Index

A

add_dates() (in module evofr.plotting.plot_functions) add_dates_sep() (in module evofr.plotting.plot_functions) add_posterior() (MultiPosterior method) add_posteriors() (MultiPosterior method) apply_delay() (in module evofr.models.renewal_model.model_functions) arg_constraints (LaplaceRandomWalk attribute) augment_data() (HierMLR method) (InnovationMLR method) (MLRNowcast method) (MLRSpline method) (ModelSpec method) (MultinomialLogisticRegression method) (PianthamModel method) (RenewalModel method) (RenewalRegressionModel method) (SingleRenewalModel method) (SplineIncidenceModel method)

B

BasisFunction (class in evofr.models.renewal_model.basis_functions.basis_fns)

BetaHazard (class in evofr.models.mlr_nowcast)

C

CaseCounts (class in evofr.data.case_counts) CaseFrequencyData (class in evofr.data.case_frequencies) combine_sites_tidy() (in module evofr.posterior.posterior_helpers)

compute_frequency_piantham() (in module evofr.models.piantham_model) continuous_dist_to_pmf() (in module evofr.models.renewal_model.model_helpers) counts_to_matrix() (in module evofr.data.data_helpers)

D

DataSpec (class in evofr.data.data_spec) default() (EvofrEncoder method) DelaySequenceCounts (class in evofr.models.mlr_nowcast) DeltaNormalPrior (class in evofr.models.mlr_innovation) DeltaPriorModel (class in evofr.models.mlr_innovation)

DeltaRegressionPrior (class in evofr.models.mlr_innovation) determine_method() (in module evofr.posterior.posterior_handler) DirMultinomialSeq (class in evofr.models.renewal_model.model_options) discrete_hazard_to_pmf_cdf() (in module evofr.models.mlr_nowcast) discretise_gamma() (in module evofr.models.renewal_model.model_helpers) discretise_lognorm() (in module evofr.models.renewal_model.model_helpers)

E

estimate_delay() (in module evofr.models.mlr_nowcast) evofr module evofr.data module evofr.data.case_counts module evofr.data.case_frequencies module evofr.data.data_helpers module evofr.data.data_spec module evofr.data.hier_cases module evofr.data.hier_frequencies module evofr.data.variant_frequencies module evofr.infer module evofr.infer.InferMCMC module evofr.infer.InferSVI module evofr.infer.MCMC_handler module evofr.infer.SVI_handler module evofr.models module evofr.models.mlr_hierarchical module evofr.models.mlr_innovation module evofr.models.mlr_nowcast module evofr.models.mlr_spline module evofr.models.model_spec module evofr.models.multinomial_logistic_regression module

evofr.models.piantham_model module evofr.models.renewal_model module evofr.models.renewal_model.basis_functions module evofr.models.renewal_model.basis_functions.basis_fns module evofr.models.renewal_model.basis_functions.hilbert_space_gaussian_process module evofr.models.renewal_model.basis_functions.splines module evofr.models.renewal_model.LAS module evofr.models.renewal_model.model_factories module evofr.models.renewal_model.model_functions module evofr.models.renewal_model.model_helpers module evofr.models.renewal_model.model_options module evofr.models.renewal_model.renewal_model module evofr.models.renewal_model.renewal_regression module evofr.models.renewal_model.renewal_single_variant module evofr.models.renewal_model.spline_incidence module evofr.plotting module evofr.plotting.plot_functions module evofr.posterior module evofr.posterior.posterior_handler module evofr.posterior.posterior_helpers module EvofrEncoder (class in evofr.posterior.posterior_helpers) expand_dates() (in module evofr.data.data_helpers)

