Man pages for seabbs/epinowcast
Flexible Hierarchical Nowcasting
| add_max_observed_delay | Add maximum observed delay |
| add_pmfs | Add probability mass functions |
| aggregate_rolling_sum | Internal function to perform rolling sum aggregation |
| as_string_formula | Converts formulas to strings |
| build_ord_obs | Build the ord_obs 'data.table'. |
| cache_location_message | Cache location message for epinowcast package |
| check_calendar_timestep | Check calendar timestep |
| check_environment_unset | Check environment setting |
| check_group | Check observations for reserved grouping variables |
| check_group_date_unique | Check observations for uniqueness of grouping variables with... |
| check_max_delay | Check appropriateness of maximum delay |
| check_module | Check a model module contains the required components |
| check_modules_compatible | Check that model modules have compatible specifications |
| check_numeric_timestep | Check Numeric Timestep |
| check_observation_indicator | Check observation indicator |
| check_quantiles | Check required quantiles are present |
| check_renviron_for_cache | Check '.Renviron' for cache location setting |
| check_timestep | Check timestep |
| check_timestep_by_date | Check timestep by date |
| check_timestep_by_group | Check timestep by group |
| coerce_date | Coerce Dates |
| coerce_dt | Coerce 'data.table's |
| construct_re | Constructs random effect terms |
| construct_rw | Constructs random walk terms |
| convolution_matrix | Construct a convolution matrix |
| create_cache_dir | Create Stan cache directory |
| date_to_numeric_modulus | Convert date column to numeric and calculate its modulus with... |
| enw_add_cumulative | Calculate cumulative reported cases from incidence of new... |
| enw_add_cumulative_membership | Add a cumulative membership effect to a 'data.frame' |
| enw_add_delay | Add a delay variable to the observations |
| enw_add_incidence | Calculate incidence of new reports from cumulative reports |
| enw_add_latest_obs_to_nowcast | Add latest observations to nowcast output |
| enw_add_max_reported | Add the maximum number of reported cases for each... |
| enw_add_metaobs_features | Add common metadata variables |
| enw_add_pooling_effect | Add a pooling effect to model design metadata |
| enw_aggregate_cumulative | Aggregate observations over a given timestep for both report... |
| enw_assign_group | Assign a group to each row of a data.table |
| enw_complete_dates | Complete missing reference and report dates |
| enw_construct_data | Construct preprocessed data |
| enw_cumulative_to_incidence | Calculate incidence of new reports from cumulative reports |
| enw_delay_metadata | Calculate reporting delay metadata for a given maximum delay |
| enw_design | A helper function to construct a design matrix from a formula |
| enw_effects_metadata | Extracts metadata from a design matrix |
| enw_example | Load a package example |
| enw_expectation | Expectation model module |
| enw_extend_date | Extend a time series with additional dates |
| enw_filter_delay | Filter observations to restrict the maximum reporting delay |
| enw_filter_reference_dates | Filter by reference dates |
| enw_filter_report_dates | Filter by report dates |
| enw_fit_opts | Format model fitting options for use with stan |
| enw_flag_observed_observations | Flag observed observations |
| enw_formula | Define a model using a formula interface |
| enw_formula_as_data_list | Format formula data for use with stan |
| enw_get_cache | Retrieve Stan cache location |
| enw_impute_na_observations | Impute NA observations |
| enw_incidence_to_cumulative | Calculate cumulative reported cases from incidence of new... |
| enw_incidence_to_linelist | Convert Aggregate Counts (Incidence) to a Line List |
| enw_latest_data | Filter observations to the latest available reported |
| enw_linelist_to_incidence | Convert a Line List to Aggregate Counts (Incidence) |
| enw_manual_formula | Define a model manually using fixed and random effects |
| enw_metadata | Extract metadata from raw data |
| enw_metadata_delay | Calculate reporting delay metadata for a given maximum delay |
| enw_missing | Missing reference data model module |
| enw_missing_reference | Extract reports with missing reference dates |
| enw_model | Load and compile the nowcasting model |
| enw_nowcast_samples | Extract posterior samples for the nowcast prediction |
| enw_nowcast_summary | Summarise the posterior nowcast prediction |
| enw_obs | Setup observation model and data |
| enw_one_hot_encode_feature | One-hot encode a variable and column-bind it to the original... |
| enw_pathfinder | Fit a CmdStan model using the pathfinder algorithm |
| enw_plot_nowcast_quantiles | Plot nowcast quantiles |
| enw_plot_obs | Generic quantile plot |
| enw_plot_pp_quantiles | Plot posterior prediction quantiles |
| enw_plot_quantiles | Generic quantile plot |
| enw_plot_theme | Package plot theme |
| enw_posterior | Summarise the posterior |
| enw_pp_summary | Posterior predictive summary |
| enw_preprocess_data | Preprocess observations |
| enw_priors_as_data_list | Convert prior 'data.frame' to list |
| enw_quantiles_to_long | Convert summarised quantiles from wide to long format |
| enw_reference | Reference date logit hazard reporting model module |
| enw_reference_by_report | Construct a lookup of references dates by report |
| enw_replace_priors | Replace default priors with user specified priors |
| enw_report | Report date logit hazard reporting model module |
| enw_reporting_triangle | Construct the reporting triangle |
| enw_reporting_triangle_to_long | Recast the reporting triangle from wide to long format |
| enw_reps_with_complete_refs | Identify report dates with complete (i.e up to the maximum... |
| enw_sample | Fit a CmdStan model using NUTS |
| enw_score_nowcast | Evaluate nowcasts using proper scoring rules |
| enw_set_cache | Set caching location for Stan models |
| enw_simulate_missing_reference | Simulate observations with a missing reference date. |
| enw_stan_to_r | Expose 'epinowcast' stan functions in R |
| enw_summarise_samples | Summarise posterior samples |
| enw_unset_cache | Unset Stan cache location |
| epinowcast | Nowcast using partially observed data |
| epinowcast-package | epinowcast: Flexible Hierarchical Nowcasting |
| extract_obs_metadata | Extract observation metadata |
| extract_sparse_matrix | Extract sparse matrix elements |
| germany_covid19_hosp | Hospitalisations in Germany by date of report and reference |
| get_internal_timestep | Get internal timestep |
| get_renviron_contents | Identify cache location in .Renviron |
| is.Date | Check an object is a Date |
| latest_obs_as_matrix | Convert latest observed data to a matrix |
| parse_formula | Parse a formula into components |
| plot.epinowcast | Plot method for epinowcast |
| re | Defines random effect terms using the lme4 syntax |
| remove_profiling | Remove profiling statements from a character vector... |
| remove_rw_terms | Remove random walk terms from a formula object |
| rw | Adds random walks with Gaussian steps to the model. |
| rw_terms | Finds random walk terms in a formula object |
| simulate_double_censored_pmf | Simulate daily double censored PMF |
| split_formula_to_terms | Split formula into individual terms |
| stan_fns_as_string | Read in a stan function file as a character string |
| subset_obs | Subset observations data table for either modelled dates or... |
| summary.epinowcast | Summary method for epinowcast |
| unset_cache_from_environ | Remove Cache Location Setting from '.Renviron' |
| update_inits | Update initial values for model fitting |
| write_stan_files_no_profile | Write copies of the .stan files of a Stan model and its... |
