Files in seabbs/epinowcast

Flexible Hierarchical Nowcasting

LICENSE.md NEWS.md R/check.R R/data-converters.R R/datasets.R R/epinowcast-package.R R/epinowcast.R R/formula-tools.R R/methods.R R/model-design-tools.R R/model-module-helpers.R R/model-modules.R R/model-tools.R R/model-validation.R R/plot.R R/postprocess.R R/preprocess.R R/simulate.R R/utils.R R/zzz.R README.Rmd README.md data-raw/load_germany_hospitalisation_data.R inst/examples/germany_dow.R inst/examples/germany_latent_renewal.R inst/examples/germany_max_delay_greater_than_data.R inst/examples/germany_missing_reference_dates.R inst/examples/germany_missing_report_dates.R inst/examples/germany_non_parametric_baseline.R inst/examples/germany_parametric_with_non_parametric_effect.R inst/examples/germany_simple.R inst/examples/germany_weekly_process_model.R inst/make_hexsticker.R inst/scripts/generate_examples.R man/add_max_observed_delay.Rd man/add_pmfs.Rd man/aggregate_rolling_sum.Rd man/as_string_formula.Rd man/build_ord_obs.Rd man/cache_location_message.Rd man/check_calendar_timestep.Rd man/check_design_matrix_sparsity.Rd man/check_environment_unset.Rd man/check_group.Rd man/check_group_date_unique.Rd man/check_max_delay.Rd man/check_module.Rd man/check_modules_compatible.Rd man/check_numeric_timestep.Rd man/check_observation_indicator.Rd man/check_quantiles.Rd man/check_renviron_for_cache.Rd man/check_timestep.Rd man/check_timestep_by_date.Rd man/check_timestep_by_group.Rd man/coerce_date.Rd man/coerce_dt.Rd man/construct_re.Rd man/construct_rw.Rd man/convolution_matrix.Rd man/create_cache_dir.Rd man/date_to_numeric_modulus.Rd man/enw_add_cumulative.Rd man/enw_add_cumulative_membership.Rd man/enw_add_delay.Rd man/enw_add_incidence.Rd man/enw_add_latest_obs_to_nowcast.Rd man/enw_add_max_reported.Rd man/enw_add_metaobs_features.Rd man/enw_add_pooling_effect.Rd man/enw_aggregate_cumulative.Rd man/enw_assign_group.Rd man/enw_complete_dates.Rd man/enw_construct_data.Rd man/enw_cumulative_to_incidence.Rd man/enw_delay_metadata.Rd man/enw_design.Rd man/enw_effects_metadata.Rd man/enw_example.Rd man/enw_expectation.Rd man/enw_extend_date.Rd man/enw_filter_delay.Rd man/enw_filter_reference_dates.Rd man/enw_filter_report_dates.Rd man/enw_fit_opts.Rd man/enw_flag_observed_observations.Rd man/enw_formula.Rd man/enw_formula_as_data_list.Rd man/enw_get_cache.Rd man/enw_impute_na_observations.Rd man/enw_incidence_to_cumulative.Rd man/enw_incidence_to_linelist.Rd man/enw_latest_data.Rd man/enw_linelist_to_incidence.Rd man/enw_manual_formula.Rd man/enw_metadata.Rd man/enw_metadata_delay.Rd man/enw_missing.Rd man/enw_missing_reference.Rd man/enw_model.Rd man/enw_nowcast_samples.Rd man/enw_nowcast_summary.Rd man/enw_obs.Rd man/enw_one_hot_encode_feature.Rd man/enw_pathfinder.Rd man/enw_plot_nowcast_quantiles.Rd man/enw_plot_obs.Rd man/enw_plot_pp_quantiles.Rd man/enw_plot_quantiles.Rd man/enw_plot_theme.Rd man/enw_posterior.Rd man/enw_pp_summary.Rd man/enw_preprocess_data.Rd man/enw_priors_as_data_list.Rd man/enw_quantiles_to_long.Rd man/enw_reference.Rd man/enw_reference_by_report.Rd man/enw_replace_priors.Rd