Package index • wweval

All functions

add_horizons(): Add columns indicating the horizon to the scores

benchmark_performance(): Benchmark performance of wastewater and hospital admissions model foreast runs

clean_and_filter_nwss_data(): Initial subsetting of NWSS data

clean_ww_data(): Clean wastewater data

cleanup_secrets(): Cleans up environment when secrets and API information is no longer needed

combine_and_summarize_ww_data(): Combine and summarize wastewater data across all forecast dates and locations

combine_hub_and_local_wis(): Combine the hosp only real-time scores and cfa real- time scores from github

combine_outputs(): Combine outputs

compute_relative_crps(): Compute relative CRPS

create_hub_submissions(): Create hub submission files

create_mock_submission_scores(): Create mock submission scores

date_of_ww_data(): Date of wastewater data

eval_fit(): Fit model for evaluation

eval_postprocess(): Postprocess model for evaluation.

exclude_hosp_outliers(): Exclude hospital outliers

flusight_location_table: flusight_location_table dataset

format_for_hub(): Format quantiles for the current COVID Forecast Hub

format_scores_for_comparison(): Format the hosp only real time scores for comparison to the other real time models

get_add_ww_metadata(): Get additional wastewater metadata

get_avg_scores_model_horizon(): Get avg of scores by horizon

get_box_plot(): Get box plot by date and scenario

get_convergence_df(): Get convergence dataframe

get_date_locs_excluded(): Get forecast date locations that we excluded in the model run

get_diagnostic_flags(): Get diagnostic flags

get_epidemic_phases_from_rt(): Get epidemic phases from R(t)

get_filepath(): Get filepath

get_full_scores(): Get the scores for ever day for a particular location and forecast date

get_growth_rate_plot(): Compare growth rates in wastewater and hospital admissions data

get_heatmap_metadata(): Get a heatmap of the metadata of reasons for excluding forecasts from analysis

get_heatmap_metadata_hub(): Get a heatmap of the metadata of Hub models submitted

get_heatmap_relative_wis(): Get heatmap of relative WIS

get_heatmap_scores(): Get heatmap of scores by scenario

get_ind_forecast_score(): Get an individual forecast score summary for a particular forecast date and location

get_input_hosp_data(): Get input hospital admissions data

get_input_ww_data(): Get input wastewater data

get_last_hosp_data_date(): Get last hospital admissions data point date

get_last_hosp_data_date_map(): Get a map of the location, forecast date, and last hospital admissions data date

get_loc_rel_crps(): Get the relative mean crps for a location

get_model_draws_w_data(): Get model draws combined with input and evaluation data

get_model_path(): Get model path

get_n_states_improved_plot(): Get bar chart of the number of states improved compared to without wastewater over each forecast date

get_plot_bias_over_time(): Get a plot of bias over time

get_plot_comb_perf_heatmap(): Plot a heatmap of the avg forecast performance by locations and forecast date for the head-to-head comparison

get_plot_hosp_data_comparison(): Get plot of hospital admissions data compared to model draws

get_plot_hub_perf_heatmap(): Plot a heatmap of the avg forecast performance by locations and forecast date for the Hub submissions

get_plot_hub_performance(): Get plot of overall hub performance

get_plot_quantile_comparison(): Get plot quantile comparison

get_plot_raw_scores(): Get plot raw scores

get_plot_rel_crps_distrib(): Get a density plot of the relative CRPS distribution

get_plot_rel_crps_heatmap(): Plot a heatmap of the relative crps by locations and forecast date for the head-to-head comparison

get_plot_rel_wis_distrib(): Get a density plot of the relative WIS distribution

get_plot_score_by_horizon_t(): Get plot of scores by horizon over time

get_plot_scores_w_data(): Get plot scores with evaluation data overlaid

get_plot_summarized_scores(): Get plot summarized scores

get_plot_theme(): Get standardized plot theme to add to figures

get_plot_wis_over_time(): Get plot of WIS over time

get_plot_ww_data_comparison(): Get plot of wastewater data compared to model draws

get_qq_plot(): Get quantile-quantile plot

get_raw_output_suffix(): Generate a standard format output suffix for saving raw output for a location/forecast date/scenario trio.

