone

bool	allele_frequencies_up_to_date

double *	allele_frequencies

double *	gamete_allele_frequencies

double *	chi1

double **	chi2

bool	all_polymorphic

vector< int >	ancestral_state

vector< poly_t >	polymorphism

vector< poly_t >	fixed_mutations

vector< int >	number_of_mutations

double	outcrossing_rate_effective

int *	genome

int *	crossovers

vector< int >	sex_gametes

double	fitness_max

stat_t	fitness_stat

stat_t *	trait_stat

double **	trait_covariance

double *	trait_weights

bool	track_genealogy

Detailed Description

HIV population with facultative drug treatment.

This class exemplifies the haploid_highd base class. It mainly adds one trait, "treatment", which is the same for all individuals and represents the presence or absence of drug treatment (in a continuous manner, \(0 \leq \) treatment \(\leq 1\)).

The replication capacity in absence of drug is encoded in the first trait. The drug resistance phenotype is represented by the second trait. Fitness is computed from traits as follows:

f[trait] = trait[0] + treatment * trait[1]

Moreover, this class fixes the length of the genome to exactly 10000 sites.

Constructor & Destructor Documentation

hivpopulation::hivpopulation	(	int	N_in = `0`,
		int	rng_seed = `0`,
		double	mutation_rate_in = `3e-5`,
		double	coinfection_rate_in = `1e-2`,
		double	crossover_rate_in = `1e-3`
	)

Construct a HIV population with certain parameters.

Parameters

N_in	number of viral particles
rng_seed	seed for the random number generator. If this is 0, time(NULL)+getpid() is used.
mutrate	mutation rate in events / generation / site
coinfection_rate	probability of coinfection of the same cell by two viral particles in events / generation
crossover_rate	probability of template switching during coinfection in events / site