Package index • wweval

All functions

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

assert_needed_env_vars(): Assert that needed environment variables are set

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

check_any_flags(): Check whether a model run had any flags.

clean_and_filter_nwss_data(): Initial subsetting of NWSS data

clean_flag_df(): Clean flags from a real-time forecast

clean_ww_data(): Clean wastewater data

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

compose_example_scores_fig(): Compose figure showing examples of forecasts and their scores.

compose_hub_fig(): Functions for creating multi-panel composite figures Make a figure showing comparisons between CFA models and other COVIDHub models

compose_pred_actual_fig(): Compose figure showing predictions and observations for three example forecasts.

compose_rel_performance_fig(): Make a multi-panel figure summarizing relative performance.

compute_flags(): Compute diagnostic flags from raw stanfit objects

compute_forecast_differences(): Compute the the posterior of the difference between model predictions.

create_hub_submissions(): Create hub submission files

create_mock_submission_scores(): Create mock submission scores

date_of_ww_data(): Date of wastewater data

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

.relative_metric_display_name(): Internal function for display names of relative metrics

eval_fit(): Fit model for evaluation

eval_postprocess(): Postprocess model for evaluation.

exclude_hosp_outliers(): Exclude hospital outliers

file_exists_object_with_suffix(): Check that a file for corresponding to a programmatically-named project output object exists.

fit_hosp_trend(): Fit a hosp trend with BRMS

fit_recent_trends(): Fit recent hospital admission and wastewater trends using BRMS

fit_ww_trend(): Fit lab-site-level recent wastewater trends with BRMS.

flusight_location_table: flusight_location_table dataset

forecast_interval_coverage_plot(): Plot interval coverage at specified ranges

forecast_output_path(): Standard path to an output directory for a specific forecast

forecast_qq_plot(): Functions for plots that assess forecast calibration Get quantile-quantile plot

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

geom_decomposed_scores(): Composite geometric object for barplots of scores decomposed into undeprediction, overprediction, and dispersion components

get_add_ww_metadata(): Get additional wastewater metadata

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_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_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_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_object_existence_checker(): Generate a function for checking whether .rds files for raw output objects exist for a location/forecast date/scenario trio.

get_object_loader(): Generate a function for loading raw output objects for a location/forecast date/scenario trio.

get_object_saver(): Generate a function for saving raw output objects for a location/forecast date/scenario trio.

get_plot_bias_over_time(): Get a plot of bias over time

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

get_plot_quantile_comparison(): Get plot quantile comparison

get_plot_raw_scores(): Get plot raw scores

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

get_plot_scores_and_forecasts(): Got a plot of forecasts and scores for a single location and date

get_plot_scores_w_data(): Get plot scores with evaluation data overlaid

get_plot_sites_vs_performance(): Make a scatterplot comparing number of wastewater sites to model performance.

get_plot_summarized_scores(): Get plot summarized scores

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

get_plot_ww_data(): Plot wastewater evaluation data

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

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

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_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_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

heatmap_scores_by_loc_date(): Plot a heatmap of avg forecast performance by location and forecast date

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

load_data_and_summarize(): Load data and summarize metadata

load_real_time_forecast(): Load a real-time forecast

load_real_time_quantile_fcsts(): Load real-time quantile outputs

make_baseline_score_table(): Make baseline score table

make_df(): Make dataframe

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

multi_location_crps_figure(): Generate bar plots of CRPS for each model in different locations

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

order_col(): Light wrapper function for converting a dataframe column to an ordered factors.

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_crps_underlay(): Make CRPS underlay figure

plot_forecast_comparison_t(): Compare two hospital admissions forecasts over time.

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

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

plot_model_hosp_t_comparison(): Make a plot comparing the fit and forecasted hospital admissions from the wastewater-informed and hospital admissions-only models.

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

plot_pred_actual_ww(): Make concentration fit and forecast figure

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

plot_rel_score_distribution(): Get a dotsinterval plot of a relative score distribution for individual location/forecast-date forecast problems.

plot_rel_score_dists(): Make a dotsinterval plot of relative scores stratified by specified variables.

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

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

plot_score_decomposed_bars(): Barplot of WIS or CRPS decomposed into overprediction, underprediction, and dispersion

plot_score_scatter(): Plot a scatterplot of scores comparing those of one model to those of another, for a given stratification.

plot_score_t(): Plotting functions for absolute forecast scores Plot average score over time for model comparison

plot_scores_by_scenario(): Barplot of scores by scenario

plot_total_admissions(): Make a figure of overall admissions (summed across locations) for context

plot_ww_conc_by_site(): Make concentration fit and forecast figure

postprocess_successful_fit(): Postprocess a successful eval fitting job.

process_recent_trend_fits(): Process BRMS log-linear fits of recent trends

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

pull_daily_nhsn(): Pull daily NHSN data from HealthData.gov

pull_hub_forecasts(): Pull hub submissions and create a scorable table as the output of scoringutils::as_forecast_quantile().

quantile_metrics: Metrics to use for quantile scores

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

read_rds_with_suffix(): Load an object from an .rds serialized file in a given output_dir, with programmatic naming.

relative_wis_histogram(): Plot a histogram of individual forecast relative WIS values

sample_metrics: Metrics to use for quantile scores

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

save_table(): Save table

scale_alpha_score_component(): ggplot scale for fill alphas by name of WIS/CRPS score component.

scale_fill_model() scale_color_model(): ggplot discrete scales for forecast models

score_hub_forecasts(): Score hub forecasts

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

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

score_samples(): Get the scores for every day for a particular location and forecast date

select_like(): Select columns from one dataframe based on the column spec of a second dataframe

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

three_location_forecast_fig(): Make a figure showing three example hospital admissions forecast timeseries and associated wastewater concentration timeseries.

with_dependencies(): Helper function to note targets dependencies not explicitly noted in the function call