Welcome to epimodels’ documentation!

This is the documentation for the implementation of a collection of three epidemiological models used in the modelling of cases observed during the COVID-19 pandemic.

• List of Epidemiology Models
  • Public Health England & Cambridge Model
    • PheSEIRModel
      • PheSEIRModel.age_groups_names()
      • PheSEIRModel.check_death_format()
      • PheSEIRModel.check_positives_format()
      • PheSEIRModel.compute_rt_trajectory()
      • PheSEIRModel.compute_transition_matrix()
      • PheSEIRModel.loglik_deaths()
      • PheSEIRModel.loglik_positive_tests()
      • PheSEIRModel.mean_deaths()
      • PheSEIRModel.mean_positives()
      • PheSEIRModel.n_outputs()
      • PheSEIRModel.n_parameters()
      • PheSEIRModel.new_infections()
      • PheSEIRModel.output_names()
      • PheSEIRModel.parameter_names()
      • PheSEIRModel.read_contact_data()
      • PheSEIRModel.read_regional_data()
      • PheSEIRModel.region_names()
      • PheSEIRModel.samples_deaths()
      • PheSEIRModel.samples_positive_tests()
      • PheSEIRModel.set_age_groups()
      • PheSEIRModel.set_outputs()
      • PheSEIRModel.set_regions()
      • PheSEIRModel.simulate()
  • Roche SEIRD Model
    • RocheSEIRModel
      • RocheSEIRModel.age_groups_names()
      • RocheSEIRModel.check_death_format()
      • RocheSEIRModel.check_positives_format()
      • RocheSEIRModel.compute_rt_trajectory()
      • RocheSEIRModel.compute_transition_matrix()
      • RocheSEIRModel.formula_SI()
      • RocheSEIRModel.loglik_deaths()
      • RocheSEIRModel.loglik_positive_tests()
      • RocheSEIRModel.mean_deaths()
      • RocheSEIRModel.mean_positives()
      • RocheSEIRModel.n_outputs()
      • RocheSEIRModel.n_parameters()
      • RocheSEIRModel.new_deaths()
      • RocheSEIRModel.new_infections()
      • RocheSEIRModel.output_names()
      • RocheSEIRModel.parameter_names()
      • RocheSEIRModel.read_contact_data()
      • RocheSEIRModel.read_npis_data()
      • RocheSEIRModel.read_regional_data()
      • RocheSEIRModel.region_names()
      • RocheSEIRModel.samples_deaths()
      • RocheSEIRModel.samples_positive_tests()
      • RocheSEIRModel.set_age_groups()
      • RocheSEIRModel.set_outputs()
      • RocheSEIRModel.set_regions()
      • RocheSEIRModel.simulate()
  • Warwick-Household Model
    • WarwickSEIRModel
      • WarwickSEIRModel.age_groups_names()
      • WarwickSEIRModel.check_death_format()
      • WarwickSEIRModel.check_new_deaths_format()
      • WarwickSEIRModel.check_new_hospital_beds_format()
      • WarwickSEIRModel.check_new_hospitalisation_format()
      • WarwickSEIRModel.check_new_icu_beds_format()
      • WarwickSEIRModel.check_new_icu_format()
      • WarwickSEIRModel.check_positives_format()
      • WarwickSEIRModel.compute_rt_trajectory()
      • WarwickSEIRModel.compute_rt_trajectory_paper()
      • WarwickSEIRModel.compute_transition_matrix()
      • WarwickSEIRModel.loglik_deaths()
      • WarwickSEIRModel.loglik_positive_tests()
      • WarwickSEIRModel.mean_deaths()
      • WarwickSEIRModel.mean_positives()
      • WarwickSEIRModel.n_outputs()
      • WarwickSEIRModel.n_parameters()
      • WarwickSEIRModel.new_deaths()
      • WarwickSEIRModel.new_hospital_beds()
      • WarwickSEIRModel.new_hospitalisations()
      • WarwickSEIRModel.new_icu()
      • WarwickSEIRModel.new_icu_beds()
      • WarwickSEIRModel.new_infections()
      • WarwickSEIRModel.output_names()
      • WarwickSEIRModel.parameter_names()
      • WarwickSEIRModel.read_contact_data()
      • WarwickSEIRModel.read_regional_data()
      • WarwickSEIRModel.region_names()
      • WarwickSEIRModel.samples_deaths()
      • WarwickSEIRModel.samples_positive_tests()
      • WarwickSEIRModel.set_age_groups()
      • WarwickSEIRModel.set_outputs()
      • WarwickSEIRModel.set_regions()
      • WarwickSEIRModel.simulate()
• Inference Classes
  • Public Health England & Cambridge Model
    • PheSEIRInfer
      • PheSEIRInfer.inference_problem_setup()
