API reference

Subpackages

• hpvsim.data package
  • Submodules
    • hpvsim.data.downloaders module
      • get_data()
      • quick_download()
      • check_downloaded()
      • remove_data()
    • hpvsim.data.loaders module
      • get_country_aliases()
      • map_entries()
      • get_age_distribution()
      • get_age_distribution_over_time()
      • get_total_pop()
      • get_death_rates()
      • get_birth_rates()
      • get_life_expectancy()

Submodules

• hpvsim.analysis module
  • Analyzer
    • Analyzer.initialize()
    • Analyzer.finalize()
    • Analyzer.apply()
    • Analyzer.shrink()
    • Analyzer.reduce()
    • Analyzer.to_json()
  • snapshot
    • snapshot.initialize()
    • snapshot.apply()
    • snapshot.finalize()
    • snapshot.get()
  • age_pyramid
    • age_pyramid.initialize()
    • age_pyramid.apply()
    • age_pyramid.finalize()
    • age_pyramid.reduce()
    • age_pyramid.plot()
  • age_results
    • age_results.initialize()
    • age_results.validate_variables()
    • age_results.convert_rname_stocks()
    • age_results.convert_rname_flows()
    • age_results.apply()
    • age_results.finalize()
    • age_results.reduce()
    • age_results.compute_mismatch()
    • age_results.get_to_plot()
    • age_results.plot_single()
    • age_results.plot()
  • age_causal_infection
    • age_causal_infection.initialize()
    • age_causal_infection.apply()
    • age_causal_infection.finalize()
  • cancer_detection
    • cancer_detection.initialize()
    • cancer_detection.apply()
  • daly_computation
    • daly_computation.initialize()
    • daly_computation.apply()
    • daly_computation.finalize()
• hpvsim.base module
  • ParsObj
    • ParsObj.update_pars()
  • Result
    • Result.sum()
    • Result.mean()
    • Result.median()
    • Result.npts
    • Result.shape
  • BaseSim
    • BaseSim.update_pars()
    • BaseSim.set_metadata()
    • BaseSim.n
    • BaseSim.get_t()
    • BaseSim.result_keys()
    • BaseSim.result_types()
    • BaseSim.copy()
    • BaseSim.export_results()
    • BaseSim.export_pars()
    • BaseSim.to_json()
    • BaseSim.to_df()
    • BaseSim.to_excel()
    • BaseSim.shrink()
    • BaseSim.save()
    • BaseSim.load()
    • BaseSim.get_interventions()
    • BaseSim.get_intervention()
    • BaseSim.get_analyzers()
    • BaseSim.get_analyzer()
  • BasePeople
    • BasePeople.initialize()
    • BasePeople.set_pars()
    • BasePeople.validate()
    • BasePeople.lock()
    • BasePeople.unlock()
    • BasePeople.filter_inds()
    • BasePeople.filter()
    • BasePeople.unfilter()
    • BasePeople.addtoself()
    • BasePeople.set()
    • BasePeople.get()
    • BasePeople.is_female
    • BasePeople.is_female_alive
    • BasePeople.is_male
    • BasePeople.is_male_alive
    • BasePeople.f_inds
    • BasePeople.m_inds
    • BasePeople.int_age
    • BasePeople.round_age
    • BasePeople.dt_age
    • BasePeople.is_active
    • BasePeople.is_female_adult
    • BasePeople.is_virgin
    • BasePeople.alive_inds
    • BasePeople.alive_level0
    • BasePeople.alive_level0_inds
    • BasePeople.n_alive
    • BasePeople.n_alive_level0
    • BasePeople.infected
    • BasePeople.abnormal
    • BasePeople.latent
    • BasePeople.precin
    • BasePeople.true()
    • BasePeople.true_by_genotype()
    • BasePeople.false_by_genotype()
    • BasePeople.false()
    • BasePeople.defined()
    • BasePeople.undefined()
    • BasePeople.count()
    • BasePeople.count_any()
    • BasePeople.count_by_genotype()
    • BasePeople.keys()
    • BasePeople.person_keys()
    • BasePeople.state_keys()
    • BasePeople.imm_keys()
    • BasePeople.intv_keys()
    • BasePeople.date_keys()
    • BasePeople.dur_keys()
    • BasePeople.layer_keys()
    • BasePeople.indices()
    • BasePeople.to_df()
    • BasePeople.to_arr()
    • BasePeople.person()
    • BasePeople.to_list()
    • BasePeople.from_list()
    • BasePeople.to_graph()
    • BasePeople.save()
