hivpopulation Member List

This is the complete list of members for hivpopulation, including all inherited members.

add_clone_to_genealogy(int locus, int dest, int parent, int left, int right, int cs, int n)	haploid_highd	protected
add_fitness_coefficient(double value, vector< int > loci)	haploid_highd	inline
add_genotype(boost::dynamic_bitset<> genotype, int n=1)	haploid_highd
add_recombinants()	haploid_highd	protected
add_trait_coefficient(double value, vector< int > loci, int t=0)	haploid_highd	inline
all_polymorphic	haploid_highd	protected
allele_frequencies	haploid_highd	protected
allele_frequencies_up_to_date	haploid_highd	protected
ancestral_state	haploid_highd	protected
bottleneck(int size_of_bottleneck)	haploid_highd
calc_allele_freqs()	haploid_highd	protected
calc_fitness_stat()	haploid_highd	protected
calc_individual_fitness(clone_t &tempgt)	haploid_highd	protected
calc_individual_fitness(int clonenum)	haploid_highd	inlineprotected
calc_individual_fitness_from_traits(clone_t *tempgt)	hivpopulation	protectedvirtual
haploid_highd::calc_individual_fitness_from_traits(clone_t &tempgt)	haploid_highd	protectedvirtual
haploid_highd::calc_individual_fitness_from_traits(int clonenum)	haploid_highd	inlineprotectedvirtual
calc_individual_traits(clone_t &tempgt)	haploid_highd	protected
calc_individual_traits(int clonenum)	haploid_highd	inlineprotected
calc_stat()	haploid_highd
calc_trait_stat()	haploid_highd	protected
carrying_capacity	haploid_highd
check_individual_maximal_fitness(clone_t &tempgt)	haploid_highd	inlineprotected
chi1	haploid_highd	protected
chi2	haploid_highd	protected
circular	haploid_highd
clear_fitness()	haploid_highd	inline
clear_trait(int t=0)	haploid_highd	inline
clear_traits()	haploid_highd	inline
crossover_pattern()	haploid_highd	protected
crossover_rate	haploid_highd
crossovers	haploid_highd	protected
distance_Hamming(unsigned int clone1, unsigned int clone2, vector< unsigned int * > *chunks=NULL, unsigned int every=1)	haploid_highd	inline
distance_Hamming(boost::dynamic_bitset<> gt1, boost::dynamic_bitset<> gt2, vector< unsigned int * > *chunks=NULL, unsigned int every=1)	haploid_highd
env	hivpopulation
evo_generator	haploid_highd	protected
evolve(int gen=1)	haploid_highd
fitness_max	haploid_highd	protected
fitness_stat	haploid_highd	protected
fixed_mutations	haploid_highd	protected
flip_single_locus(int locus)	haploid_highd
flip_single_locus(unsigned int clonenum, int locus)	haploid_highd	protected
gamete_allele_frequencies	haploid_highd	protected
genealogy	haploid_highd
generation	haploid_highd	protected
genome	haploid_highd	protected
get_allele_frequency(int l)	haploid_highd	inline
get_chi(int l)	haploid_highd	inline
get_chi2(int locus1, int locus2)	haploid_highd	inline
get_clone_size(int n)	haploid_highd	inline
get_derived_allele_frequency(int l)	haploid_highd	inline
get_derived_chi(int l)	haploid_highd	inline
get_divergence_histogram(gsl_histogram **hist, unsigned int bins=10, vector< unsigned int * > *chunks=NULL, unsigned int every=1, unsigned int n_sample=1000)	haploid_highd
get_divergence_statistics(unsigned int n_sample=1000)	haploid_highd
get_diversity_histogram(gsl_histogram **hist, unsigned int bins=10, vector< unsigned int * > *chunks=NULL, unsigned int every=1, unsigned int n_sample=1000)	haploid_highd
get_diversity_statistics(unsigned int n_sample=1000)	haploid_highd
get_fitness(int n)	haploid_highd	inline
get_fitness_histogram(gsl_histogram **hist, unsigned int bins=10, unsigned int n_sample=1000)	haploid_highd
get_fitness_statistics()	haploid_highd	inline
get_fixed_mutations()	haploid_highd	inline
get_generation()	haploid_highd	inline
get_genotype_string(unsigned int i)	haploid_highd	inline
get_LD(int locus1, int locus2)	haploid_highd	inline
get_logmean_expfitness()	haploid_highd	protected
get_max_fitness()	haploid_highd	inline
get_moment(int locus1, int locus2)	haploid_highd	inline
get_mutation_rate()	haploid_highd	inline
