- a -

• age : tree_key_t
• all_polymorphic : haploid_highd
• allele_frequencies : haploid_highd
• allele_frequencies_up_to_date : haploid_highd
• ancestral_state : haploid_highd

- b -

• bins : sample
• birth : poly_t

- c -

• carrying_capacity : haploid_highd , haploid_lowd
• chi1 : haploid_highd
• chi2 : haploid_highd
• child_edges : node_t
• circular : haploid_highd , haploid_lowd
• clone_size : clone_t , node_t
• coeff : hypercube_lowd
• coefficients_epistasis : hypercube_highd
• coefficients_single_locus : hypercube_highd
• crossover : node_t
• crossover_rate : haploid_highd
• crossovers : haploid_highd

- d -

• dim : hypercube_highd , hypercube_lowd
• distribution : sample

- e -

• edges : rooted_tree
• effect : poly_t
• end : hivgene
• env : hivpopulation
• epistatic_std : hypercube_highd
• evo_generator : haploid_highd

- f -

• fitness : clone_t , node_t , haploid_lowd , poly_t
• fitness_max : haploid_highd
• fitness_stat : haploid_highd
• fitness_variance : poly_t
• fixed_mutations : haploid_highd
• func : hypercube_lowd

- g -

• gamete_allele_frequencies : haploid_highd
• genealogy : haploid_highd
• generation : haploid_lowd , haploid_highd
• genome : haploid_highd
• genotype : clone_t , genotype_value_pair_t
• growth_rate : haploid_highd

- h -

• hypercube_mean : hypercube_highd

- i -

• index : index_value_pair_t , tree_key_t

- l -

• label_generator : haploid_highd
• last_clone : haploid_highd
• leafs : rooted_tree
• length : edge_t
• loci : coeff_t , multi_locus_genealogy
• locus : coeff_single_locus_t
• long_time_generation : haploid_lowd

- m -

• mean : stat_t , sample
• mem_dis : sample
• mem_values : sample
• MRCA : rooted_tree
• mutants : haploid_lowd
• mutation_rate : haploid_highd
• mutation_rates : haploid_lowd

- n -

• newGenerations : multi_locus_genealogy
• nodes : rooted_tree
• number_of_clones : haploid_highd
• number_of_loci : haploid_highd , haploid_lowd
• number_of_mutations : haploid_highd
• number_of_offspring : node_t , edge_t
• number_of_traits : haploid_highd
• number_of_values : sample

- o -

• order : coeff_t , hypercube_lowd
• outcrossing_rate : haploid_lowd , haploid_highd
• outcrossing_rate_effective : haploid_highd
• own_key : node_t , edge_t

- p -

• parent_node : node_t , edge_t
• participation_ratio : haploid_highd
• polymorphism : haploid_highd
• population : haploid_highd , haploid_lowd
• population_size : haploid_lowd , haploid_highd
• pos : step_t

- r -

• random_sample : haploid_highd
• range_max : sample
• range_min : sample
• recombinants : haploid_lowd
• recombination_model : haploid_highd , haploid_lowd
• recombination_patterns : haploid_lowd
• rng : haploid_lowd , hypercube_lowd
• rng_offset : hypercube_highd
• root : rooted_tree

- s -

• seed : haploid_highd , hypercube_lowd , haploid_lowd
• segment : edge_t
• sex_gametes : haploid_highd
• start : hivgene
• state : hypercube_lowd
• step : step_t
• sweep_time : poly_t

- t -

• track_genealogy : haploid_highd
• trait : clone_t , haploid_highd
• trait_covariance : haploid_highd
• trait_stat : haploid_highd
• trait_weights : haploid_highd
• trees : multi_locus_genealogy

- v -

• val : index_value_pair_t , genotype_value_pair_t
• value : coeff_single_locus_t , coeff_t
• values : sample
• variance : stat_t , sample

- w -

• weight_distribution : node_t
• with_range : sample