    • BasePeople.load()
    • BasePeople.init_contacts()
    • BasePeople.add_contacts()
    • BasePeople.make_edgelist()
    • BasePeople.remove_duplicates()
  • Person
  • FlexDict
    • FlexDict.keys()
    • FlexDict.values()
    • FlexDict.items()
  • Contacts
    • Contacts.add_layer()
    • Contacts.pop_layer()
    • Contacts.to_graph()
  • Layer
    • Layer.members
    • Layer.meta_keys()
    • Layer.validate()
    • Layer.get_inds()
    • Layer.pop_inds()
    • Layer.append()
    • Layer.to_df()
    • Layer.from_df()
    • Layer.to_graph()
    • Layer.find_contacts()
    • Layer.update()
• hpvsim.calibration module
  • Calibration
    • Calibration.run_sim()
    • Calibration.update_dict_pars()
    • Calibration.update_dict_pars_from_trial()
    • Calibration.update_dict_pars_init_and_bounds()
    • Calibration.get_full_pars()
    • Calibration.trial_pars_to_sim_pars()
    • Calibration.sim_to_sample_pars()
    • Calibration.trial_to_sim_pars()
    • Calibration.run_trial()
    • Calibration.worker()
    • Calibration.run_workers()
    • Calibration.remove_db()
    • Calibration.make_study()
    • Calibration.calibrate()
    • Calibration.parse_study()
    • Calibration.to_json()
    • Calibration.plot()
• hpvsim.defaults module
  • default_float
  • default_int
  • get_default_plots()
• hpvsim.hiv module
  • HIVsim
    • HIVsim.update_pars()
    • HIVsim.init_states()
    • HIVsim.init_results()
    • HIVsim.set_hiv_prognoses()
    • HIVsim.check_hiv_death()
    • HIVsim.update_cd4()
    • HIVsim.step()
    • HIVsim.new_hiv_infections()
    • HIVsim.update_hpv_progs()
    • HIVsim.update_hiv_results()
    • HIVsim.get_hiv_data()
    • HIVsim.load_data()
    • HIVsim.finalize()
• hpvsim.immunity module
  • init_immunity()
  • update_peak_immunity()
  • check_immunity()
  • precompute_waning()
  • exp_decay()
  • linear_decay()
  • linear_growth()
• hpvsim.interventions module
  • Intervention
    • Intervention.disp()
    • Intervention.initialize()
    • Intervention.finalize()
    • Intervention.apply()
    • Intervention.shrink()
    • Intervention.plot_intervention()
    • Intervention.to_json()
  • RoutineDelivery
    • RoutineDelivery.initialize()
  • CampaignDelivery
    • CampaignDelivery.initialize()
  • dynamic_pars
    • dynamic_pars.initialize()
    • dynamic_pars.apply()
  • EventSchedule
    • EventSchedule.initialize()
    • EventSchedule.apply()
  • set_intervention_attributes()
  • BaseVaccination
    • BaseVaccination.initialize()
    • BaseVaccination.check_eligibility()
    • BaseVaccination.apply()
    • BaseVaccination.shrink()
  • routine_vx
    • routine_vx.initialize()
  • campaign_vx
    • campaign_vx.initialize()
  • BaseTest
    • BaseTest.initialize()
    • BaseTest.deliver()
    • BaseTest.check_eligibility()
  • BaseScreening
    • BaseScreening.check_eligibility()
    • BaseScreening.apply()
  • routine_screening
    • routine_screening.initialize()
  • campaign_screening
    • campaign_screening.initialize()
  • BaseTriage
    • BaseTriage.check_eligibility()
    • BaseTriage.apply()
  • routine_triage
    • routine_triage.initialize()
  • campaign_triage
    • campaign_triage.initialize()
  • BaseTreatment
    • BaseTreatment.initialize()
    • BaseTreatment.check_eligibility()
    • BaseTreatment.get_accept_inds()
    • BaseTreatment.get_candidates()
    • BaseTreatment.apply()
  • treat_num
    • treat_num.add_to_queue()
    • treat_num.get_candidates()
    • treat_num.apply()
  • treat_delay
    • treat_delay.add_to_schedule()
    • treat_delay.get_candidates()
    • treat_delay.apply()
  • BaseTxVx
    • BaseTxVx.deliver()
  • routine_txvx
    • routine_txvx.initialize()
    • routine_txvx.apply()
  • campaign_txvx
    • campaign_txvx.initialize()
    • campaign_txvx.apply()
  • linked_txvx
    • linked_txvx.apply()
  • dx
    • dx.default_value
    • dx.administer()
  • tx
