Index

A

age_groups_names() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

C

change_age_groups() (epimodels.ContactMatrix method) (epimodels.RegionMatrix method) change_region_name() (epimodels.RegionMatrix method) check_death_format() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) check_new_deaths_format() (epimodels.WarwickSEIRModel method) check_new_hospital_beds_format() (epimodels.WarwickSEIRModel method) check_new_hospitalisation_format() (epimodels.WarwickSEIRModel method) check_new_icu_beds_format() (epimodels.WarwickSEIRModel method) check_new_icu_format() (epimodels.WarwickSEIRModel method) check_positives_format() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

compute_dom_eigenvalue() (epimodels.UniNextGenMatrix method) compute_prob_infectivity_matrix() (epimodels.MultiTimesInfectivity method) (epimodels.UniInfectivityMatrix method) compute_reproduction_number() (epimodels.MultiTimesInfectivity method) (epimodels.UniInfectivityMatrix method) compute_rt_trajectory() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) compute_rt_trajectory_paper() (epimodels.WarwickSEIRModel method) compute_transition_matrix() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) ContactMatrix (class in epimodels)

F

formula_SI() (epimodels.RocheSEIRModel method)

G

get_age_groups() (epimodels.ContactMatrix method)

get_next_gen_matrix() (epimodels.UniNextGenMatrix method)

I

identify_current_contacts() (epimodels.MultiTimesContacts method) inference_problem_setup() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method)

L

loglik_deaths() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

loglik_positive_tests() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

M

mean_deaths() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) mean_positives() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

MultiTimesContacts (class in epimodels) MultiTimesInfectivity (class in epimodels)

N

n_outputs() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) n_parameters() (epimodels.inference.PHELogLik method) (epimodels.inference.PHELogPrior method) (epimodels.inference.RocheLogLik method) (epimodels.inference.RocheLogPrior method) (epimodels.inference.WarwickLogLik method) (epimodels.inference.WarwickLogPrior method) (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

new_deaths() (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) new_hospital_beds() (epimodels.WarwickSEIRModel method) new_hospitalisations() (epimodels.WarwickSEIRModel method) new_icu() (epimodels.WarwickSEIRModel method) new_icu_beds() (epimodels.WarwickSEIRModel method) new_infections() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

O

optimisation_problem_setup() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method)

output_names() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

P

parameter_names() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) PheDiseaseParameters (class in epimodels) PheICs (class in epimodels) PHELogLik (class in epimodels.inference) PHELogPrior (class in epimodels.inference)

PheParametersController (class in epimodels) PheRegParameters (class in epimodels) PheSEIRInfer (class in epimodels.inference) PheSEIRModel (class in epimodels) PheSimParameters (class in epimodels) plot_heat_map() (epimodels.ContactMatrix method) (epimodels.RegionMatrix method)

R

read_contact_data() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) read_deaths_data() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method) read_delay_data() (epimodels.inference.WarwickSEIRInfer method) read_extended_contact_matrices() (epimodels.inference.WarwickSEIRInfer method) read_extended_population_structure() (epimodels.inference.WarwickSEIRInfer method) read_model_data() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method) read_npis_data() (epimodels.inference.RocheSEIRInfer method) (epimodels.RocheSEIRModel method) read_regional_data() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) read_serology_data() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method)

region_names() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) RegionMatrix (class in epimodels) return_loglikelihood() (epimodels.inference.PheSEIRInfer method) (epimodels.inference.RocheSEIRInfer method) (epimodels.inference.WarwickSEIRInfer method) RocheCompartmentTimes (class in epimodels) RocheICs (class in epimodels) RocheLogLik (class in epimodels.inference) RocheLogPrior (class in epimodels.inference) RocheParametersController (class in epimodels) RocheProportions (class in epimodels) RocheSEIRInfer (class in epimodels.inference) RocheSEIRModel (class in epimodels) RocheSimParameters (class in epimodels) RocheTransmission (class in epimodels)

S

samples_deaths() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) samples_positive_tests() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) set_age_groups() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) set_fixed_parameters() (epimodels.inference.PHELogLik method) (epimodels.inference.RocheLogLik method) (epimodels.inference.WarwickLogLik method)

set_outputs() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) set_regions() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method) simulate() (epimodels.PheSEIRModel method) (epimodels.RocheSEIRModel method) (epimodels.WarwickSEIRModel method)

U

UniInfectivityMatrix (class in epimodels)

UniNextGenMatrix (class in epimodels)

W

WarwickDiseaseParameters (class in epimodels) WarwickICs (class in epimodels) WarwickLogLik (class in epimodels.inference) WarwickLogPrior (class in epimodels.inference) WarwickParametersController (class in epimodels)

WarwickRegParameters (class in epimodels) WarwickSEIRInfer (class in epimodels.inference) WarwickSEIRModel (class in epimodels) WarwickSimParameters (class in epimodels) WarwickSocDistParameters (class in epimodels) WarwickTransmission (class in epimodels)