Index

_

__init__() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.classes.host method), [1] (transmission_models.classes.host.host method), [1] (transmission_models.classes.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.same_location_prior_tree method), [1] (transmission_models.classes.MCMC method), [1] (transmission_models.classes.mcmc.mcmc.MCMC method), [1] (transmission_models.classes.same_location_prior_tree method), [1] (transmission_models.didelot_unsampled method) (transmission_models.genetic_prior_tree method) (transmission_models.host method) (transmission_models.location_distance_prior_tree method) (transmission_models.MCMC method) (transmission_models.same_location_prior_tree method)

__int__() (transmission_models.classes.host method), [1] (transmission_models.classes.host.host method), [1] (transmission_models.host method) __str__() (transmission_models.classes.host method), [1] (transmission_models.classes.host.host method), [1] (transmission_models.host method)

A

add_genetic_prior() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) add_remove_step() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) add_root() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

add_same_location_prior() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) add_unsampled_with_times() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) average_mutations() (in module transmission_models.classes.host), [1]

B

binom_mutation() (in module transmission_models.classes.host), [1]

build_infection_based_network() (in module transmission_models.utils), [1], [2], [3]

C

cast_types() (in module transmission_models.utils), [1], [2], [3] check_attribute_sampling() (in module transmission_models.classes.partial_sampled_utils), [1] choose_successors() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) compute_Delta_loc_prior() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

create_genome() (in module transmission_models.classes.host), [1] create_transmision_phylogeny_nets() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

D

Delta_log_gamma() (in module transmission_models.utils), [1], [2], [3] Delta_log_infection() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) Delta_log_likelihood_host() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) Delta_log_offspring() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

Delta_log_prior() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.genetic_prior_tree method) Delta_log_sampling() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) didelot_unsampled (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.didelot_unsampled), [1]

G

genetic_prior_tree (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.genetic_prior), [1] get_candidates_to_chain() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_closest_sampling_siblings() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.classes.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.same_location_prior_tree method), [1] (transmission_models.classes.same_location_prior_tree method), [1] (transmission_models.genetic_prior_tree method) (transmission_models.location_distance_prior_tree method) (transmission_models.same_location_prior_tree method) get_genetic_str() (transmission_models.classes.host method), [1] (transmission_models.classes.host.host method), [1] (transmission_models.host method) get_host_from_dict() (in module transmission_models.utils), [1], [2], [3] get_infection_model_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_infection_model_log_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_log_likelihood_transmission() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_log_posterior_transmission_tree() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1] (transmission_models.didelot_unsampled method) get_mut_time_dist() (transmission_models.classes.genetic_prior.genetic_prior_tree static method), [1] (transmission_models.classes.genetic_prior_tree static method), [1] (transmission_models.classes.location_distance_prior_tree static method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree static method), [1] (transmission_models.classes.location_prior.same_location_prior_tree static method), [1] (transmission_models.classes.same_location_prior_tree static method), [1] (transmission_models.genetic_prior_tree static method) (transmission_models.location_distance_prior_tree static method) (transmission_models.same_location_prior_tree static method)

get_N_candidates_to_chain() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_newick() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_offspring_model_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_offspring_model_log_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_root_subtrees() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_roots_data_subtrees() (in module transmission_models.classes.genetic_prior), [1] (transmission_models.classes.location_prior.same_location_prior_tree static method), [1] (transmission_models.classes.same_location_prior_tree static method), [1] (transmission_models.same_location_prior_tree static method) get_sampling_model_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_sampling_model_log_likelihood() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) get_unsampled_hosts() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

H

hierarchy_pos() (in module transmission_models.utils), [1], [2], [3] hierarchy_pos_times() (in module transmission_models.utils), [1], [2], [3]

host (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.host), [1]

I

infection_time_from_infection_model_step() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

infection_time_from_sampling_step() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

J

json_to_tree() (in module transmission_models.utils), [1], [2], [3] (transmission_models.classes.didelot_unsampled class method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled class method), [1] (transmission_models.didelot_unsampled class method)

L

location_distance_prior_tree (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.location_prior), [1] log_likelihood_host() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) log_likelihood_hosts_list() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) log_likelihood_transmission_tree() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) log_likelihood_transmission_tree_old() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1] (transmission_models.didelot_unsampled method) log_posterior_transmission_tree() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1] (transmission_models.didelot_unsampled method)

log_prior_host() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.genetic_prior_tree method) log_prior_host_list() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.genetic_prior_tree method) log_prior_T() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.classes.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.same_location_prior_tree method), [1] (transmission_models.classes.same_location_prior_tree method), [1] (transmission_models.genetic_prior_tree method) (transmission_models.location_distance_prior_tree method) (transmission_models.same_location_prior_tree method)