      • PheSEIRInfer.optimisation_problem_setup()
      • PheSEIRInfer.read_deaths_data()
      • PheSEIRInfer.read_model_data()
      • PheSEIRInfer.read_serology_data()
      • PheSEIRInfer.return_loglikelihood()
    • PHELogLik
      • PHELogLik.n_parameters()
      • PHELogLik.set_fixed_parameters()
    • PHELogPrior
      • PHELogPrior.n_parameters()
  • Roche SEIRD Model
    • RocheSEIRInfer
      • RocheSEIRInfer.inference_problem_setup()
      • RocheSEIRInfer.optimisation_problem_setup()
      • RocheSEIRInfer.read_deaths_data()
      • RocheSEIRInfer.read_model_data()
      • RocheSEIRInfer.read_npis_data()
      • RocheSEIRInfer.read_serology_data()
      • RocheSEIRInfer.return_loglikelihood()
    • RocheLogLik
      • RocheLogLik.n_parameters()
      • RocheLogLik.set_fixed_parameters()
    • RocheLogPrior
      • RocheLogPrior.n_parameters()
  • Warwick-Household Model
    • WarwickSEIRInfer
      • WarwickSEIRInfer.inference_problem_setup()
      • WarwickSEIRInfer.optimisation_problem_setup()
      • WarwickSEIRInfer.read_deaths_data()
      • WarwickSEIRInfer.read_delay_data()
      • WarwickSEIRInfer.read_extended_contact_matrices()
      • WarwickSEIRInfer.read_extended_population_structure()
      • WarwickSEIRInfer.read_model_data()
      • WarwickSEIRInfer.read_serology_data()
      • WarwickSEIRInfer.return_loglikelihood()
    • WarwickLogLik
      • WarwickLogLik.n_parameters()
      • WarwickLogLik.set_fixed_parameters()
    • WarwickLogPrior
      • WarwickLogPrior.n_parameters()
• Setup Matrices
  • Contact Population Matrix
    • ContactMatrix
      • ContactMatrix.change_age_groups()
      • ContactMatrix.get_age_groups()
      • ContactMatrix.plot_heat_map()
  • Region-specific Susceptibility Matrix
    • RegionMatrix
      • RegionMatrix.change_age_groups()
      • RegionMatrix.change_region_name()
      • RegionMatrix.plot_heat_map()
  • Mono Time&Region-specific New Infections Matrix
    • UniNextGenMatrix
      • UniNextGenMatrix.compute_dom_eigenvalue()
      • UniNextGenMatrix.get_next_gen_matrix()
  • Multi Time&Region-specific Contact Matrix
    • MultiTimesContacts
      • MultiTimesContacts.identify_current_contacts()
  • Mono Time&Region-specific Infectivity Matrix and Reproduction Number Computer
    • UniInfectivityMatrix
      • UniInfectivityMatrix.compute_prob_infectivity_matrix()
      • UniInfectivityMatrix.compute_reproduction_number()
  • Multi Time&Region-specific Infectivity Matrix and Reproduction Number Computer
    • MultiTimesInfectivity
      • MultiTimesInfectivity.compute_prob_infectivity_matrix()
      • MultiTimesInfectivity.compute_reproduction_number()
• Model Parameters Classes
  • Parameter Classes for the PHE Model
  • Initial Conditions Parameters
    • PheICs
  • Regional and Time Dependent Parameters
    • PheRegParameters
  • Disease Specific Parameters
    • PheDiseaseParameters
  • Simulation Method Parameters
    • PheSimParameters
  • Parameters Controller
    • PheParametersController
  • Parameter Classes for the Roche SEIRD Model
  • Initial Conditions Parameters
    • RocheICs
  • Average Times in Compartments Parameters
    • RocheCompartmentTimes
  • Proportions of Asymptomatic, Super-spreader and Dead Parameters
    • RocheProportions
  • Transmission Specific Parameters
    • RocheTransmission
  • Simulation Method Parameters
    • RocheSimParameters
  • Parameters Controller
    • RocheParametersController
  • Parameter Classes for the Warwick-Household Model
  • Initial Conditions Parameters
    • WarwickICs
  • Regional and Time Dependent Parameters
    • WarwickRegParameters
  • Disease Specific Parameters
    • WarwickDiseaseParameters
  • Transmission Specific Parameters
    • WarwickTransmission
  • Simulation Method Parameters
    • WarwickSimParameters
  • Social Distancing Parameters
    • WarwickSocDistParameters
  • Parameters Controller
    • WarwickParametersController

Indices and tables

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