F

fit() (InferMCMC method) (InferNUTS_from_MAP method) (InferSVI method) (MCMCHandler method) (SVIHandler method) FixedGA (class in evofr.models.renewal_model.model_options) forecast_dates() (in module evofr.data.data_helpers)

forecast_frequencies() (HierMLR static method) (MultinomialLogisticRegression static method) format_var_names() (in module evofr.data.data_helpers) forward_simulate_EC() (in module evofr.models.renewal_model.model_functions) forward_simulate_I() (in module evofr.models.renewal_model.model_functions) forward_simulate_I_and_prev() (in module evofr.models.renewal_model.model_functions) FreeGrowth (class in evofr.models.renewal_model.model_options)

G

GAPRW (class in evofr.models.renewal_model.model_options) GARW (class in evofr.models.renewal_model.model_options) get() (MultiPosterior method) get_data_dict() (PosteriorHandler method) get_freq() (in module evofr.posterior.posterior_helpers) get_growth_advantage() (in module evofr.posterior.posterior_helpers) get_infections() (in module evofr.models.renewal_model.model_functions) get_infections_intros() (in module evofr.models.renewal_model.model_functions)

get_median() (in module evofr.posterior.posterior_helpers) get_quantile() (in module evofr.posterior.posterior_helpers) get_quantiles() (in module evofr.posterior.posterior_helpers) get_site() (PosteriorHandler method) get_site_by_variant() (in module evofr.posterior.posterior_helpers) get_sites_quantiles_json() (in module evofr.posterior.posterior_helpers) get_sites_variants_json() (in module evofr.posterior.posterior_helpers) get_sites_variants_tidy() (in module evofr.posterior.posterior_helpers) get_standard_delays() (in module evofr.models.renewal_model.model_helpers)

H

HazardModel (class in evofr.models.mlr_nowcast) hier_MLR_numpyro() (in module evofr.models.mlr_hierarchical) HierarchicalCFData (class in evofr.data.case_frequencies)

HierCases (class in evofr.data.hier_cases) HierFrequencies (class in evofr.data.hier_frequencies) HierMLR (class in evofr.models.mlr_hierarchical) HSGaussianProcess (class in evofr.models.renewal_model.basis_functions.hilbert_space_gaussian_process)

I

InferFullRank (class in evofr.infer.InferSVI) InferMAP (class in evofr.infer.InferSVI) InferMCMC (class in evofr.infer.InferMCMC) InferNUTS (class in evofr.infer.InferMCMC) InferNUTS_from_MAP (class in evofr.infer.InferMCMC)

InferSVI (class in evofr.infer.InferSVI) init_svi() (SVIHandler method) init_to_MAP() (in module evofr.infer.InferSVI) InnovationMLR (class in evofr.models.mlr_innovation) InnovationSequenceCounts (class in evofr.models.mlr_innovation) is_obs_idx() (in module evofr.models.renewal_model.model_helpers)

L

lam() (HSGaussianProcess static method) LaplaceRandomWalk (class in evofr.models.renewal_model.LAS) LAS_Laplace() (in module evofr.models.renewal_model.LAS) LinearHazard (class in evofr.models.mlr_nowcast) load_data() (in module evofr.posterior.posterior_handler) load_posterior() (PosteriorHandler method)

load_state() (MCMCHandler method) (SVIHandler method) log_prob() (LaplaceRandomWalk method) LogitRWHazard (class in evofr.models.mlr_nowcast) LogitSplineHazard (class in evofr.models.mlr_nowcast) losses (SVIHandler property)