get_rel_wis_all_time(): Get the relative wis from the hub formatted

get_rel_wis_real_time(): Get the relative wis for the real time scores

get_scenario_site_ids(): Get scenario site ids

get_scores_from_quantiles(): Get the scores for every day for a location, forecast date, and scenario from the quantiles during the forecast period

get_secret(): Interface for getting information needed for API interfacing

get_state_level_quantiles(): Get quantiles for state-level generated quantities

get_state_level_ww_quantiles(): Get quantiles for site-lab level wastewater

get_stats_imp_forecasts_wis(): Get stats on number of improved forecasts in real time from wis

get_stats_improved_forecasts(): Get stats on number of improved forecasts

get_summary_metadata(): Get a summary table of the number of forecasts excluded for each reason

get_summary_table_fig3(): Get a summary of a single states crps

get_summary_ww_table(): Get wastewater data summary tables

get_table_sufficient_ww(): Get table of location-forecast dates with sufficient wastewater

get_ww_data_flags(): Get table of location-forecast dates with sufficient wastewater

load_data_and_summarize(): Load data and summarize metadata

loc_abbr_to_flusight_code(): Convert a two-letter location abbreviation to a two-character FluSight location code

make_baseline_score_table(): Make baseline score table

make_df(): Make dataframe

make_fig2(): Make figure 2

make_fig2_ct(): Make concentration fit and forecast figure

make_fig2_ct_supp(): Make concentration fit and forecast figure for supplement

make_fig2_hosp_t(): Make a plot comparing the fit and forecasted hospital admissions from the wastewater and hospital admissions model for a few example states

make_fig3(): Title

make_fig3_crps_underlay_fig(): Make CRPS underlay figure

make_fig3_forecast_comp_fig(): Make hospital forecast comparison figure

make_fig3_single_loc_comp(): Make head to head CRPS distribution comparison plot for a single location

make_fig4(): Make Figure 4

make_fig4_admissions_overall(): Make a figure of overall admissions for context

make_fig4_avg_crps_over_time(): Plot average CRPS over time for model comparison

make_fig4_avg_wis_over_time(): Plot average WIS over time for model comparison

make_fig4_heatmap_rel_wis(): Get a plot of the relative wis from the real-time models

make_fig4_pct_better_w_ww(): Make a figure of the percent of locations with a better forecast with ww over time

make_fig4_rel_crps_by_location(): Make figure that stratifies scores by location across forecast dates

make_fig4_rel_crps_by_phase(): Make figure that plots distribution of relative crps stratified by epidemic phase

make_fig4_rel_crps_over_time(): Make a CRPS density plot for a subset of locations

make_fig4_rel_crps_overall(): Make figure that stratifies across location and forecast dates

make_fig4_rel_wis_by_location(): Make figure that stratifies scores by location across forecast dates

make_fig4_rel_wis_over_time(): Make a CRPS density plot for a subset of locations

make_fig4_results_table(): Make a summary of the with and without wastewater comparison scores

make_fig5(): Make Fig 5

make_fig5_average_wis(): Get plot of WIS over time

make_fig5_bar_chart(): Make plot of WIS scores in Hub models overall

make_fig5_density_rank(): Make a figure of the distribution of standardized WIS rank

make_fig5_heatmap_relative_wis(): Make a heatmap of relative WIS across locations

make_fig5_hub_performance(): Get plot of overall hub performance, grouped by period

make_fig5_qq_plot(): Make a quantile quantile plot for the Hub

make_fig5_table_and_plot(): Make summary table of WIS scores in Hub models overall

make_plot_coverage_range(): Plot coverage at specified ranges

make_qq_plot_overall(): Make a qq plot

make_sfig_crps_by_phase(): Make figure that plots distribution of absolute crps stratified by epidemic phase

nhsn_soda_query(): Construct a Socrata open data API (SODA) query for the NSHN dataset

order_horizons(): Get the order of the categorical horizons for plotting

order_locations(): Get the order of the locations for plotting

order_periods(): Get the order of the time periods for plotting

order_phases(): Get the order of the categorical horizons for plotting

plot_benchmarks(): Plot benchmark summaries

plot_components(): Get plot components (colors for now)

plot_quantiles(): Plot a timeseries of quantiles

postprocess_successful_fit(): Postprocess a successful eval fitting job.

pull_and_write_hosp_data(): Pull and save the current state of NHSN data on HealthData.gov

pull_nhsn(): Pull NHSN data from HealthData.gov

query_and_select_models(): Query Zoltar for models to include in the analysis

save_table(): Save table

score_hub_submissions(): Score hub submissions

score_real_time_outputs(): Load in and score the real-time outputs

setup_secrets(): Handles values needed to retrieve data from APIs to run pipeline

soql_is_in(): Return a soql::soql_where() construct for a given column being in a list of values

summarize_std_rank(): Summarize standardize rank with medians and 25th,75th percentiles

to_rds_with_suffix(): Save an object to .rds in a given output_dir, with programmatic naming.

trajectories_to_quantiles(): Aggregate individual trajectory timeseries or forecasts to quantile timeseries or forecasts