Index

_

__init__() (haploid_highd method) (haploid_lowd method) (hivpopulation method) (multi_locus_genealogy method) (tree_key method) (tree_step method) __repr__() (haploid_highd method) (haploid_lowd method) (hivpopulation method) (multi_locus_genealogy method) (polymorphism method) (rooted_tree method) (tree_edge method) (tree_key method) (tree_node method) (tree_step method)

__str__() (haploid_highd method) (haploid_lowd method) (hivpopulation method) (multi_locus_genealogy method) (polymorphism method) (rooted_tree method) (tree_edge method) (tree_key method) (tree_node method) (tree_step method)

A

add_fitness_coefficient() (haploid_highd method) add_genotype() (haploid_highd method) add_trait_coefficient() (haploid_highd method)

age (tree_key attribute) allele_entropy() (haploid_lowd method) ancestors_at_age() (rooted_tree method)

B

binarify() (in module FFPopSim) birth (polymorphism attribute)

bottleneck() (haploid_highd method)

C

calc_stat() (haploid_highd method) calc_weight_distribution() (rooted_tree method) carrying_capacity (haploid_highd attribute) (haploid_lowd attribute) child_edges (tree_node attribute) circular (haploid_highd attribute) (haploid_lowd attribute) clear_fitness() (haploid_highd method) clear_trait() (haploid_highd method)

clear_traits() (haploid_highd method) clone (class in FFPopSim) clone_size (clone attribute) (tree_node attribute) copy() (haploid_highd method) (haploid_lowd method) (hivpopulation method) create_subtree_from_keys() (rooted_tree method) crossover (tree_node attribute) crossover_rate (haploid_highd attribute)

D

distance_Hamming() (haploid_highd method)

dump() (haploid_highd method)

E

edges (rooted_tree attribute) effect (polymorphism attribute) end (hivgene attribute) env (hivpopulation attribute)

evolve() (haploid_highd method) (haploid_lowd method) evolve_deterministic() (haploid_lowd method) evolve_norec() (haploid_lowd method) external_branch_length() (rooted_tree method)

F

FFPopSim (module) fitness (clone attribute) (polymorphism attribute) (tree_node attribute)

fitness_variance (polymorphism attribute) flip_single_locus() (haploid_highd method)

G

genealogy (haploid_highd attribute) generation (haploid_highd attribute) (haploid_lowd attribute) genotype (clone attribute) (genotype_value_pair attribute) genotype_entropy() (haploid_lowd method) genotype_value_pair (class in FFPopSim) get_allele_frequencies() (haploid_highd method) (haploid_lowd method) get_allele_frequency() (haploid_highd method) (haploid_lowd method) get_chi() (haploid_highd method) (haploid_lowd method) get_chi2() (haploid_highd method) (haploid_lowd method) get_clone() (haploid_highd method) get_clone_size() (haploid_highd method) get_clone_sizes() (haploid_highd method) get_divergence_histogram() (haploid_highd method) (haploid_lowd method) get_divergence_statistics() (haploid_highd method) (haploid_lowd method) get_diversity_histogram() (haploid_highd method) (haploid_lowd method) get_diversity_statistics() (haploid_highd method) (haploid_lowd method) get_fitness() (haploid_highd method) (haploid_lowd method) get_fitness_histogram() (haploid_highd method) (haploid_lowd method) get_fitness_statistics() (haploid_highd method)

get_fitnesses() (haploid_highd method) (haploid_lowd method) get_genotype() (haploid_highd method) get_genotype_frequencies() (haploid_lowd method) get_genotype_frequency() (haploid_lowd method) get_genotypes() (haploid_highd method) get_LD() (haploid_highd method) (haploid_lowd method) get_moment() (haploid_highd method) (haploid_lowd method) get_mutation_rates() (haploid_lowd method) get_pair_frequency() (haploid_highd method) (haploid_lowd method) get_recombination_rates() (haploid_lowd method) get_replication_additive() (hivpopulation method), [1] get_resistance_additive() (hivpopulation method), [1] get_trait() (haploid_highd method) get_trait_additive() (haploid_highd method) get_trait_covariance() (haploid_highd method) get_trait_epistasis() (haploid_highd method) get_trait_statistics() (haploid_highd method) get_traits() (haploid_highd method) get_tree() (multi_locus_genealogy method)

