API reference¶
Subpackages¶
Submodules¶
- hpvsim.analysis module
- hpvsim.base module
ParsObjResultBaseSimBaseSim.update_pars()BaseSim.set_metadata()BaseSim.nBaseSim.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()
BasePeopleBasePeople.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_femaleBasePeople.is_female_aliveBasePeople.is_maleBasePeople.is_male_aliveBasePeople.f_indsBasePeople.m_indsBasePeople.int_ageBasePeople.round_ageBasePeople.dt_ageBasePeople.is_activeBasePeople.is_female_adultBasePeople.is_virginBasePeople.alive_indsBasePeople.alive_level0BasePeople.alive_level0_indsBasePeople.n_aliveBasePeople.n_alive_level0BasePeople.infectedBasePeople.abnormalBasePeople.latentBasePeople.precinBasePeople.cin1BasePeople.cin2BasePeople.cin3BasePeople.cinBasePeople.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()
PersonFlexDictContactsLayer
- hpvsim.calibration module
CalibrationCalibration.run_sim()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
- hpvsim.hiv module
- hpvsim.immunity module
- hpvsim.interventions module
InterventionRoutineDeliveryCampaignDeliverydynamic_parsEventScheduleset_intervention_attributes()BaseVaccinationroutine_vxcampaign_vxBaseTestBaseScreeningroutine_screeningcampaign_screeningBaseTriageroutine_triagecampaign_triageBaseTreatmenttreat_numtreat_delayBaseTxVxroutine_txvxcampaign_txvxlinked_txvxdxtxvxradiationdefault_dx()default_tx()default_vx()
- hpvsim.misc module
- hpvsim.parameters module
- hpvsim.people module
PeoplePeople.init_flows()People.scale_flows()People.increment_age()People.initialize()People.update_states_pre()People.set_prognoses()People.set_severity()People.update_severity()People.dissolve_partnerships()People.create_partnerships()People.check_inds()People.check_inds_true()People.check_transformation()People.check_progress()People.check_cin1()People.check_cin2()People.check_cin3()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
- hpvsim.population module
- hpvsim.run module
make_metapars()MultiSimMultiSim.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()
ScenariosSweepsingle_run()multi_run()parallel()
- hpvsim.settings module
- hpvsim.sim module
SimSim.load_data()Sim.initialize()Sim.layer_keys()Sim.reset_layer_pars()Sim.validate_layer_pars()Sim.validate_pars()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_summary()Sim.summarize()Sim.plot()Sim.compute_fit()
AlreadyRunErrordiff_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()true()false()defined()undefined()itrue()ifalse()idefined()iundefined()itruei()ifalsei()idefinedi()iundefinedi()dtround()find_cutoff()
- hpvsim.version module