HPVsim documentation

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

Full contents

• 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 with Scenarios
  • T4 - People, populations, and networks
    • Demographic data
    • People and contact network layers
    • Assortative mixing
  • 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 2.0.2 (2024-03-05)
  • Version 2.0.1 (2024-02-14)
  • Version 2.0.0 (2023-11-29)
  • Version 1.2.7 (2023-09-22)
  • Version 1.2.6 (2023-09-22)
  • 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
  • analysis
    • Analyzer
    • snapshot
    • age_pyramid
    • age_results
    • age_causal_infection
    • cancer_detection
    • dalys
  • base
    • ParsObj
    • Result
    • BaseSim
    • BasePeople
    • Person
    • FlexDict
    • Contacts
    • Layer
  • calibration
    • Calibration
  • defaults
    • default_float
    • default_int
    • get_default_plots
  • hiv
    • HIVsim
  • immunity
    • check_immunity
    • exp_decay
    • init_immunity
    • linear_decay
    • linear_growth
    • precompute_waning
    • update_peak_immunity
  • interventions
    • Intervention
    • RoutineDelivery
    • CampaignDelivery
    • dynamic_pars
    • EventSchedule
    • 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
    • set_intervention_attributes
    • default_dx
    • default_tx
    • default_vx
  • misc
    • 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
  • parameters
    • make_pars
    • reset_layer_pars
  • people
    • People
  • plotting
    • plot_sim
    • plot_scens
    • plot_scen_age_results
    • plot_result
    • plot_people
  • population
    • make_people
    • make_contacts
  • run
    • MultiSim
    • Scenarios
    • Sweep
    • make_metapars
    • single_run
    • multi_run
    • parallel
  • settings
  • sim
    • Sim
    • diff_sims
    • hpvsim.sim.AlreadyRunError
  • utils
    • 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
  • downloaders
    • get_data
    • quick_download
    • check_downloaded
    • remove_data
  • loaders
    • 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