H

haploid_highd (class in FFPopSim) haploid_lowd (class in FFPopSim)

hivgene (class in FFPopSim) hivpopulation (class in FFPopSim)

I

index (index_value_pair attribute) (tree_key attribute) index_value_pair (class in FFPopSim)

integerify() (in module FFPopSim)

L

L (haploid_highd attribute) (haploid_lowd attribute) leafs (rooted_tree attribute) length (tree_edge attribute)

load_haploid_highd() (in module FFPopSim) loci (multi_locus_genealogy attribute)

M

max_fitness (haploid_highd attribute) mean (stat attribute)

multi_locus_genealogy (class in FFPopSim) mutation_rate (haploid_highd attribute)

N

N (haploid_highd attribute) (haploid_lowd attribute) nodes (rooted_tree attribute) number_of_clones (haploid_highd attribute)

number_of_loci (haploid_highd attribute) (haploid_lowd attribute) number_of_offspring (tree_edge attribute) number_of_traits (clone attribute) (haploid_highd attribute)

O

outcrossing_rate (haploid_highd attribute) (haploid_lowd attribute)

own_key (tree_edge attribute) (tree_node attribute)

P

parent_node (tree_edge attribute) (tree_node attribute) participation_ratio (haploid_highd attribute) plot_divergence_histogram() (haploid_highd method) (haploid_lowd method) plot_diversity_histogram() (haploid_highd method) (haploid_lowd method) plot_fitness_histogram() (haploid_highd method) (haploid_lowd method)

polymorphism (class in FFPopSim) population_size (haploid_highd attribute) (haploid_lowd attribute) pos (tree_step attribute) print_newick() (rooted_tree method)

R

random_clone() (haploid_highd method) random_clones() (haploid_highd method) random_genomes() (haploid_highd method) (haploid_lowd method) read_replication_coefficients() (hivpopulation method), [1] read_resistance_coefficients() (hivpopulation method), [1]

recombination_model (haploid_highd attribute) (haploid_lowd attribute) reset() (multi_locus_genealogy method) reset_but_loci() (multi_locus_genealogy method) rooted_tree (class in FFPopSim)

S

segment (tree_edge attribute) set_allele_frequencies() (haploid_highd method) (haploid_lowd method) set_fitness_additive() (haploid_highd method) (haploid_lowd method) set_fitness_coefficients() (haploid_lowd method) set_fitness_function() (haploid_lowd method) set_genotypes() (haploid_highd method) (haploid_lowd method) set_mutation_rates() (haploid_lowd method) set_random_epistasis() (haploid_highd method) set_random_trait_epistasis() (haploid_highd method) set_recombination_rates() (haploid_lowd method) set_replication_additive() (hivpopulation method), [1] set_replication_landscape() (hivpopulation method), [1]

set_resistance_additive() (hivpopulation method), [1] set_resistance_landscape() (hivpopulation method), [1] set_trait_additive() (haploid_highd method) set_trait_landscape() (hivpopulation method), [1] set_wildtype() (haploid_highd method) (haploid_lowd method) start (hivgene attribute) stat (class in FFPopSim) status() (haploid_highd method) (haploid_lowd method) step (tree_step attribute) subtree_newick() (rooted_tree method) sweep_time (polymorphism attribute)

T

thisown (hivpopulation attribute) to_Biopython_tree() (rooted_tree method) total_branch_length() (rooted_tree method) track_locus() (multi_locus_genealogy method) track_locus_genealogy() (haploid_highd method) trait (clone attribute)

trait_weights (haploid_highd attribute) treatment (hivpopulation attribute), [1] tree_edge (class in FFPopSim) tree_key (class in FFPopSim) tree_node (class in FFPopSim) tree_step (class in FFPopSim)

U

unique_clones() (haploid_highd method)

V

val (genotype_value_pair attribute) (index_value_pair attribute)

variance (stat attribute)

W

weight_distribution (tree_node attribute) write_genotypes() (hivpopulation method), [1]

write_genotypes_compressed() (hivpopulation method), [1]