diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..b33858a --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,9 @@ +template: + includes: + in_header: | + + + diff --git a/docs/404.html b/docs/404.html index 9c6542a..621b090 100644 --- a/docs/404.html +++ b/docs/404.html @@ -16,6 +16,12 @@ + + + diff --git a/docs/articles/covidHubUtils-overview.html b/docs/articles/covidHubUtils-overview.html index 40f98c7..34aae74 100644 --- a/docs/articles/covidHubUtils-overview.html +++ b/docs/articles/covidHubUtils-overview.html @@ -17,6 +17,12 @@ + + + diff --git a/docs/articles/covidHubUtils-zoltar_sqlite_setup.html b/docs/articles/covidHubUtils-zoltar_sqlite_setup.html index 737ea13..2d4ff60 100644 --- a/docs/articles/covidHubUtils-zoltar_sqlite_setup.html +++ b/docs/articles/covidHubUtils-zoltar_sqlite_setup.html @@ -17,6 +17,12 @@ + + + diff --git a/docs/articles/index.html b/docs/articles/index.html index f8b80cd..ebedf96 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -2,7 +2,13 @@ Articles • covidHubUtils + + + +
diff --git a/docs/authors.html b/docs/authors.html index 30f7987..a1eec5a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -2,7 +2,13 @@ Authors and Citation • covidHubUtils + + + +
diff --git a/docs/index.html b/docs/index.html index 5414434..a1b6c99 100644 --- a/docs/index.html +++ b/docs/index.html @@ -20,6 +20,12 @@ + + + diff --git a/docs/news/index.html b/docs/news/index.html index 74b3538..2fc7d09 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -2,7 +2,13 @@ Changelog • covidHubUtils + + + +
diff --git a/docs/reference/aggregate_to_weekly.html b/docs/reference/aggregate_to_weekly.html index 54b9f55..842d3b9 100644 --- a/docs/reference/aggregate_to_weekly.html +++ b/docs/reference/aggregate_to_weekly.html @@ -3,7 +3,13 @@ previous Saturday in that week"> + + + +
diff --git a/docs/reference/align_forecasts.html b/docs/reference/align_forecasts.html index f2edf85..f4c716d 100644 --- a/docs/reference/align_forecasts.html +++ b/docs/reference/align_forecasts.html @@ -2,7 +2,13 @@ Add reference dates and relative horizons to a dataframe of forecasts — align_forecasts • covidHubUtils + + + +
diff --git a/docs/reference/align_forecasts_one_temporal_resolution.html b/docs/reference/align_forecasts_one_temporal_resolution.html index 9b16ca7..6847787 100644 --- a/docs/reference/align_forecasts_one_temporal_resolution.html +++ b/docs/reference/align_forecasts_one_temporal_resolution.html @@ -11,7 +11,13 @@ at the daily resolution or the weekly resolution."> + + + +
diff --git a/docs/reference/as_covid_hub_forecasts.html b/docs/reference/as_covid_hub_forecasts.html index df89974..2415552 100644 --- a/docs/reference/as_covid_hub_forecasts.html +++ b/docs/reference/as_covid_hub_forecasts.html @@ -17,7 +17,13 @@ reference dates, locations, horizons, and targets."> + + + +
diff --git a/docs/reference/calc_cramers_dist_equal_space.html b/docs/reference/calc_cramers_dist_equal_space.html index b292f47..05ae0be 100644 --- a/docs/reference/calc_cramers_dist_equal_space.html +++ b/docs/reference/calc_cramers_dist_equal_space.html @@ -5,7 +5,13 @@ F and G that are represented by a collection of equally-spaced quantiles."> + + + +
diff --git a/docs/reference/calc_cramers_dist_one_model_pair.html b/docs/reference/calc_cramers_dist_one_model_pair.html index 158da29..c37ad6d 100644 --- a/docs/reference/calc_cramers_dist_one_model_pair.html +++ b/docs/reference/calc_cramers_dist_one_model_pair.html @@ -8,7 +8,13 @@ approximation rule."> + + + +