M

make_data_dict() (CaseCounts method) (CaseFrequencyData method) (DataSpec method) (DelaySequenceCounts method) (HierarchicalCFData method) (HierCases method) (HierFrequencies method) (InnovationSequenceCounts method) (VariantFrequencies method) make_features() (BasisFunction method) (Matern method) (Spline method) (SplineDeriv method) (SquaredExponential method) make_model() (RenewalModel method) (RenewalRegressionModel method) (SingleRenewalModel method) (SplineIncidenceModel method) make_ols_feature() (HierMLR static method) (MultinomialLogisticRegression static method) Matern (class in evofr.models.renewal_model.basis_functions.hilbert_space_gaussian_process) matrix() (Spline static method) (SplineDeriv static method) MCMCHandler (class in evofr.infer.MCMC_handler) mean (LaplaceRandomWalk property) MLR_innovation_model() (in module evofr.models.mlr_innovation) MLR_innovation_model_time_varying() (in module evofr.models.mlr_innovation) MLR_nowcast_model() (in module evofr.models.mlr_nowcast) MLR_numpyro() (in module evofr.models.multinomial_logistic_regression) MLR_spline_numpyro() (in module evofr.models.mlr_spline) MLRNowcast (class in evofr.models.mlr_nowcast) MLRSpline (class in evofr.models.mlr_spline) model() (BetaHazard method) (DeltaNormalPrior method) (DeltaPriorModel method) (DeltaRegressionPrior method) (DirMultinomialSeq method) (FixedGA method) (FreeGrowth method) (GAPRW method) (GARW method) (HazardModel method) (LinearHazard method) (LogitRWHazard method) (LogitSplineHazard method) (MultinomialSeq method) (NegBinomCases method) (PoisCases method) (ZINegBinomCases method) (ZIPoisCases method)

model_fn (ModelSpec attribute) ModelSpec (class in evofr.models.model_spec) module evofr evofr.data evofr.data.case_counts evofr.data.case_frequencies evofr.data.data_helpers evofr.data.data_spec evofr.data.hier_cases evofr.data.hier_frequencies evofr.data.variant_frequencies evofr.infer evofr.infer.InferMCMC evofr.infer.InferSVI evofr.infer.MCMC_handler evofr.infer.SVI_handler evofr.models evofr.models.mlr_hierarchical evofr.models.mlr_innovation evofr.models.mlr_nowcast evofr.models.mlr_spline evofr.models.model_spec evofr.models.multinomial_logistic_regression evofr.models.piantham_model evofr.models.renewal_model evofr.models.renewal_model.basis_functions evofr.models.renewal_model.basis_functions.basis_fns evofr.models.renewal_model.basis_functions.hilbert_space_gaussian_process evofr.models.renewal_model.basis_functions.splines evofr.models.renewal_model.LAS evofr.models.renewal_model.model_factories evofr.models.renewal_model.model_functions evofr.models.renewal_model.model_helpers evofr.models.renewal_model.model_options evofr.models.renewal_model.renewal_model evofr.models.renewal_model.renewal_regression evofr.models.renewal_model.renewal_single_variant evofr.models.renewal_model.spline_incidence evofr.plotting evofr.plotting.plot_functions evofr.posterior evofr.posterior.posterior_handler evofr.posterior.posterior_helpers MultinomialLogisticRegression (class in evofr.models.multinomial_logistic_regression) MultinomialSeq (class in evofr.models.renewal_model.model_options) MultiPosterior (class in evofr.posterior.posterior_handler)

N

NegBinomCases (class in evofr.models.renewal_model.model_options)

O

optim_state (SVIHandler property)

P

pad_delays() (in module evofr.models.renewal_model.model_helpers) pad_to_obs() (in module evofr.models.renewal_model.model_helpers) params (MCMCHandler property) (SVIHandler property) phi() (HSGaussianProcess static method) phi_matrix() (HSGaussianProcess static method) Piantham_model_numpyro() (in module evofr.models.piantham_model) PianthamModel (class in evofr.models.piantham_model) plot_cases() (in module evofr.plotting.plot_functions) plot_ga_time_censored() (in module evofr.plotting.plot_functions) plot_growth_advantage() (in module evofr.plotting.plot_functions) plot_little_r_censored() (in module evofr.plotting.plot_functions) plot_observed_frequency() (in module evofr.plotting.plot_functions) plot_observed_frequency_size() (in module evofr.plotting.plot_functions) plot_posterior_average_R() (in module evofr.plotting.plot_functions) plot_posterior_frequency() (in module evofr.plotting.plot_functions) plot_posterior_I() (in module evofr.plotting.plot_functions) plot_posterior_smooth_EC() (in module evofr.plotting.plot_functions) plot_posterior_time() (in module evofr.plotting.plot_functions) plot_ppc_cases() (in module evofr.plotting.plot_functions)

