Index

A

abnormal (BasePeople property) add_births() (People method) add_contacts() (BasePeople method) add_layer() (Contacts method) add_to_queue() (treat_num method) add_to_schedule() (treat_delay method) addtoself() (BasePeople method) administer() (dx method) (radiation method) (tx method) (vx method) age_causal_infection (class in hpvsim.analysis) age_pyramid (class in hpvsim.analysis) age_results (class in hpvsim.analysis) alive_inds (BasePeople property) alive_level0 (BasePeople property) alive_level0_inds (BasePeople property) AlreadyRunError Analyzer (class in hpvsim.analysis) append() (Layer method)

apply() (age_causal_infection method) (age_pyramid method) (age_results method) (Analyzer method) (BaseScreening method) (BaseTreatment method) (BaseTriage method) (BaseVaccination method) (campaign_txvx method) (cancer_detection method) (daly_computation method) (dynamic_pars method) (EventSchedule method) (Intervention method) (linked_txvx method) (routine_txvx method) (snapshot method) (treat_delay method) (treat_num method) apply_death_rates() (People method)

B

BasePeople (class in hpvsim.base) BaseScreening (class in hpvsim.interventions) BaseSim (class in hpvsim.base) BaseTest (class in hpvsim.interventions) BaseTreatment (class in hpvsim.interventions) BaseTriage (class in hpvsim.interventions)

BaseTxVx (class in hpvsim.interventions) BaseVaccination (class in hpvsim.interventions) binomial_arr() (in module hpvsim.utils) binomial_filter() (in module hpvsim.utils) brief() (MultiSim method) (Scenarios method)

C

calibrate() (Calibration method) Calibration (class in hpvsim.calibration) campaign_screening (class in hpvsim.interventions) campaign_triage (class in hpvsim.interventions) campaign_txvx (class in hpvsim.interventions) campaign_vx (class in hpvsim.interventions) CampaignDelivery (class in hpvsim.interventions) cancer_detection (class in hpvsim.analysis) check_cancer() (People method) check_cancer_deaths() (People method) check_cin() (People method) check_clearance() (People method) check_downloaded() (in module hpvsim.data.downloaders) check_eligibility() (BaseScreening method) (BaseTest method) (BaseTreatment method) (BaseTriage method) (BaseVaccination method) check_hiv_death() (HIVsim method) check_immunity() (in module hpvsim.immunity) check_inds() (People method) check_inds_true() (People method) check_migration() (People method) check_progress() (People method) check_save_version() (in module hpvsim.misc)

check_version() (in module hpvsim.misc) choose() (in module hpvsim.utils) choose_r() (in module hpvsim.utils) choose_w() (in module hpvsim.utils) combine() (MultiSim method) (Sweep method) compare() (MultiSim method) (Scenarios method) (Sweep method) compute_age_mean() (Sim method) compute_fit() (Sim method) compute_gof() (in module hpvsim.misc) compute_mismatch() (age_results method) compute_results() (Sim method) compute_states() (Sim method) compute_summary() (Sim method) Contacts (class in hpvsim.base) convert_rname_flows() (age_results method) convert_rname_stocks() (age_results method) copy() (BaseSim method) count() (BasePeople method) count_any() (BasePeople method) count_by_genotype() (BasePeople method) create_partnerships() (People method) create_sims() (Sweep method)

D

daly_computation (class in hpvsim.analysis) date() (in module hpvsim.misc) date_keys() (BasePeople method) date_range() (in module hpvsim.misc) day() (in module hpvsim.misc) daydiff() (in module hpvsim.misc) default_dx() (in module hpvsim.interventions) default_float (in module hpvsim.defaults) default_int (in module hpvsim.defaults) default_tx() (in module hpvsim.interventions) default_value (dx property) default_vx() (in module hpvsim.interventions) defined() (BasePeople method) (in module hpvsim.utils)

deliver() (BaseTest method) (BaseTxVx method) diff_sims() (in module hpvsim.sim) disp() (Intervention method) (MultiSim method) (Scenarios method) dissolve_partnerships() (People method) dt_age (BasePeople property) dtround() (in module hpvsim.utils) dur_keys() (BasePeople method) dx (class in hpvsim.interventions) dynamic_pars (class in hpvsim.interventions)