diff --git a/docs/reference/calc_cramers_dist_unequal_space.html b/docs/reference/calc_cramers_dist_unequal_space.html index 647f38a..46c9279 100644 --- a/docs/reference/calc_cramers_dist_unequal_space.html +++ b/docs/reference/calc_cramers_dist_unequal_space.html @@ -5,7 +5,13 @@ F and G that are represented by a collection of unequally-spaced quantiles."> + + + +
diff --git a/docs/reference/calc_forecast_week_end_date.html b/docs/reference/calc_forecast_week_end_date.html index f579bb9..0134358 100644 --- a/docs/reference/calc_forecast_week_end_date.html +++ b/docs/reference/calc_forecast_week_end_date.html @@ -8,7 +8,13 @@ Saturday of EW12 (the current week) for Tuesday through Saturday of EW12.'> + + + +
diff --git a/docs/reference/calc_submission_due_date.html b/docs/reference/calc_submission_due_date.html index 407b312..bcd2ce6 100644 --- a/docs/reference/calc_submission_due_date.html +++ b/docs/reference/calc_submission_due_date.html @@ -3,7 +3,13 @@ finds the nearest Monday for which a submission could have been made"> + + + +
diff --git a/docs/reference/calc_target_end_date.html b/docs/reference/calc_target_end_date.html index 10de149..99745cd 100644 --- a/docs/reference/calc_target_end_date.html +++ b/docs/reference/calc_target_end_date.html @@ -2,7 +2,13 @@ Calculate end date for a forecast is targeting. — calc_target_end_date • covidHubUtils + + + +
diff --git a/docs/reference/calc_target_week_end_date.html b/docs/reference/calc_target_week_end_date.html index fc5dd4f..774fcd6 100644 --- a/docs/reference/calc_target_week_end_date.html +++ b/docs/reference/calc_target_week_end_date.html @@ -9,7 +9,13 @@ EW12.'> + + + +
diff --git a/docs/reference/covidHubUtils.html b/docs/reference/covidHubUtils.html index 3c22b39..30ab963 100644 --- a/docs/reference/covidHubUtils.html +++ b/docs/reference/covidHubUtils.html @@ -2,7 +2,13 @@ covidHubUtils - Utility functions for the COVID-19 forecast hub — covidHubUtils • covidHubUtils + + + +
diff --git a/docs/reference/date_to_datetime.html b/docs/reference/date_to_datetime.html index e8cf6fe..829732c 100644 --- a/docs/reference/date_to_datetime.html +++ b/docs/reference/date_to_datetime.html @@ -7,7 +7,13 @@ Then, return the converted date time in UTC timezone.'> + + + +
diff --git a/docs/reference/date_to_week_end_date.html b/docs/reference/date_to_week_end_date.html index 5cc9593..18081b8 100644 --- a/docs/reference/date_to_week_end_date.html +++ b/docs/reference/date_to_week_end_date.html @@ -8,7 +8,13 @@ of epidemic week from a specified date"> + + + +
diff --git a/docs/reference/download_raw_nytimes.html b/docs/reference/download_raw_nytimes.html index 156c6c3..9437af8 100644 --- a/docs/reference/download_raw_nytimes.html +++ b/docs/reference/download_raw_nytimes.html @@ -5,7 +5,13 @@ updates to the NYTimes data stopped in March 2023."> + + + +
diff --git a/docs/reference/download_raw_usafacts.html b/docs/reference/download_raw_usafacts.html index 1638f1d..4246c0b 100644 --- a/docs/reference/download_raw_usafacts.html +++ b/docs/reference/download_raw_usafacts.html @@ -2,7 +2,13 @@ Download raw truth data from USAFacts — download_raw_usafacts • covidHubUtils + + + +
diff --git a/docs/reference/get_all_models.html b/docs/reference/get_all_models.html index c360976..c297e7d 100644 --- a/docs/reference/get_all_models.html +++ b/docs/reference/get_all_models.html @@ -2,7 +2,13 @@ Get all valid model names — get_all_models • covidHubUtils + + + +