plot_ppc_frequency() (in module evofr.plotting.plot_functions) plot_ppc_seq_counts() (in module evofr.plotting.plot_functions) plot_R() (in module evofr.plotting.plot_functions) plot_R_censored() (in module evofr.plotting.plot_functions) plot_site() (in module evofr.plotting.plot_functions) plot_time_varying_single() (in module evofr.plotting.plot_functions) plot_time_varying_variant() (in module evofr.plotting.plot_functions) plot_total_by_median_frequency() (in module evofr.plotting.plot_functions) plot_total_by_obs_frequency() (in module evofr.plotting.plot_functions) PoisCases (class in evofr.models.renewal_model.model_options) PosteriorHandler (class in evofr.posterior.posterior_handler) predict() (DeltaRegressionPrior method) (MCMCHandler method) (SVIHandler method) prep_cases() (in module evofr.data.data_helpers) prep_clade_list() (in module evofr.models.mlr_innovation) prep_dates() (in module evofr.data.data_helpers) prep_posterior_for_plot() (in module evofr.plotting.plot_functions) prep_sequence_counts() (in module evofr.data.data_helpers) prep_sequence_counts_delay() (in module evofr.models.mlr_nowcast)

R

registry (DataSpec attribute) (ModelSpec attribute) renewal_regression_model_factory() (in module evofr.models.renewal_model.renewal_regression) RenewalModel (class in evofr.models.renewal_model.renewal_model)

RenewalRegressionModel (class in evofr.models.renewal_model.renewal_regression) reparametrized_params (LaplaceRandomWalk attribute) reporting_to_vec() (in module evofr.models.renewal_model.model_functions) reset_state() (SVIHandler method) rt_from_incidence() (in module evofr.models.renewal_model.renewal_regression)

S

sample() (LaplaceRandomWalk method) save_data() (in module evofr.posterior.posterior_handler) save_json() (in module evofr.posterior.posterior_helpers) save_posterior() (PosteriorHandler method) save_state() (MCMCHandler method) (SVIHandler method) simulate_hier_mlr() (in module evofr.models.mlr_hierarchical) simulate_MLR() (in module evofr.models.multinomial_logistic_regression) simulate_MLR_freq() (in module evofr.models.multinomial_logistic_regression)

SingleRenewalModel (class in evofr.models.renewal_model.renewal_single_variant) spd() (Matern static method) (SquaredExponential static method) Spline (class in evofr.models.renewal_model.basis_functions.splines) SplineDeriv (class in evofr.models.renewal_model.basis_functions.splines) SplineIncidenceModel (class in evofr.models.renewal_model.spline_incidence) SquaredExponential (class in evofr.models.renewal_model.basis_functions.hilbert_space_gaussian_process) support (LaplaceRandomWalk attribute) SVIHandler (class in evofr.infer.SVI_handler)

T

to_survivor_function() (in module evofr.models.renewal_model.model_helpers)

tree_flatten() (LaplaceRandomWalk method) tree_unflatten() (LaplaceRandomWalk class method)

U

unpack_posterior() (PosteriorHandler method)

V

v_fs_I() (in module evofr.models.renewal_model.model_functions) variance (LaplaceRandomWalk property)

variant_counts_to_dataframe() (in module evofr.data.variant_frequencies) VariantFrequencies (class in evofr.data.variant_frequencies)

Z

ZINegBinomCases (class in evofr.models.renewal_model.model_options)

ZIPoisCases (class in evofr.models.renewal_model.model_options)