E

EventSchedule (class in hpvsim.interventions) exp_decay() (in module hpvsim.immunity)

export_pars() (BaseSim method) export_results() (BaseSim method)

F

f_inds (BasePeople property) false() (BasePeople method) (in module hpvsim.utils) false_by_genotype() (BasePeople method) filter() (BasePeople method) filter_inds() (BasePeople method) finalize() (age_causal_infection method) (age_pyramid method) (age_results method) (Analyzer method) (daly_computation method) (HIVsim method) (Intervention method) (Sim method) (snapshot method)

finalize_analyzers() (Sim method) find_contacts() (Layer method) find_cutoff() (in module hpvsim.utils) FlexDict (class in hpvsim.base) from_df() (Layer method) from_list() (BasePeople method)

G

get() (BasePeople method) (snapshot method) get_accept_inds() (BaseTreatment method) get_age_distribution() (in module hpvsim.data.loaders) get_age_distribution_over_time() (in module hpvsim.data.loaders) get_analyzer() (BaseSim method) get_analyzers() (BaseSim method) get_birth_rates() (in module hpvsim.data.loaders) get_candidates() (BaseTreatment method) (treat_delay method) (treat_num method) get_country_aliases() (in module hpvsim.data.loaders) get_data() (in module hpvsim.data.downloaders) get_death_rates() (in module hpvsim.data.loaders) get_default_plots() (in module hpvsim.defaults)

get_doubling_time() (in module hpvsim.misc) get_full_pars() (Calibration method) get_hiv_data() (HIVsim method) get_inds() (Layer method) get_intervention() (BaseSim method) get_interventions() (BaseSim method) get_life_expectancy() (in module hpvsim.data.loaders) get_pdf() (in module hpvsim.utils) get_people_in_state() (tx method) get_png_metadata() (in module hpvsim.misc) get_t() (BaseSim method) get_to_plot() (age_results method) get_total_pop() (in module hpvsim.data.loaders) get_version_pars() (in module hpvsim.misc) git_info() (in module hpvsim.misc)

H

help() (in module hpvsim.misc) HIVsim (class in hpvsim.hiv) hpvsim module hpvsim.analysis module hpvsim.base module hpvsim.calibration module hpvsim.data module hpvsim.data.downloaders module hpvsim.data.loaders module hpvsim.defaults module hpvsim.hiv module hpvsim.immunity module

hpvsim.interventions module hpvsim.misc module hpvsim.parameters module hpvsim.people module hpvsim.plotting module hpvsim.population module hpvsim.run module hpvsim.settings module hpvsim.sim module hpvsim.utils module hpvsim.version module

I

idefined() (in module hpvsim.utils) idefinedi() (in module hpvsim.utils) ifalse() (in module hpvsim.utils) ifalsei() (in module hpvsim.utils) imm_keys() (BasePeople method) increment_age() (People method) indices() (BasePeople method) infect() (People method) infected (BasePeople property) init_analyzers() (Sim method) init_contacts() (BasePeople method) init_flows() (People method) init_genotypes() (Sim method) init_hiv() (Sim method) init_immunity() (in module hpvsim.immunity) (Sim method) init_interventions() (Sim method) init_people() (Sim method) init_results() (HIVsim method) (Sim method) init_sims() (MultiSim method) init_states() (HIVsim static method) (Sim method) init_time_vecs() (Sim method) initialize() (age_causal_infection method) (age_pyramid method) (age_results method) (Analyzer method) (BasePeople method) (BaseTest method) (BaseTreatment method) (BaseVaccination method) (campaign_screening method) (campaign_triage method) (campaign_txvx method) (campaign_vx method) (CampaignDelivery method) (cancer_detection method) (daly_computation method) (dynamic_pars method) (EventSchedule method) (Intervention method) (People method) (routine_screening method) (routine_triage method) (routine_txvx method) (routine_vx method) (RoutineDelivery method) (Sim method) (snapshot method)