diff --git a/docs/reference/get_forecast_file_path.html b/docs/reference/get_forecast_file_path.html index 156a9c4..cf9c1ff 100644 --- a/docs/reference/get_forecast_file_path.html +++ b/docs/reference/get_forecast_file_path.html @@ -2,7 +2,13 @@ Generate paths to forecast files submitted on a range of forecast dates from selected models — get_forecast_file_path • covidHubUtils + + + +
diff --git a/docs/reference/get_hub_locations.html b/docs/reference/get_hub_locations.html index 9283a21..4531375 100644 --- a/docs/reference/get_hub_locations.html +++ b/docs/reference/get_hub_locations.html @@ -2,7 +2,13 @@ Create data/hub_locations.rda for loading data from zoltar and covidData — get_hub_locations • covidHubUtils + + + +
diff --git a/docs/reference/get_model_designations.html b/docs/reference/get_model_designations.html index 94050ee..bf26301 100644 --- a/docs/reference/get_model_designations.html +++ b/docs/reference/get_model_designations.html @@ -2,7 +2,13 @@ Get model designations from metadata — get_model_designations • covidHubUtils + + + +
diff --git a/docs/reference/get_model_forecast_history_local_zoltar.html b/docs/reference/get_model_forecast_history_local_zoltar.html index 740b79c..d0fff15 100644 --- a/docs/reference/get_model_forecast_history_local_zoltar.html +++ b/docs/reference/get_model_forecast_history_local_zoltar.html @@ -2,7 +2,13 @@ Get forecast submission history of a specified model from local zoltar sqlite file — get_model_forecast_history_local_zoltar • covidHubUtils + + + +
diff --git a/docs/reference/get_model_metadata.html b/docs/reference/get_model_metadata.html index ff19263..cc5ea04 100644 --- a/docs/reference/get_model_metadata.html +++ b/docs/reference/get_model_metadata.html @@ -2,7 +2,13 @@ Get Hub model metadata — get_model_metadata • covidHubUtils + + + +
diff --git a/docs/reference/get_models_local_zoltar.html b/docs/reference/get_models_local_zoltar.html index 93c3aec..63cf71c 100644 --- a/docs/reference/get_models_local_zoltar.html +++ b/docs/reference/get_models_local_zoltar.html @@ -5,7 +5,13 @@ from local zoltar sqlite file"> + + + +
diff --git a/docs/reference/get_plot_forecast_data.html b/docs/reference/get_plot_forecast_data.html index c2d5d74..4a948dd 100644 --- a/docs/reference/get_plot_forecast_data.html +++ b/docs/reference/get_plot_forecast_data.html @@ -2,7 +2,13 @@ Combine load_truth() and pivot_forecasts_wider() — get_plot_forecast_data • covidHubUtils + + + +
diff --git a/docs/reference/get_truth_path.html b/docs/reference/get_truth_path.html index 13feed8..b3c89e7 100644 --- a/docs/reference/get_truth_path.html +++ b/docs/reference/get_truth_path.html @@ -2,7 +2,13 @@ Construct the file path to a truth file — get_truth_path • covidHubUtils + + + +
diff --git a/docs/reference/get_valid_target_list.html b/docs/reference/get_valid_target_list.html index 17a5388..2a1e9bc 100644 --- a/docs/reference/get_valid_target_list.html +++ b/docs/reference/get_valid_target_list.html @@ -2,7 +2,13 @@ Create data/hub_targets_us.rda and data/hub_targets_ecdc.rda — get_valid_target_list • covidHubUtils + + + +
diff --git a/docs/reference/get_zoltar_project_id_local_zoltar.html b/docs/reference/get_zoltar_project_id_local_zoltar.html index 564f1e1..428b133 100644 --- a/docs/reference/get_zoltar_project_id_local_zoltar.html +++ b/docs/reference/get_zoltar_project_id_local_zoltar.html @@ -2,7 +2,13 @@ Get Zoltar project id from local zoltar sqlite file — get_zoltar_project_id_local_zoltar • covidHubUtils + + + +