M

MCMC (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.mcmc.mcmc), [1] MCMC_iteration() (transmission_models.classes.MCMC method), [1] (transmission_models.classes.mcmc.mcmc.MCMC method), [1] (transmission_models.MCMC method) MCMC_step() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) module transmission_models transmission_models.classes, [1] transmission_models.classes.genetic_prior, [1] transmission_models.classes.host, [1] transmission_models.classes.location_prior, [1] transmission_models.classes.mcmc, [1] transmission_models.classes.mcmc.mcmc, [1] transmission_models.classes.partial_sampled_utils, [1] transmission_models.utils, [1], [2], [3] transmission_models.utils.topology_movements, [1]

O

one_mutation() (in module transmission_models.classes.host), [1] out_degree() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

P

parent() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) pdf_in_between() (in module transmission_models.utils), [1], [2], [3] plot_transmision_network() (in module transmission_models.utils), [1], [2], [3] prior_host() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.classes.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree method), [1] (transmission_models.classes.location_prior.same_location_prior_tree method), [1] (transmission_models.classes.same_location_prior_tree method), [1] (transmission_models.genetic_prior_tree method) (transmission_models.location_distance_prior_tree method) (transmission_models.same_location_prior_tree method)

prior_pair() (transmission_models.classes.genetic_prior.genetic_prior_tree method), [1] (transmission_models.classes.genetic_prior_tree method), [1] (transmission_models.genetic_prior_tree method)

R

random() (in module transmission_models.classes.mcmc), [1] (in module transmission_models.utils), [1], [2], [3] random_combination() (in module transmission_models.utils), [1], [2], [3]

read_tree_dict() (in module transmission_models.utils), [1], [2], [3] remove_unsampled_with_times() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

S

same_location_prior_tree (class in transmission_models) (class in transmission_models.classes), [1] (class in transmission_models.classes.location_prior), [1] samp_t_inf_between() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1] (transmission_models.didelot_unsampled method) sample_in_between() (in module transmission_models.utils), [1], [2], [3] save_json() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) search_first_sampled_parent() (in module transmission_models.classes.location_prior), [1] (in module transmission_models.utils), [1], [2], [3] (transmission_models.classes.genetic_prior.genetic_prior_tree static method), [1] (transmission_models.classes.genetic_prior_tree static method), [1] (transmission_models.genetic_prior_tree static method) search_first_sampleed_parent() (transmission_models.classes.location_distance_prior_tree static method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree static method), [1] (transmission_models.location_distance_prior_tree static method) search_firsts_sampled_siblings() (in module transmission_models.utils), [1], [2], [3] (transmission_models.classes.genetic_prior.genetic_prior_tree static method), [1] (transmission_models.classes.genetic_prior_tree static method), [1] (transmission_models.classes.location_distance_prior_tree static method), [1] (transmission_models.classes.location_prior.location_distance_prior_tree static method), [1] (transmission_models.classes.location_prior.same_location_prior_tree static method), [1] (transmission_models.classes.same_location_prior_tree static method), [1] (transmission_models.genetic_prior_tree static method) (transmission_models.location_distance_prior_tree static method) (transmission_models.same_location_prior_tree static method)

search_partial_sampled_parent() (in module transmission_models.classes.partial_sampled_utils), [1] search_partial_sampled_siblings() (in module transmission_models.classes.partial_sampled_utils), [1] set_T() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1] (transmission_models.didelot_unsampled method) show_log_likelihoods() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method) successors() (transmission_models.classes.didelot_unsampled method), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled method), [1], [2], [3] (transmission_models.didelot_unsampled method)

T

T (transmission_models.classes.didelot_unsampled property), [1] (transmission_models.classes.didelot_unsampled.didelot_unsampled property), [1] (transmission_models.didelot_unsampled property) t_inf (transmission_models.classes.host property), [1] (transmission_models.classes.host.host property), [1] (transmission_models.host property) transmission_models module transmission_models.classes module, [1] transmission_models.classes.genetic_prior module, [1] transmission_models.classes.host module, [1] transmission_models.classes.location_prior module, [1]

transmission_models.classes.mcmc module, [1] transmission_models.classes.mcmc.mcmc module, [1] transmission_models.classes.partial_sampled_utils module, [1] transmission_models.utils module, [1], [2], [3] transmission_models.utils.topology_movements module, [1] tree_slicing_step() (in module transmission_models.utils.topology_movements), [1] tree_slicing_to_chain() (in module transmission_models.utils.topology_movements), [1] tree_slicing_to_offspring() (in module transmission_models.utils.topology_movements), [1] tree_to_dict() (in module transmission_models.utils), [1], [2], [3] tree_to_json() (in module transmission_models.utils), [1], [2], [3] tree_to_newick() (in module transmission_models.utils), [1], [2], [3]