Man pages for reichlab/cdcfluutils
Utility functions for CDC flu forecasts for team Kernel of Truth
| assemble_predictions | Assemble leave-one-season-out or test phase predictions made... |
| assemble_stacking_inputs | Assemble a data frame of inputs to stacking |
| calc_median_from_binned_probs | Calculation of median value from binned probability... |
| cdcfluutils | cdcfluutils - Utility functions for CDC flu forecasts for... |
| compute_competition_log_score | Calculate "log scores" for the purpose of the competition -... |
| create_ILI_revision_tables | create tables of ILI trajectory revisions by epiweek |
| download_and_preprocess_flu_data | Download and preprocess the latest CDC flu data, both... |
| download_and_preprocess_hosp_data | Download and preprocess the latest CDC hospitalization data |
| download_and_preprocess_state_flu_data | Download and preprocess the latest CDC flu data, state-level |
| fetch_delphi_data_multi_issue | Fetch and combine data from the Delphi Epidata API |
| first_season_week_below_baseline | Find the first season week incidence goes below baseline and... |
| fit_kde_log_peak_week_inc | Estimate KDE for LOG peak week incidence |
| fit_kde_onset_week | Estimate KDE for onset week |
| fit_kde_peak_week | Estimate KDE for peak week |
| fit_kde_weekly_inc | Fit a GAM for weekly incidence |
| fit_kernel_smoothed_stacked_model_fixed_bw | Estimate weights for a linear combination of predictive... |
| fit_region_kdes | Fits and saves KDE models for all region-year combinations |
| fit_region_sarima | Estimate SARIMA model using data up to but not including... |
| fit_stacked_model | Fit a stacking model that assigns weights to component models... |
| fit_unregularized_stacked_model | Estimate "optimal" unregularized weights for a linear... |
| flu_data | Regional influenza incidence in the US (1997 - 2019) |
| flu_onset_baselines | Flu season "onset thresholds" from the US CDC. |
| get_inc_bin | return the bin name for a given incidence |
| get_num_MMWR_weeks_in_first_season_year | return integer that's either 52 or 53: number of weeks in the... |
| get_num_MMWR_weeks_in_year | return integer that's either 52 or 53: number of MMWR weeks... |
| get_observed_seasonal_quantities | Compute season onset, peak week, and peak incidence |
| get_official_observed_seasonal_quantities | Compute season onset, peak week, and peak incidence |
| get_onset_baseline | Get the onset baseline for a combination of region and season |
| get_onset_week | Utility function to compute onset week based on a trajectory... |
| get_partially_revised_ilinet | Wrapper function around epiforecast::mimicPastEpidataDF to... |
| get_submission_one_region_via_trajectory_simulation | Get samples in for each prediction target in a predx data... |
| historical_vars_regional | Variances of historical revisions to ilinet data |
| ILI_revision_tables | A list of historical revisions to ilinet data at the national... |
| logspace_add | Calculate log(exp(logx) + exp(logy)) in a somewhat... |
| logspace_sub | Calculate log(exp(logx) - exp(logy)) in a somewhat... |
| logspace_sub_matrix_rows | Calculate logspace difference of matrix rows in a somewhat... |
| logspace_sum | Calculate log(sum(exp(logx))) in a somewhat numerically... |
| logspace_sum_matrix_rows | Calculate logspace summation of matrix rows in a somewhat... |
| make_kde_region_prediction | Make a KDE prediction for one region |
| make_one_kde_prediction_file | Wrapper for prediction of a single time-point from KDE fits |
| make_predictions_plots | Make plots of prediction submissions for flu contest: so far,... |
| merge_predx_samples | merge predx samples by location and target |
| mmwr_week_to_season | get season in which an mmwr week falls |
| mmwr_week_to_season_week | Convert mmwr week to season week |
| move_k_week_ahead | Utility function to move k week ahead |
| my_plot_weekahead | Plots Week Ahead Forecasts |
| nat_reg_flu_data_with_backfill | National and Regional influenza incidence in the US (1997 -... |
| pick_week | For each week specified by a vector of dates giving the week... |
| predict_kde_log_peak_week_inc | Compute predictive distribution for peak week incidence from... |
| predict_kde_log_weekly_inc | Compute predictive distribution for weekly incidence from GAM... |
| predict_kde_onset_week | Functions for predicting from KDE fits |
| predict_kde_peak_week | Compute predictive distribution for peak week from KDE fit |
| predict_region_kde | Wrapper for prediction and evaluation of KDE fits |
| predx_to_submission_df | Converts predx format forecasts into a data frame suitable... |
| preprocess_and_augment_trajectory_samples | Given a set of sampled trajectories for future disease... |
| preprocess_reg_data_for_GPthingy_stan | Preprocess state level flu data and set up a data object to... |
| rRevisedILI | sample revised ILI trajectories |
| rRevisedILI_cached | sample revised ILI trajectories |
| rRevisedILI_fast | sample revised ILI trajectories using normal approximation |
| sample_predictive_trajectories_arima_wrapper | A wrapper around simulate.sarimaTD suitable for use as the... |
| season_week_to_mmwr_year | return mmwr year corresponding to a given season week |
| season_week_to_year_week | Convert season week to year week |
| simulate_trajectories_kcde | Simulate predictive distributions from KCDE/copulas model;... |
| state_flu_data | State-level influenza incidence in the US (1997 - 2018) |
| to_standard_location_code | Convert a location name to standardized name as given here:... |
| weighted_combine_predictions | Compute a weighted combination of prediction results |
| year_week_to_season_week | Convert year week to season week (deprecated - use... |