diff --git a/docs/reference/get_zoltar_project_url.html b/docs/reference/get_zoltar_project_url.html index 4163684..ff6b8de 100644 --- a/docs/reference/get_zoltar_project_url.html +++ b/docs/reference/get_zoltar_project_url.html @@ -2,7 +2,13 @@ Get Zoltar project URL — get_zoltar_project_url • covidHubUtils + + + +
diff --git a/docs/reference/hub_locations.html b/docs/reference/hub_locations.html index f32cb25..e2fc3cc 100644 --- a/docs/reference/hub_locations.html +++ b/docs/reference/hub_locations.html @@ -2,7 +2,13 @@ Information on locations in the COVID-19 Forecast Hub — hub_locations • covidHubUtils + + + +
diff --git a/docs/reference/hub_locations_ecdc.html b/docs/reference/hub_locations_ecdc.html index a924fee..617b446 100644 --- a/docs/reference/hub_locations_ecdc.html +++ b/docs/reference/hub_locations_ecdc.html @@ -2,7 +2,13 @@ Available locations in the ECDC Hub — hub_locations_ecdc • covidHubUtils + + + +
diff --git a/docs/reference/hub_locations_flusight.html b/docs/reference/hub_locations_flusight.html index 9fb932e..5e86009 100644 --- a/docs/reference/hub_locations_flusight.html +++ b/docs/reference/hub_locations_flusight.html @@ -2,7 +2,13 @@ Available locations in the FluSight Hub — hub_locations_flusight • covidHubUtils + + + +
diff --git a/docs/reference/hub_targets_ecdc.html b/docs/reference/hub_targets_ecdc.html index 4accdfc..87320b9 100644 --- a/docs/reference/hub_targets_ecdc.html +++ b/docs/reference/hub_targets_ecdc.html @@ -2,7 +2,13 @@ Available targets in the ECDC Hub — hub_targets_ecdc • covidHubUtils + + + +
diff --git a/docs/reference/hub_targets_flusight.html b/docs/reference/hub_targets_flusight.html index 9c512b4..28d3ca6 100644 --- a/docs/reference/hub_targets_flusight.html +++ b/docs/reference/hub_targets_flusight.html @@ -2,7 +2,13 @@ Available targets in the FluSight Hub — hub_targets_flusight • covidHubUtils + + + +
diff --git a/docs/reference/hub_targets_us.html b/docs/reference/hub_targets_us.html index 96a484d..6276fcf 100644 --- a/docs/reference/hub_targets_us.html +++ b/docs/reference/hub_targets_us.html @@ -2,7 +2,13 @@ Available targets in the US Hub — hub_targets_us • covidHubUtils + + + +
diff --git a/docs/reference/index.html b/docs/reference/index.html index 66596e2..ffa60bb 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -2,7 +2,13 @@ Function reference • covidHubUtils + + + +
diff --git a/docs/reference/join_with_hub_locations.html b/docs/reference/join_with_hub_locations.html index 671c5e6..3ded4e6 100644 --- a/docs/reference/join_with_hub_locations.html +++ b/docs/reference/join_with_hub_locations.html @@ -5,7 +5,13 @@ data with the correct stored location data"> + + + +
diff --git a/docs/reference/load_forecast_files_repo.html b/docs/reference/load_forecast_files_repo.html index 323dad2..40b9eda 100644 --- a/docs/reference/load_forecast_files_repo.html +++ b/docs/reference/load_forecast_files_repo.html @@ -5,7 +5,13 @@ without rows having NULLs in value column."> + + + +
diff --git a/docs/reference/load_forecasts.html b/docs/reference/load_forecasts.html index 3dbe910..b1ec491 100644 --- a/docs/reference/load_forecasts.html +++ b/docs/reference/load_forecasts.html @@ -14,7 +14,13 @@ "> + + + +
diff --git a/docs/reference/load_forecasts_local_zoltar.html b/docs/reference/load_forecasts_local_zoltar.html index 4ab5c22..7793045 100644 --- a/docs/reference/load_forecasts_local_zoltar.html +++ b/docs/reference/load_forecasts_local_zoltar.html @@ -4,7 +4,13 @@ See http://reichlab.io/covidHubUtils/articles/covidHubUtils-zoltar_sqlite_setup.htmlvignette for more details."> + + + +