man/enw_report.Rd man/enw_reporting_triangle.Rd man/enw_reporting_triangle_to_long.Rd man/enw_reps_with_complete_refs.Rd man/enw_sample.Rd man/enw_score_nowcast.Rd man/enw_set_cache.Rd man/enw_simulate_missing_reference.Rd man/enw_stan_to_r.Rd man/enw_summarise_samples.Rd man/enw_unset_cache.Rd man/epinowcast-package.Rd man/epinowcast.Rd man/extract_obs_metadata.Rd man/extract_sparse_matrix.Rd man/germany_covid19_hosp.Rd man/get_internal_timestep.Rd man/get_renviron_contents.Rd man/is.Date.Rd man/latest_obs_as_matrix.Rd man/parse_formula.Rd man/plot.epinowcast.Rd man/re.Rd man/remove_profiling.Rd man/remove_rw_terms.Rd man/roxygen/meta.R man/rw.Rd man/rw_terms.Rd man/simulate_double_censored_pmf.Rd man/split_formula_to_terms.Rd man/stan_fns_as_string.Rd man/subset_obs.Rd man/summary.epinowcast.Rd man/unset_cache_from_environ.Rd man/update_inits.Rd man/write_stan_files_no_profile.Rd tests/spelling.R tests/testthat.R tests/testthat/_snaps/build_ord_obs.md tests/testthat/_snaps/check_max_delay.md tests/testthat/_snaps/convolution_matrix.md tests/testthat/_snaps/enw_add_latest_obs_to_nowcast.md tests/testthat/_snaps/enw_complete_dates.md tests/testthat/_snaps/enw_expectation.md tests/testthat/_snaps/enw_filter_reference_dates.md tests/testthat/_snaps/enw_fit_opts.md tests/testthat/_snaps/enw_formula.md tests/testthat/_snaps/enw_formula_as_data_list.md tests/testthat/_snaps/enw_incidence_to_linelist.md tests/testthat/_snaps/enw_linelist_to_incidence.md tests/testthat/_snaps/enw_manual_formula.md tests/testthat/_snaps/enw_missing.md tests/testthat/_snaps/enw_nowcast_samples.md tests/testthat/_snaps/enw_nowcast_summary.md tests/testthat/_snaps/enw_obs.md tests/testthat/_snaps/enw_posterior.md tests/testthat/_snaps/enw_pp_summary.md tests/testthat/_snaps/enw_quantiles_to_long.md tests/testthat/_snaps/enw_reference.md tests/testthat/_snaps/enw_report.md tests/testthat/_snaps/enw_set_cache.md tests/testthat/_snaps/enw_summarise_samples.md tests/testthat/_snaps/ewn_design.md tests/testthat/_snaps/subset_obs.md tests/testthat/helper-expectations.R tests/testthat/helper-functions.R tests/testthat/helper-state.R tests/testthat/setup-options.R tests/testthat/setup.R tests/testthat/test-add_max_observed_delay.R tests/testthat/test-add_pmfs.R tests/testthat/test-build_ord_obs.R tests/testthat/test-cache_location_message.R tests/testthat/test-check_design_matrix_sparsity.R tests/testthat/test-check_group.R tests/testthat/test-check_group_date_unique.R tests/testthat/test-check_max_delay.R tests/testthat/test-check_module.R tests/testthat/test-check_modules_compatible.R tests/testthat/test-check_observation_indicator.R tests/testthat/test-check_quantiles.R tests/testthat/test-check_timestep.R tests/testthat/test-check_timestep_by_date.R tests/testthat/test-check_timestep_by_group.R tests/testthat/test-coerce_date.R tests/testthat/test-convolution_matrix.R tests/testthat/test-create_cache_dir.R tests/testthat/test-datatable-disconnection.R tests/testthat/test-date_to_numeric_modulus.R tests/testthat/test-enw_add_cumulative.R tests/testthat/test-enw_add_cumulative_membership.R