int_age (BasePeople property) Intervention (class in hpvsim.interventions) intv_keys() (BasePeople method) is_active (BasePeople property) is_female (BasePeople property) is_female_adult (BasePeople property) is_female_alive (BasePeople property) is_male (BasePeople property) is_male_alive (BasePeople property) is_virgin (BasePeople property) items() (FlexDict method) itrue() (in module hpvsim.utils) itruei() (in module hpvsim.utils) iundefined() (in module hpvsim.utils) iundefinedi() (in module hpvsim.utils)

K

keys() (BasePeople method) (FlexDict method)

L

latent (BasePeople property) Layer (class in hpvsim.base) layer_keys() (BasePeople method) (Sim method) linear_decay() (in module hpvsim.immunity) linear_growth() (in module hpvsim.immunity) linked_txvx (class in hpvsim.interventions) load() (BasePeople static method) (BaseSim static method) (in module hpvsim.misc) (MultiSim static method) (Scenarios static method)

load_data() (HIVsim method) (in module hpvsim.misc) (Sim method) lock() (BasePeople method)

M

m_inds (BasePeople property) make_contacts() (in module hpvsim.population) make_edgelist() (BasePeople method) make_metapars() (in module hpvsim.run) make_naive() (People method) make_pars() (in module hpvsim.parameters) make_people() (in module hpvsim.population) make_study() (Calibration method) map_entries() (in module hpvsim.data.loaders) mean() (MultiSim method) (Result method) (Sweep method) median() (MultiSim method) (Result method) (Sweep method) members (Layer property) merge() (MultiSim static method) (Scenarios static method) meta_keys() (Layer method) module hpvsim hpvsim.analysis hpvsim.base hpvsim.calibration hpvsim.data hpvsim.data.downloaders hpvsim.data.loaders hpvsim.defaults hpvsim.hiv hpvsim.immunity hpvsim.interventions hpvsim.misc hpvsim.parameters hpvsim.people hpvsim.plotting hpvsim.population hpvsim.run hpvsim.settings hpvsim.sim hpvsim.utils hpvsim.version

multi_run() (in module hpvsim.run) MultiSim (class in hpvsim.run)

N

n (BaseSim property) n_alive (BasePeople property) n_alive_level0 (BasePeople property) n_binomial() (in module hpvsim.utils)

n_multinomial() (in module hpvsim.utils) n_neg_binomial() (in module hpvsim.utils) n_poisson() (in module hpvsim.utils) new_hiv_infections() (HIVsim method) npts (Result property)

P

parallel() (in module hpvsim.run) parse_study() (Calibration method) ParsObj (class in hpvsim.base) participation_filter() (in module hpvsim.utils) People (class in hpvsim.people) Person (class in hpvsim.base) person() (BasePeople method) person_keys() (BasePeople method) plot() (age_pyramid method) (age_results method) (Calibration method) (MultiSim method) (People method) (Scenarios method) (Sim method)

plot_age_results() (Scenarios method) plot_compare() (MultiSim method) plot_heatmap() (Sweep method) plot_intervention() (Intervention method) plot_people() (in module hpvsim.plotting) plot_result() (in module hpvsim.plotting) (MultiSim method) plot_scen_age_results() (in module hpvsim.plotting) plot_scens() (in module hpvsim.plotting) plot_sim() (in module hpvsim.plotting) plot_single() (age_results method) poisson() (in module hpvsim.utils) pop_inds() (Layer method) pop_layer() (Contacts method) precin (BasePeople property) precompute_waning() (in module hpvsim.immunity)