diff --git a/docs/reference/load_forecasts_repo.html b/docs/reference/load_forecasts_repo.html index 8bb8705..4b6cafc 100644 --- a/docs/reference/load_forecasts_repo.html +++ b/docs/reference/load_forecasts_repo.html @@ -6,7 +6,13 @@ locations, types and target."> + + + +
diff --git a/docs/reference/load_forecasts_zoltar.html b/docs/reference/load_forecasts_zoltar.html index 3ac907c..652bd97 100644 --- a/docs/reference/load_forecasts_zoltar.html +++ b/docs/reference/load_forecasts_zoltar.html @@ -4,7 +4,13 @@ locations, types and target."> + + + +
diff --git a/docs/reference/load_from_coviddata.html b/docs/reference/load_from_coviddata.html index d698d43..7f46b29 100644 --- a/docs/reference/load_from_coviddata.html +++ b/docs/reference/load_from_coviddata.html @@ -2,7 +2,13 @@ load truth data from covidData — load_from_coviddata • covidHubUtils + + + +
diff --git a/docs/reference/load_from_hub_repo.html b/docs/reference/load_from_hub_repo.html index f942fe9..47021d8 100644 --- a/docs/reference/load_from_hub_repo.html +++ b/docs/reference/load_from_hub_repo.html @@ -2,7 +2,13 @@ load truth data from a local clone of forecast hub repo — load_from_hub_repo • covidHubUtils + + + +
diff --git a/docs/reference/load_latest_forecasts.html b/docs/reference/load_latest_forecasts.html index 469e790..e8091fc 100644 --- a/docs/reference/load_latest_forecasts.html +++ b/docs/reference/load_latest_forecasts.html @@ -8,7 +8,13 @@ Please use load_forecasts() instead."> + + + +
diff --git a/docs/reference/load_latest_forecasts_repo.html b/docs/reference/load_latest_forecasts_repo.html index 0ede38f..86b2b15 100644 --- a/docs/reference/load_latest_forecasts_repo.html +++ b/docs/reference/load_latest_forecasts_repo.html @@ -4,7 +4,13 @@ on forecast_dates from a local clone of reichlab/covid19-forecast-hub repo. — load_latest_forecasts_repo"> + + + +
diff --git a/docs/reference/load_latest_forecasts_zoltar.html b/docs/reference/load_latest_forecasts_zoltar.html index c5bb988..7179ec8 100644 --- a/docs/reference/load_latest_forecasts_zoltar.html +++ b/docs/reference/load_latest_forecasts_zoltar.html @@ -6,7 +6,13 @@ locations, types and target."> + + + +
diff --git a/docs/reference/load_truth.html b/docs/reference/load_truth.html index 1a6d623..e214996 100644 --- a/docs/reference/load_truth.html +++ b/docs/reference/load_truth.html @@ -7,7 +7,13 @@ for all US locations."> + + + +
diff --git a/docs/reference/name_to_fips.html b/docs/reference/name_to_fips.html index 7214984..c8a08e8 100644 --- a/docs/reference/name_to_fips.html +++ b/docs/reference/name_to_fips.html @@ -2,7 +2,13 @@ Get FIPS or CBSA codes from county or metropolitan area locations — name_to_fips • covidHubUtils + + + +
diff --git a/docs/reference/pivot_forecasts_wider.html b/docs/reference/pivot_forecasts_wider.html index fd5e1e5..f729757 100644 --- a/docs/reference/pivot_forecasts_wider.html +++ b/docs/reference/pivot_forecasts_wider.html @@ -2,7 +2,13 @@ Return a data frame of forecasts with predictive quantiles in columns. — pivot_forecasts_wider • covidHubUtils + + + +
diff --git a/docs/reference/plot_forecast.html b/docs/reference/plot_forecast.html index 00f024b..a8d1732 100644 --- a/docs/reference/plot_forecast.html +++ b/docs/reference/plot_forecast.html @@ -8,7 +8,13 @@ Please use plot_forecasts() instead."> + + + +