tests/testthat/test-enw_add_delay.R tests/testthat/test-enw_add_incidence.R tests/testthat/test-enw_add_latest_obs_to_nowcast.R tests/testthat/test-enw_add_max_reported.R tests/testthat/test-enw_add_metaobs_features.R tests/testthat/test-enw_add_pooling_effect.R tests/testthat/test-enw_aggregate_cumulative.R tests/testthat/test-enw_assign_group.R tests/testthat/test-enw_complete_dates.R tests/testthat/test-enw_delay_filter.R tests/testthat/test-enw_effects_metadata.R tests/testthat/test-enw_example.R tests/testthat/test-enw_expectation.R tests/testthat/test-enw_extend_date.R tests/testthat/test-enw_filter_delay.R tests/testthat/test-enw_filter_reference_dates.R tests/testthat/test-enw_filter_report_dates.R tests/testthat/test-enw_fit_opts.R tests/testthat/test-enw_flag_observed_observations.R tests/testthat/test-enw_formula.R tests/testthat/test-enw_formula_as_data_list.R tests/testthat/test-enw_get_cache.R tests/testthat/test-enw_impute_na_observations.R tests/testthat/test-enw_incidence_to_linelist.R tests/testthat/test-enw_latest_data.R tests/testthat/test-enw_linelist_to_incidence.R tests/testthat/test-enw_manual_formula.R tests/testthat/test-enw_metadata.R tests/testthat/test-enw_metadata_delay.R tests/testthat/test-enw_missing.R tests/testthat/test-enw_missing_reference.R tests/testthat/test-enw_model.R tests/testthat/test-enw_nowcast_samples.R tests/testthat/test-enw_nowcast_summary.R tests/testthat/test-enw_obs.R tests/testthat/test-enw_plot_obs.R tests/testthat/test-enw_posterior.R tests/testthat/test-enw_pp_summary.R tests/testthat/test-enw_preprocess_data.R tests/testthat/test-enw_priors_as_data_list.R tests/testthat/test-enw_quantiles_to_long.R tests/testthat/test-enw_reference.R tests/testthat/test-enw_reference_by_report.R tests/testthat/test-enw_replace_priors.R tests/testthat/test-enw_report.R tests/testthat/test-enw_reps_with_complete_refs.R tests/testthat/test-enw_score_nowcast.R tests/testthat/test-enw_set_cache.R tests/testthat/test-enw_simulate_missing_reference.R tests/testthat/test-enw_stan_to_r.R tests/testthat/test-enw_summarise_samples.R tests/testthat/test-enw_unset_cache.R tests/testthat/test-epinowcast.R tests/testthat/test-ewn_design.R tests/testthat/test-extract_obs_metadata.R tests/testthat/test-extract_sparse_matrix.R tests/testthat/test-get_internal_timestep.R tests/testthat/test-plot.epinowcast.R tests/testthat/test-simulate_double_censored_pmf.R tests/testthat/test-stan_discretised_logit_hazard.R tests/testthat/test-stan_expected_obs.R tests/testthat/test-stan_fns_as_string.R tests/testthat/test-subset_obs.R tests/testthat/test-summary.epinowcast.R touchstone/footer.R touchstone/header.R touchstone/missing-setup.R touchstone/multigroup-setup.R touchstone/preprocessing.R touchstone/script.R touchstone/setup.R touchstone/threaded-setup.R vignettes/chunks/_readme-install-epinowcast.Rmd vignettes/distributions.Rmd vignettes/epinowcast.Rmd vignettes/germany-age-stratified-nowcasting.Rmd vignettes/model.Rmd vignettes/package-use-cases.Rmd vignettes/precompile.R vignettes/single-timeseries-rt-estimation.Rmd vignettes/stan-help.Rmd