Index

_

_SliderComponent (class in branchpro)

A

add_collapsed_text() (branchpro.BranchProDashApp method) add_data() (branchpro.IncidenceNumberPlot method) add_ground_truth_rt() (branchpro.ReproductionNumberPlot method)

add_interval_rt() (branchpro.ReproductionNumberPlot method) add_simulation() (branchpro.IncidenceNumberPlot method) add_slider() (branchpro._SliderComponent method) add_text() (branchpro.BranchProDashApp method)

B

big_pdf() (branchpro.GammaDist method) branchpro.figures module BranchProDashApp (class in branchpro)

BranchProInferenceApp (class in branchpro) BranchProModel (class in branchpro) BranchProPosterior (class in branchpro) BranchProPosteriorMultSI (class in branchpro)

D

DatasetLibrary (class in branchpro)

E

evaluateS1() (branchpro.MultiCatPoissonBranchProLogLik method) (branchpro.PoissonBranchProLogLik method)

F

ForwardModel (class in branchpro)

french_flu() (branchpro.DatasetLibrary method)

G

GammaDist (class in branchpro) get_contact_matrix() (branchpro.MultiCatPoissonBranchProModel method) get_intervals() (branchpro.BranchProPosterior method) (branchpro.BranchProPosteriorMultSI method) get_mean_contact() (branchpro.PoiBinBranchProModel method) get_next_gen() (branchpro.PoiBinBranchProModel method) get_overdispersion() (branchpro.LocImpNegBinBranchProModel method) (branchpro.NegBinBranchProLogLik method) (branchpro.NegBinBranchProModel method)

get_r_profile() (branchpro.BranchProModel method) get_serial_intervals() (branchpro.BranchProModel method) (branchpro.BranchProPosterior method) (branchpro.BranchProPosteriorMultSI method) (branchpro.MultiCatPoissonBranchProLogLik method) (branchpro.MultiCatPoissonBranchProModel method) (branchpro.PoissonBranchProLogLik method) get_sliders_div() (branchpro._SliderComponent method) get_transmissibility() (branchpro.MultiCatPoissonBranchProModel method)

I

IncidenceNumberPlot (class in branchpro)

IncidenceNumberSimulationApp (class in branchpro)

L

last_time_r_threshold() (branchpro.BranchProPosterior method) LocImpBranchProModel (class in branchpro) LocImpBranchProPosterior (class in branchpro)

LocImpBranchProPosteriorMultSI (class in branchpro) LocImpMultiCatPoissonBranchProModel (class in branchpro) LocImpNegBinBranchProModel (class in branchpro)

M

module branchpro.figures

MultiCatPoissonBranchProLogLik (class in branchpro) MultiCatPoissonBranchProLogPosterior (class in branchpro) MultiCatPoissonBranchProModel (class in branchpro)

N

n_parameters() (branchpro.MultiCatPoissonBranchProLogLik method) (branchpro.NegBinBranchProLogLik method) (branchpro.PoissonBranchProLogLik method)

NegBinBranchProLogLik (class in branchpro) NegBinBranchProLogPosterior (class in branchpro) NegBinBranchProModel (class in branchpro)

P

parse_contents() (branchpro.BranchProDashApp method) plot_forward_simulations() (in module branchpro.figures) plot_r_inference() (in module branchpro.figures)

PoiBinBranchProModel (class in branchpro) PoissonBranchProLogLik (class in branchpro) PoissonBranchProLogPosterior (class in branchpro) proportion_time_r_more_than_1() (branchpro.BranchProPosterior method)

R

refresh_user_data_json() (branchpro.BranchProDashApp method) ReproductionNumberPlot (class in branchpro) return_loglikelihood() (branchpro.MultiCatPoissonBranchProLogPosterior method) (branchpro.PoissonBranchProLogPosterior method) return_logposterior() (branchpro.MultiCatPoissonBranchProLogPosterior method) (branchpro.PoissonBranchProLogPosterior method) return_logprior() (branchpro.MultiCatPoissonBranchProLogPosterior method) (branchpro.PoissonBranchProLogPosterior method) run() (branchpro.SimulationController method)

run_inference() (branchpro.BranchProPosterior method) (branchpro.BranchProPosteriorMultSI method) (branchpro.LocImpBranchProPosterior method) (branchpro.LocImpBranchProPosteriorMultSI method) (branchpro.MultiCatPoissonBranchProLogPosterior method) (branchpro.NegBinBranchProLogPosterior method) (branchpro.PoissonBranchProLogPosterior method) run_optimisation() (branchpro.MultiCatPoissonBranchProLogPosterior method) (branchpro.NegBinBranchProLogPosterior method) (branchpro.PoissonBranchProLogPosterior method)

S

set_contact_matrix() (branchpro.MultiCatPoissonBranchProModel method) set_epsilon() (branchpro.LocImpBranchProModel method) (branchpro.LocImpBranchProPosterior method) (branchpro.LocImpMultiCatPoissonBranchProModel method) (branchpro.PoissonBranchProLogLik method) set_imported_cases() (branchpro.LocImpBranchProModel method) (branchpro.LocImpMultiCatPoissonBranchProModel method) set_mean_contact() (branchpro.PoiBinBranchProModel method) set_next_gen() (branchpro.PoiBinBranchProModel method) set_overdispersion() (branchpro.LocImpNegBinBranchProModel method) (branchpro.NegBinBranchProLogLik method) (branchpro.NegBinBranchProModel method) set_r_profile() (branchpro.BranchProModel method) set_serial_intervals() (branchpro.BranchProModel method) (branchpro.BranchProPosterior method) (branchpro.BranchProPosteriorMultSI method) (branchpro.MultiCatPoissonBranchProLogLik method) (branchpro.MultiCatPoissonBranchProModel method) (branchpro.PoissonBranchProLogLik method)

set_transmissibility() (branchpro.MultiCatPoissonBranchProModel method) show_figure() (branchpro.IncidenceNumberPlot method) (branchpro.ReproductionNumberPlot method) simulate() (branchpro.BranchProModel method) (branchpro.ForwardModel method) (branchpro.LocImpBranchProModel method) (branchpro.LocImpMultiCatPoissonBranchProModel method) (branchpro.LocImpNegBinBranchProModel method) (branchpro.MultiCatPoissonBranchProModel method) (branchpro.NegBinBranchProModel method) (branchpro.PoiBinBranchProModel method) (branchpro.StochasticLocImpNegBinBranchProModel method) (branchpro.StochasticNegBinBranchProModel method) SimulationController (class in branchpro) slider_ids() (branchpro._SliderComponent method) StochasticLocImpNegBinBranchProModel (class in branchpro) StochasticNegBinBranchProModel (class in branchpro) switch_resolution() (branchpro.SimulationController method)

U

update_data_figure() (branchpro.BranchProInferenceApp method) update_figure() (branchpro.IncidenceNumberSimulationApp method) update_inference_figure() (branchpro.BranchProInferenceApp method) update_labels() (branchpro.IncidenceNumberPlot method) (branchpro.ReproductionNumberPlot method)

update_posterior() (branchpro.BranchProInferenceApp method) update_simulation() (branchpro.IncidenceNumberSimulationApp method) update_sliders() (branchpro.BranchProInferenceApp method) (branchpro.IncidenceNumberSimulationApp method)