    • tx.get_people_in_state()
    • tx.administer()
  • vx
    • vx.administer()
  • radiation
    • radiation.administer()
  • default_dx()
  • default_tx()
  • default_vx()
• hpvsim.misc module
  • date()
  • day()
  • daydiff()
  • date_range()
  • load_data()
  • load()
  • save()
  • savefig()
  • git_info()
  • check_version()
  • check_save_version()
  • get_version_pars()
  • get_png_metadata()
  • get_doubling_time()
  • compute_gof()
  • help()
• hpvsim.parameters module
  • make_pars()
  • reset_layer_pars()
• hpvsim.people module
  • People
    • People.init_flows()
    • People.scale_flows()
    • People.increment_age()
    • People.initialize()
    • People.update_states_pre()
    • People.update_states_post()
    • People.set_prognoses()
    • People.set_severity()
    • People.dissolve_partnerships()
    • People.create_partnerships()
    • People.check_inds()
    • People.check_inds_true()
    • People.check_progress()
    • People.check_cin()
    • People.check_cancer()
    • People.check_cancer_deaths()
    • People.check_clearance()
    • People.apply_death_rates()
    • People.add_births()
    • People.check_migration()
    • People.make_naive()
    • People.infect()
    • People.remove_people()
    • People.plot()
    • People.story()
• hpvsim.plotting module
  • plot_sim()
  • plot_scens()
  • plot_scen_age_results()
  • plot_result()
  • plot_people()
• hpvsim.population module
  • make_people()
  • make_contacts()
• hpvsim.run module
  • make_metapars()
  • MultiSim
    • MultiSim.result_keys()
    • MultiSim.init_sims()
    • MultiSim.run()
    • MultiSim.shrink()
    • MultiSim.reset()
    • MultiSim.reduce()
    • MultiSim.mean()
    • MultiSim.median()
    • MultiSim.combine()
    • MultiSim.compare()
    • MultiSim.plot()
    • MultiSim.plot_result()
    • MultiSim.plot_compare()
    • MultiSim.save()
    • MultiSim.load()
    • MultiSim.merge()
    • MultiSim.split()
    • MultiSim.disp()
    • MultiSim.summarize()
    • MultiSim.brief()
    • MultiSim.to_json()
    • MultiSim.to_excel()
  • Scenarios
    • Scenarios.result_keys()
    • Scenarios.run()
    • Scenarios.compare()
    • Scenarios.plot()
    • Scenarios.plot_age_results()
    • Scenarios.to_json()
    • Scenarios.to_excel()
    • Scenarios.save()
    • Scenarios.load()
    • Scenarios.disp()
    • Scenarios.summarize()
    • Scenarios.brief()
    • Scenarios.merge()
  • Sweep
    • Sweep.create_sims()
    • Sweep.run()
    • Sweep.reduce()
    • Sweep.combine()
    • Sweep.mean()
    • Sweep.median()
    • Sweep.compare()
    • Sweep.plot_heatmap()
  • single_run()
  • multi_run()
  • parallel()
• hpvsim.settings module
• hpvsim.sim module
  • Sim
    • Sim.load_data()
    • Sim.initialize()
    • Sim.layer_keys()
    • Sim.reset_layer_pars()
    • Sim.validate_layer_pars()
    • Sim.validate_dt()
    • Sim.validate_pars()
    • Sim.init_time_vecs()
    • Sim.validate_init_conditions()
    • Sim.init_genotypes()
    • Sim.init_results()
    • Sim.init_interventions()
    • Sim.init_people()
    • Sim.init_analyzers()
    • Sim.init_immunity()
    • Sim.init_hiv()
    • Sim.finalize_analyzers()
    • Sim.init_states()
    • Sim.step()
    • Sim.run()
    • Sim.finalize()
    • Sim.compute_results()
    • Sim.compute_states()
    • Sim.compute_age_mean()
    • Sim.compute_summary()
    • Sim.summarize()
    • Sim.plot()
    • Sim.compute_fit()
  • AlreadyRunError
  • diff_sims()
• hpvsim.utils module
  • sample()
  • get_pdf()
  • set_seed()
  • n_binomial()
  • binomial_filter()
  • binomial_arr()
  • n_multinomial()
  • poisson()
  • n_poisson()
  • n_neg_binomial()
  • choose()
  • choose_r()
  • choose_w()
  • participation_filter()
  • true()
  • false()
  • defined()
  • undefined()
  • itrue()
  • ifalse()
  • idefined()
  • iundefined()
  • itruei()
  • ifalsei()
  • idefinedi()
  • iundefinedi()
  • dtround()
  • find_cutoff()
• hpvsim.version module