get_nonempty_clones()	haploid_highd
get_number_of_clones()	haploid_highd	inline
get_number_of_loci()	haploid_highd	inline
get_number_of_mutations()	haploid_highd	inline
get_number_of_traits()	haploid_highd	inline
get_pair_frequencies(vector< vector< int > > *loci)	haploid_highd
get_pair_frequency(int locus1, int locus2)	haploid_highd
get_participation_ratio()	haploid_highd	inline
get_polymorphisms()	haploid_highd	inline
get_population_size()	haploid_highd	inline
get_random_seed()	haploid_highd	protected
get_trait(int n, int t=0)	haploid_highd	inline
get_trait_covariance(int t1, int t2)	haploid_highd	inline
get_trait_difference(clone_t &tempgt1, clone_t &tempgt2, vector< int > &diffpos, int traitnum)	haploid_highd	protected
get_trait_epistasis(int t=0)	haploid_highd	inline
get_trait_statistics(int t=0)	haploid_highd	inline
get_trait_weight(int t)	haploid_highd	inline
get_treatment()	hivpopulation	inline
growth_rate	haploid_highd
haploid_highd(int L=0, int rng_seed=0, int number_of_traits=1, bool all_polymorphic=false)	haploid_highd
hivpopulation(int N=0, int rng_seed=0, double mutation_rate=3e-5, double coinfection_rate=1e-2, double crossover_rate=1e-3)	hivpopulation
is_all_polymorphic()	haploid_highd	inline
L()	haploid_highd	inline
label_generator	haploid_highd	protected
last_clone	haploid_highd	protected
mutate()	haploid_highd	protected
mutation_rate	haploid_highd	protected
N()	haploid_highd	inline
new_generation()	haploid_highd	protected
number_of_clones	haploid_highd	protected
number_of_loci	haploid_highd	protected
number_of_mutations	haploid_highd	protected
number_of_traits	haploid_highd	protected
outcrossing_rate	haploid_highd
outcrossing_rate_effective	haploid_highd	protected
participation_ratio	haploid_highd	protected
partition_cumulative(vector< unsigned int > &partition_cum)	haploid_highd	protected
polymorphism	haploid_highd	protected
population	haploid_highd
population_size	haploid_highd	protected
print_allele_frequencies(ostream &out)	haploid_highd
produce_random_sample(int size=1000)	haploid_highd	protected
provide_at_least(int n)	haploid_highd	protected
random_clone()	haploid_highd
random_clones(unsigned int n_o_individuals, vector< int > *sample)	haploid_highd
random_sample	haploid_highd	protected
read_ms_sample(istream &gts, int skip_locus, int multiplicity)	haploid_highd
read_ms_sample_sparse(istream &gts, int skip_locus, int multiplicity, int distance)	haploid_highd
read_replication_coefficients(istream &model)	hivpopulation
read_resistance_coefficients(istream &model)	hivpopulation
reassortment_pattern()	haploid_highd	protected
recombination_model	haploid_highd
recombine(int parent1, int parent2)	haploid_highd	protected
recombine_crossover(int parent1, int parent2, int ng)	haploid_highd	protected
relaxation_value()	haploid_highd	protected
select_gametes()	haploid_highd	protected
set_allele_frequencies(double *frequencies, unsigned long N)	haploid_highd
set_generation(int g)	haploid_highd	inline
set_genotypes(vector< genotype_value_pair_t > gt)	haploid_highd
set_mutation_rate(double m)	haploid_highd	inline
set_random_epistasis(double epistasis_std)	haploid_highd	inline
set_random_trait_epistasis(double epistasis_std, int traitnumber=0)	haploid_highd	inline
set_trait_weights(double *weights)	haploid_highd	inline
set_treatment(double t)	hivpopulation	inline
set_wildtype(unsigned long N)	haploid_highd
sex_gametes	haploid_highd	protected
shuffle_genotypes()	haploid_highd	protected
track_genealogy	haploid_highd	protected
track_locus_genealogy(vector< int > loci)	haploid_highd
trait	haploid_highd
trait_covariance	haploid_highd	protected
trait_stat	haploid_highd	protected
trait_weights	haploid_highd	protected
unique_clones()	haploid_highd
update_fitness()	haploid_highd
update_traits()	haploid_highd
write_genotypes(ostream &out_genotypes, int sample_size, string gt_label="", int start=0, int length=0)	hivpopulation
~haploid_highd()	haploid_highd	virtual
~hivpopulation()	hivpopulation	virtual