Function reference • covidHubUtils

All functions
`aggregate_to_weekly()`	Aggregate daily data to weekly data
`align_forecasts()`	Add reference dates and relative horizons to a dataframe of forecasts
`align_forecasts_one_temporal_resolution()`	Internal function that add reference dates and relative horizons to a dataframe of forecasts. This function requires that the forecasts data frame contains only forecasts one temporal_resolution, i.e., only at the daily resolution or the weekly resolution.
`as_covid_hub_forecasts()`	Reformat model outputs stored as a `model_output_tbl` class (or similar) to that of a `data.frame` formatted according to standards of the COVID-19 Forecasting Hub which can be processed by functions from the `covidHubUtils` package such as `score_forecasts()` or `plot_forecasts()`. The supplied `model_output_tbl` should have columns defining properties akin to reference dates, locations, horizons, and targets.
`calc_cramers_dist_equal_space()`	Approximate the Cramer’s distance between a pair of distributions F and G that are represented by a collection of equally-spaced quantiles.
`calc_cramers_dist_one_model_pair()`	Calculate the approximated Cramer’s distance between a pair of distributions F and G that are represented by a collection of quantiles using a specific approximation rule.
`calc_cramers_dist_unequal_space()`	Approximate the Cramer’s distance between a pair of distributions F and G that are represented by a collection of unequally-spaced quantiles.
`calc_forecast_week_end_date()`	Calculate end date for the week a forecast was made.
`calc_submission_due_date()`	Calculate the submission date that corresponds to a given forecast date
`calc_target_end_date()`	Calculate end date for a forecast is targeting.
`calc_target_week_end_date()`	Calculate end date for the week a forecast is targeting.
`covidHubUtils` `covidHubUtils-package`	covidHubUtils - Utility functions for the COVID-19 forecast hub
`date_to_datetime()`	Create a datetime by appending time and/or UTC timezone to the given date string, if necessary
`date_to_week_end_date()`	Calculate the date of the Saturday that ends the MMWR epidemic week for the given date,offset a specified number of epidemic week from a specified date
`download_raw_nytimes()`	Download historical raw truth data from NYTimes and write to CSV files. Note: updates to the NYTimes data stopped in March 2023.
`get_all_models()`	Get all valid model names
`get_forecast_file_path()`	Generate paths to forecast files submitted on a range of forecast dates from selected models
`get_hub_locations()`	Create data/hub_locations.rda for loading data from `zoltar` and `covidData`
`get_model_designations()`	Get model designations from metadata
`get_model_forecast_history_local_zoltar()`	Get forecast submission history of a specified model from local zoltar sqlite file
`get_model_metadata()`	Get Hub model metadata
`get_models_local_zoltar()`	Get id and abbrevations of all models available in a specified project from local zoltar sqlite file
`get_plot_forecast_data()`	Combine `load_truth()` and `pivot_forecasts_wider()`
`get_truth_path()`	Construct the file path to a truth file
`get_valid_target_list()`	Create data/hub_targets_us.rda and data/hub_targets_ecdc.rda
`get_zoltar_project_id_local_zoltar()`	Get Zoltar project id from local zoltar sqlite file
`get_zoltar_project_url()`	Get Zoltar project URL
`hub_locations` `hub_locations`	Information on locations in the COVID-19 Forecast Hub
`hub_locations_ecdc`	Available locations in the ECDC Hub
`hub_locations_flusight`	Available locations in the FluSight Hub
`hub_targets_ecdc`	Available targets in the ECDC Hub
`hub_targets_flusight`	Available targets in the FluSight Hub
`hub_targets_us`	Available targets in the US Hub
`join_with_hub_locations()`	Add stored information about location name and population by joining the data with the correct stored location data
`load_forecast_files_repo()`	Read in a set of forecast files from a repository without rows having NULLs in value column.
`load_forecasts()`	Load all available forecasts submitted around forecast dates from Zoltar, local Zoltar module or local hub repo.
`load_forecasts_local_zoltar()`	Load all available forecasts submitted on `forecast_dates` from local Zoltar module.
`load_forecasts_repo()`	Load all available forecasts submitted on `forecast_dates` from a local clone of `reichlab/covid19-forecast-hub` repo.
`load_forecasts_zoltar()`	Load all available forecasts submitted on `forecast_dates` from Zoltar.
`load_from_coviddata()`	load truth data from covidData
`load_from_hub_repo()`	load truth data from a local clone of forecast hub repo
`load_latest_forecasts()`	Load covid forecasts from local hub repo or Zoltar. Return the most recent forecast from each model within forecast_date_window_size days of the last_forecast_date
`load_latest_forecasts_repo()`	Load the most recent forecasts of all that were submitted on `forecast_dates` from a local clone of `reichlab/covid19-forecast-hub` repo.
`load_latest_forecasts_zoltar()`	Load the most recent forecasts of all that were submitted on `forecast_dates` from Zoltar.
`load_truth()`	Load truth data under multiple target variables from multiple truth sources
`name_to_fips()`	Get FIPS or CBSA codes from county or metropolitan area locations
`pivot_forecasts_wider()`	Return a data frame of forecasts with predictive quantiles in columns.
`plot_forecast()`	Plot forecasts and optional truth for only one selected target variable. Faceted plots for multiple models, locations and forecast dates are supported with specified facet formula.
`plot_forecasts()`	Plot forecasts and optional truth for only one selected target variable.
`preprocess_hospitalization()`	Preprocess raw hospitalization data into Cumulative/Incident hospitalizations and write to CSVs
`preprocess_jhu()`	Preprocess historical raw truth data from JHU CSSE into Cumulative/Incident - Deaths/Cases and write to CSVs. Note: updates to the JHU CSSE data stopped in March 2023.
`preprocess_nytimes()`	Preprocess raw truth data from NYTimes into Cumulative/Incident - Deaths/Cases and write to CSVs. Note: updates to the NYTimes data stopped in March 2023.
`preprocess_visualization_truth()`	Preprocess raw truth data from JHU CSSE into Cumulative/Incident - Deaths/Cases for visualization purpose and write to JSON files. Note: updates to the JHU CSSE data stopped in March 2023.
`reformat_forecasts()`	Reformat forecast data frame returned from zoltar query This function will throw a warning and return an empty data.frame with columns `model`, `forecast_date`, `location`, `type`, `quantile` and `value`, when no forecasts are available in `zoltar_query_result`.
`score_forecasts()`	Score forecasts
`setup_zoltar_connection()`	Set up Zoltar connection

Reference

All functions