API for ImperialCollegeLondon/epidemia
Modeling of Epidemics using Hierarchical Bayesian Models
| Global functions | |
|---|---|
| .cnms | Source code |
| .cnms.epimodel | Source code |
| .flist | Source code |
| .flist.epimodel | Source code |
| .format_pars | Source code |
| .get_group | Source code |
| .get_obs | Source code |
| .get_time | Source code |
| .max_treedepth | Source code |
| .median_and_madsd | Source code |
| .mixed_check | Source code |
| .print_covariance_prior | Source code |
| .print_scalar_prior | Source code |
| .print_vector_prior | Source code |
| .printfr | Source code |
| EnglandNewCases | Man page |
| EuropeCovid | Man page |
| EuropeCovid2 | Man page |
| R | Source code |
| STOP_no_draws | Source code |
| STOP_sampling_only | Source code |
| VarCorr.epimodel | Source code |
| `%ORifNULL%` | Source code |
| add_median | Source code |
| add_xlev | Source code |
| all_obs_types | Man page Source code |
| all_obs_types.epimodel | Man page Source code |
| all_vars | Source code |
| as.array.epimodel | Man page Source code |
| as.character.expr | Source code |
| as.data.frame.epimodel | Man page Source code |
| as.matrix.epimodel | Man page Source code |
| as.string.formula | Source code |
| base_plot | Source code |
| by100k | Source code |
| cauchy | Man page |
| check_all_in_set | Source code |
| check_all_vars_data | Source code |
| check_alpha | Source code |
| check_character | Source code |
| check_consecutive_dates | Source code |
| check_data | Source code |
| check_data.frame | Source code |
| check_dates | Source code |
| check_df | Source code |
| check_draws | Source code |
| check_formula | Source code |
| check_group_as_factor | Source code |
| check_group_subset | Source code |
| check_groups_data | Source code |
| check_has_rows | Source code |
| check_in_set | Source code |
| check_inf | Source code |
| check_integer | Source code |
| check_levels | Source code |
| check_list | Source code |
| check_logical | Source code |
| check_missing_pars | Source code |
| check_name_conflicts_data | Source code |
| check_non_negative | Source code |
| check_numeric | Source code |
| check_obs | Source code |
| check_obs_formula | Source code |
| check_offset | Source code |
| check_pops | Source code |
| check_pops_unique | Source code |
| check_positive | Source code |
| check_prior | Source code |
| check_reTrms | Source code |
| check_rhats | Source code |
| check_rm | Source code |
| check_rt | Source code |
| check_rt_formula | Source code |
| check_scalar | Source code |
| check_smooth | Source code |
| check_sum_to_one | Source code |
| check_time_as_date | Source code |
| collect_pars | Source code |
| crps | Source code |
| cumul | Source code |
| cumulate | Source code |
| cumulate.epiobs_ | Source code |
| daily_coverage | Source code |
| daily_error | Source code |
| decov | Man page |
| epidemia | Man page |
| epidemia-package | Man page |
| epiinf | Man page Source code |
| epim | Man page Source code |
| epimodel | Source code |
| epimodel-objects | Man page |
| epiobs | Man page Source code |
| epiobs_ | Source code |
| epirt | Man page Source code |
| epirt_ | Source code |
| evaluate_forecast | Man page Source code |
| exclude_lp_and_ppd | Source code |
| exponential | Man page |
| fancy_scientific | Source code |
| formula.epiformula | Source code |
| formula.epimodel | Man page Source code |
| geom_stepribbon | Source code |
| get_autocor_gr | Source code |
| get_autocor_time | Source code |
| get_gr | Source code |
| get_gr.epiobs_ | Source code |
| get_grs | Source code |
| get_i2o | Source code |
| get_i2o.epiobs_ | Source code |
| get_labels | Source code |
| get_obs | Source code |
| get_obs.epiobs_ | Source code |
| get_quantiles | Source code |
| get_samps | Man page Source code |
| get_time | Source code |
| get_time.epiobs_ | Source code |
| get_times | Source code |
| get_x | Man page Source code |
| get_x.default | Source code |
| get_x.mixed | Source code |
| get_z | Man page Source code |
| get_z.mixed | Source code |
| gr_subset | Source code |
| grep_for_pars | Source code |
| group_date_col_data | Source code |
| handle_glm_prior | Source code |
| hexp | Man page Source code |
| hs | Man page |
| hs_plus | Man page |
| is.epimodel | Source code |
| is.mixed | Source code |
| is.mixed.epimodel | Source code |
| is.mixed.formula | Source code |
| is.scalar | Source code |
| is_autocor | Source code |
| justRE | Source code |
| just_fe | Source code |
| laplace | Man page |
| lasso | Man page |
| last_dimnames | Source code |
| lhs | Source code |
| linear_predictor | Source code |
| linear_predictor.default | Source code |
