HPV agent-based Simulator (HPVsim) documentation

HPVsim is a stochastic agent-based simulator, written in Python, for exploring and analyzing human papillomavirus (HPV) transmission.

Full contents

• HPVsim overview
  • Installation
  • Usage and documentation
  • Contributing
  • Disclaimer
• Tutorials
  • T1 - Getting started
    • Hello world
    • Defining parameters and genotypes, and running simulations
    • Plotting results
    • Full usage example
  • T2 - Plotting, printing, and saving
    • Global plotting configuration
    • Printing objects
    • Plotting options
    • Customizing plots
    • Saving options
  • T3 - Running scenarios
    • Running with MultiSims
      • Running one sim with uncertainty
      • Running different sims
      • Advanced usage
    • Running with Scenarios
  • T4 - People, populations, and networks
    • Demographic data
    • People and contact network layers
  • T5 - Using interventions
    • Products and interventions
    • Screening and treatment interventions
    • Prophylactic vaccination
    • Therapeutic vaccination
  • T6 - Using analyzers
    • Results by age
    • Snapshots
    • Age pyramids
  • T7 - Calibration
    • Data types supported by HPVsim
    • The Calibration object
• What’s new
  • Version 1.2.5 (2023-09-21)
  • Version 1.2.4 (2023-09-19)
  • Version 1.2.3 (2023-08-30)
  • Version 1.2.2 (2023-08-11)
  • Version 1.2.1 (2023-07-09)
  • Version 1.2.0 (2023-05-31)
  • Version 1.1.5 (2023-03-23)
  • Version 1.1.4 (2023-03-15)
  • Version 1.1.3 (2023-03-14)
  • Version 1.1.2 (2023-03-13)
  • Version 1.1.1 (2023-03-01)
  • Version 1.1.0 (2023-02-16)
  • Version 1.0.1 (2023-02-09)
  • Version 1.0.0 (2023-01-31)
  • Version 0.4.17 (2023-01-31)
  • Version 0.4.16 (2023-01-30)
  • Version 0.4.15 (2023-01-13)
  • Version 0.4.14 (2023-01-11)
  • Version 0.4.13 (2023-01-09)
  • Version 0.4.12 (2023-01-02)
  • Version 0.4.11 (2022-12-21)
  • Version 0.4.10 (2022-12-19)
  • Version 0.4.9 (2022-12-16)
  • Version 0.4.8 (2022-12-14)
  • Version 0.4.7 (2022-12-13)
  • Version 0.4.6 (2022-12-12)
  • Version 0.4.5 (2022-12-06)
  • Version 0.4.4 (2022-12-05)
  • Version 0.4.3 (2022-12-01)
  • Version 0.4.2 (2022-11-21)
  • Version 0.4.1 (2022-11-21)
  • Version 0.4.0 (2022-11-16)
  • Version 0.3.9 (2022-11-15)
  • Version 0.3.8 (2022-11-02)
  • Version 0.3.7 (2022-11-01)
  • Version 0.3.6 (2022-11-01)
  • Version 0.3.5 (2022-10-31)
  • Version 0.3.4 (2022-10-31)
  • Version 0.3.3 (2022-10-30)
  • Version 0.3.2 (2022-10-26)
  • Version 0.3.1 (2022-10-26)
  • Version 0.3.0 (2022-10-26)
  • Version 0.2.11 (2022-10-25)
  • Version 0.2.10 (2022-10-24)
  • Version 0.2.9 (2022-10-18)
  • Version 0.2.8 (2022-10-17)
  • Version 0.2.7 (2022-10-14)
  • Version 0.2.6 (2022-10-12)
  • Version 0.2.5 (2022-10-07)
  • Version 0.2.4 (2022-10-07)
  • Version 0.2.3 (2022-09-01)
  • Version 0.2.2 (2022-08-22)
  • Version 0.2.1 (2022-08-19)
  • Version 0.2.0 (2022-08-19)
  • Version 0.1.0 (2022-08-01)
  • Version 0.0.3 (2022-07-18)
  • Version 0.0.2 (2022-06-15)
  • Version 0.0.1 (2022-04-04)
• API reference
  • Subpackages
    • hpvsim.data package
      • Submodules
  • Submodules
    • hpvsim.analysis module
      • Analyzer
      • snapshot
      • age_pyramid
      • age_results
      • age_causal_infection
      • cancer_detection
      • daly_computation
    • hpvsim.base module
      • ParsObj
      • Result
      • BaseSim
      • BasePeople
      • Person
      • FlexDict
      • Contacts
      • Layer
    • hpvsim.calibration module
      • Calibration
    • hpvsim.defaults module
      • default_float
      • default_int
      • get_default_plots()
    • hpvsim.hiv module
      • HIVsim
    • hpvsim.immunity module
      • init_immunity()
      • update_peak_immunity()
      • check_immunity()
      • precompute_waning()
      • exp_decay()
      • linear_decay()
      • linear_growth()
    • hpvsim.interventions module
      • Intervention
      • RoutineDelivery
      • CampaignDelivery
      • dynamic_pars
      • EventSchedule
      • set_intervention_attributes()
      • BaseVaccination
      • routine_vx
      • campaign_vx
      • BaseTest
      • BaseScreening
      • routine_screening
      • campaign_screening
      • BaseTriage
      • routine_triage
      • campaign_triage
      • BaseTreatment
      • treat_num
      • treat_delay
      • BaseTxVx
      • routine_txvx
      • campaign_txvx
      • linked_txvx
      • dx
      • tx
      • vx
      • radiation
      • 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
    • 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
      • Scenarios
      • Sweep
      • single_run()
      • multi_run()
      • parallel()
    • hpvsim.settings module
    • hpvsim.sim module
      • Sim
      • 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()
      • true()
      • false()
      • defined()
      • undefined()
      • itrue()
      • ifalse()
      • idefined()
      • iundefined()
      • itruei()
      • ifalsei()
      • idefinedi()
      • iundefinedi()
      • dtround()
      • find_cutoff()
    • hpvsim.version module