diff --git a/docs/reference/plot_forecasts.html b/docs/reference/plot_forecasts.html index c68f7ab..917cc6c 100644 --- a/docs/reference/plot_forecasts.html +++ b/docs/reference/plot_forecasts.html @@ -3,7 +3,13 @@ supported with specified facet formula."> + + + +
diff --git a/docs/reference/preprocess_hospitalization.html b/docs/reference/preprocess_hospitalization.html index fd8987f..122ebb4 100644 --- a/docs/reference/preprocess_hospitalization.html +++ b/docs/reference/preprocess_hospitalization.html @@ -2,7 +2,13 @@ Preprocess raw hospitalization data into Cumulative/Incident hospitalizations and write to CSVs — preprocess_hospitalization • covidHubUtils + + + +
diff --git a/docs/reference/preprocess_jhu.html b/docs/reference/preprocess_jhu.html index 489356a..da7fbfd 100644 --- a/docs/reference/preprocess_jhu.html +++ b/docs/reference/preprocess_jhu.html @@ -5,7 +5,13 @@ Note: updates to the JHU CSSE data stopped in March 2023."> + + + +
diff --git a/docs/reference/preprocess_nytimes.html b/docs/reference/preprocess_nytimes.html index 7868893..91cb54a 100644 --- a/docs/reference/preprocess_nytimes.html +++ b/docs/reference/preprocess_nytimes.html @@ -5,7 +5,13 @@ Note: updates to the NYTimes data stopped in March 2023."> + + + +
diff --git a/docs/reference/preprocess_truth_for_zoltar.html b/docs/reference/preprocess_truth_for_zoltar.html index dbe89ee..a7ee7cc 100644 --- a/docs/reference/preprocess_truth_for_zoltar.html +++ b/docs/reference/preprocess_truth_for_zoltar.html @@ -5,7 +5,13 @@ It only includes national and state-level truth data."> + + + +
diff --git a/docs/reference/preprocess_usafacts.html b/docs/reference/preprocess_usafacts.html index abfc697..06822fb 100644 --- a/docs/reference/preprocess_usafacts.html +++ b/docs/reference/preprocess_usafacts.html @@ -2,7 +2,13 @@ Preprocess raw truth data from USAFacts into Cumulative/Incident - Deaths/Cases and write to CSVs — preprocess_usafacts • covidHubUtils + + + +
diff --git a/docs/reference/preprocess_visualization_truth.html b/docs/reference/preprocess_visualization_truth.html index 9dcae2f..e421b0e 100644 --- a/docs/reference/preprocess_visualization_truth.html +++ b/docs/reference/preprocess_visualization_truth.html @@ -5,7 +5,13 @@ purpose and write to JSON files. Note: updates to the JHU CSSE data stopped in March 2023."> + + + +
diff --git a/docs/reference/reformat_forecasts.html b/docs/reference/reformat_forecasts.html index 084d7b9..08aece3 100644 --- a/docs/reference/reformat_forecasts.html +++ b/docs/reference/reformat_forecasts.html @@ -11,7 +11,13 @@ no forecasts are available in zoltar_query_result."> + + + +
diff --git a/docs/reference/save_truth_for_zoltar.html b/docs/reference/save_truth_for_zoltar.html index 999d53a..1b92e2f 100644 --- a/docs/reference/save_truth_for_zoltar.html +++ b/docs/reference/save_truth_for_zoltar.html @@ -8,7 +8,13 @@ It only includes national and state-level truth data."> + + + +
diff --git a/docs/reference/score_forecasts.html b/docs/reference/score_forecasts.html index 3da5cd0..98e83b7 100644 --- a/docs/reference/score_forecasts.html +++ b/docs/reference/score_forecasts.html @@ -2,7 +2,13 @@ Score forecasts — score_forecasts • covidHubUtils + + + +
diff --git a/docs/reference/setup_zoltar_connection.html b/docs/reference/setup_zoltar_connection.html index bf2623b..ce8522d 100644 --- a/docs/reference/setup_zoltar_connection.html +++ b/docs/reference/setup_zoltar_connection.html @@ -2,7 +2,13 @@ Set up Zoltar connection — setup_zoltar_connection • covidHubUtils + + + +