| linear_predictor.matrix | Source code |
| lkj | Man page |
| make_Sigma_nms | Source code |
| make_V | Source code |
| make_b_nms | Source code |
| make_glmerControl | Source code |
| make_inf_nms | Source code |
| make_oaux_nms | Source code |
| make_obeta_nms | Source code |
| make_obs_ac_nms | Source code |
| make_ointercept_nms | Source code |
| make_rw_nms | Source code |
| make_rw_sigma_nms | Source code |
| make_stan_summary | Source code |
| maybe_broadcast | Source code |
| mcmc_function_name | Source code |
| mflevels | Source code |
| model.frame.epimodel | Man page Source code |
| needs_chains | Source code |
| new_inf_stanmat | Source code |
| new_names | Source code |
| new_rw_stanmat | Source code |
| ngrps | Man page |
| ngrps.mixed | Man page Source code |
| nobs | Source code |
| nobs.epiobs_ | Source code |
| normal | Man page |
| norws | Source code |
| obs_to_int | Source code |
| pad | Source code |
| pad_reTrms | Source code |
| pairs.epimodel | Man page Source code |
| pars | Source code |
| parse_all_terms | Source code |
| parse_data | Source code |
| parse_formula | Source code |
| parse_latent | Source code |
| parse_mm | Source code |
| parse_new_data | Source code |
| parse_obs | Source code |
| parse_rw_labels | Source code |
| parse_term | Source code |
| plot.epimodel | Man page Source code |
| plot_coverage | Man page Source code |
| plot_infections | Man page Source code |
| plot_infections.epimodel | Man page Source code |
| plot_infectious | Man page Source code |
| plot_infectious.epimodel | Man page Source code |
| plot_linpred | Man page Source code |
| plot_linpred.epimodel | Man page Source code |
| plot_metrics | Man page Source code |
| plot_obs | Man page Source code |
| plot_obs.epimodel | Man page Source code |
| plot_rt | Man page Source code |
| plot_rt.epimodel | Man page Source code |
| posterior_coverage | Man page Source code |
| posterior_infections | Man page Source code |
| posterior_infections.epimodel | Man page Source code |
| posterior_infectious | Man page Source code |
| posterior_infectious.epimodel | Man page Source code |
| posterior_latent | Man page Source code |
| posterior_latent.epimodel | Man page Source code |
| posterior_linpred | Man page Source code |
| posterior_metrics | Man page Source code |
| posterior_predict | Man page |
| posterior_predict.epimodel | Man page Source code |
| posterior_rt | Man page Source code |
| posterior_rt.epimodel | Man page Source code |
| posterior_sample_size | Man page Source code |
| posterior_sample_size.epimodel | Man page Source code |
| posterior_sims | Source code |
| pp_b_ord | Source code |
| pp_eta | Source code |
| pp_eta_ac | Source code |
| pp_eta_fe | Source code |
| pp_eta_re | Source code |
| pp_stanmat | Source code |
| print.epimodel | Man page Source code |
| print.prior_summary.epimodel | Man page Source code |
| print.prior_summary_reg.epimodel | Man page Source code |
| print.summary.epimodel | Man page Source code |
| prior_summary | Man page |
| prior_summary.epimodel | Man page Source code |
| process_x | Source code |
| product_normal | Man page |
| reexports | Man page |
| restrict_pars | Source code |
| rhs | Source code |
| rw | Man page Source code |
| scaled_logit | Man page Source code |
| select_cols_data | Source code |
| set_plotting_args | Source code |
| set_plotting_fun | Source code |
| set_prior_scale | Source code |
| shifted_gamma | Man page Source code |
| smooth_obs | Source code |
| spaghetti_base | Source code |
| spaghetti_infections | Man page Source code |
| spaghetti_obs | Man page Source code |
| spaghetti_rt | Man page Source code |
| standata_all | Source code |
| standata_autocor | Source code |
| standata_data | Source code |
| standata_inf | Source code |
| standata_obs | Source code |
| standata_reg | Source code |
| standata_rt | Source code |
| student_t | Man page |
| sub_ | Source code |
| subsamp | Source code |
| subset_data | Source code |
| subset_for_dates | Source code |
| summarize_glm_prior | Source code |
| summary.epimodel | Man page Source code |
| terms.epimodel | Man page |
| terms_rw | Man page Source code |
| transformTheta_L | Source code |
| transform_obs | Source code |
| transform_rt | Source code |
| unpad_reTrms | Source code |
| unpad_reTrms.array | Source code |
| unpad_reTrms.default | Source code |
| used.sampling | Source code |
| used.variational | Source code |
| validate_neff_ratio | Source code |
| validate_parameter_value | Source code |
| validate_plotfun_for_opt_or_vb | Source code |
| validate_rhat | Source code |
| warn_sum_to_one | Source code |