Q

quick_download() (in module hpvsim.data.downloaders)

R

radiation (class in hpvsim.interventions) reduce() (age_pyramid static method) (age_results static method) (Analyzer static method) (MultiSim method) (Sweep method) remove_data() (in module hpvsim.data.downloaders) remove_db() (Calibration method) remove_duplicates() (BasePeople static method) remove_people() (People method) reset() (MultiSim method) reset_layer_pars() (in module hpvsim.parameters) (Sim method) Result (class in hpvsim.base) result_keys() (BaseSim method) (MultiSim method) (Scenarios method)

result_types() (BaseSim method) round_age (BasePeople property) routine_screening (class in hpvsim.interventions) routine_triage (class in hpvsim.interventions) routine_txvx (class in hpvsim.interventions) routine_vx (class in hpvsim.interventions) RoutineDelivery (class in hpvsim.interventions) run() (MultiSim method) (Scenarios method) (Sim method) (Sweep method) run_sim() (Calibration method) run_trial() (Calibration method) run_workers() (Calibration method)

S

sample() (in module hpvsim.utils) save() (BasePeople method) (BaseSim method) (in module hpvsim.misc) (MultiSim method) (Scenarios method) savefig() (in module hpvsim.misc) scale_flows() (People method) Scenarios (class in hpvsim.run) set() (BasePeople method) set_hiv_prognoses() (HIVsim method) set_intervention_attributes() (in module hpvsim.interventions) set_metadata() (BaseSim method) set_pars() (BasePeople method) set_prognoses() (People method) set_seed() (in module hpvsim.utils) set_severity() (People method) shape (Result property)

shrink() (Analyzer method) (BaseSim method) (BaseVaccination method) (Intervention method) (MultiSim method) Sim (class in hpvsim.sim) sim_to_sample_pars() (Calibration method) single_run() (in module hpvsim.run) snapshot (class in hpvsim.analysis) split() (MultiSim method) state_keys() (BasePeople method) step() (HIVsim method) (Sim method) story() (People method) sum() (Result method) summarize() (MultiSim method) (Scenarios method) (Sim method) Sweep (class in hpvsim.run)

T

to_arr() (BasePeople method) to_df() (BasePeople method) (BaseSim method) (Layer method) to_excel() (BaseSim method) (MultiSim method) (Scenarios method) to_graph() (BasePeople method) (Contacts method) (Layer method) to_json() (Analyzer method) (BaseSim method) (Calibration method) (Intervention method) (MultiSim method) (Scenarios method)

to_list() (BasePeople method) treat_delay (class in hpvsim.interventions) treat_num (class in hpvsim.interventions) trial_pars_to_sim_pars() (Calibration method) trial_to_sim_pars() (Calibration method) true() (BasePeople method) (in module hpvsim.utils) true_by_genotype() (BasePeople method) tx (class in hpvsim.interventions)

U

undefined() (BasePeople method) (in module hpvsim.utils) unfilter() (BasePeople method) unlock() (BasePeople method) update() (Layer method) update_cd4() (HIVsim method) update_dict_pars() (Calibration static method) update_dict_pars_from_trial() (Calibration method)

update_dict_pars_init_and_bounds() (Calibration method) update_hiv_results() (HIVsim method) update_hpv_progs() (HIVsim method) update_pars() (BaseSim method) (HIVsim method) (ParsObj method) update_peak_immunity() (in module hpvsim.immunity) update_states_post() (People method) update_states_pre() (People method)

V

validate() (BasePeople method) (Layer method) validate_dt() (Sim method) validate_init_conditions() (Sim method)

validate_layer_pars() (Sim method) validate_pars() (Sim method) validate_variables() (age_results method) values() (FlexDict method) vx (class in hpvsim.interventions)

W

worker() (Calibration method)