Index

_ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W

_

__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]