diff --git a/_targets.R b/_targets.R index 4a72c5d2..2f77ddd4 100644 --- a/_targets.R +++ b/_targets.R @@ -250,7 +250,7 @@ list( ), - ## Fit the model ------------------------------------------------------------ + # # Fit the model ------------------------------------------------------------ # # get a stacked long dataframe containing the quantiles(estimated # # from all draws) and 100 samples of the draws from the posterior for the # # generated quantities and the parameters @@ -285,7 +285,7 @@ list( name = plot_single_location_hosp_draws_id, command = get_plot_draws(grouped_df_id, "pred_hosp", - figure_file_path, + figure_output_subdirectory, show_calibration_data = FALSE ), pattern = map(grouped_df_id), @@ -296,7 +296,7 @@ list( name = plot_single_location_comb_quantiles_id, command = get_combo_quantile_plot( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -306,7 +306,7 @@ list( name = plot_ww_site_level_quantiles_id, command = get_ww_site_plots( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -316,7 +316,7 @@ list( name = plot_single_location_ww_draws_id, command = get_plot_labsite_ww_draws( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -326,7 +326,7 @@ list( name = plot_rt_id, command = get_rt_from_draws( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -336,7 +336,7 @@ list( name = plot_rt_site_level, command = get_rt_site_level( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -346,7 +346,7 @@ list( name = plot_params_id, command = get_plot_param_distribs( grouped_df_id, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_id), iteration = "list", @@ -365,8 +365,8 @@ list( deployment = "main" ), tar_target( - name = figure_file_path, - command = get_figure_file_path( + name = figure_output_subdirectory, + command = get_figure_output_subdirectory( output_dir_ho ), deployment = "main" @@ -463,7 +463,7 @@ list( name = plot_single_location_hosp_draws_ho, command = get_plot_draws(grouped_df, "pred_hosp", - figure_file_path, + figure_output_subdirectory, show_calibration_data = FALSE ), pattern = map(grouped_df), @@ -474,7 +474,7 @@ list( name = plot_rt_ho, command = get_rt_from_draws( grouped_df, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df), iteration = "list", @@ -484,7 +484,7 @@ list( name = plot_params_ho, command = get_plot_param_distribs( grouped_df, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df), iteration = "list", @@ -553,7 +553,10 @@ list( ), tar_target( name = single_plot_data_sa, - command = plot_combined_data(grouped_data_sa, figure_file_path), + command = plot_combined_data( + grouped_data_sa, + figure_output_subdirectory + ), pattern = map(grouped_data_sa), iteration = "list", deployment = "main" @@ -607,7 +610,7 @@ list( name = plot_single_location_hosp_draws_sa, command = get_plot_draws(grouped_df_sa, "pred_hosp", - figure_file_path, + figure_output_subdirectory, show_calibration_data = FALSE ), pattern = map(grouped_df_sa), @@ -618,7 +621,7 @@ list( name = plot_single_location_ww_draws_sa, command = get_plot_draws(df_of_filepaths_us, "pred_ww", - figure_file_path, + figure_output_subdirectory, show_calibration_data = FALSE ), deployment = "main" @@ -627,7 +630,7 @@ list( name = plot_rt_sa, command = get_rt_from_draws( grouped_df_sa, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_sa), iteration = "list", @@ -637,7 +640,7 @@ list( name = plot_params_sa, command = get_plot_param_distribs( grouped_df_sa, - figure_file_path + figure_output_subdirectory ), pattern = map(grouped_df_sa), iteration = "list", @@ -647,7 +650,7 @@ list( name = plot_single_location_comb_quantiles_sa, command = get_combo_quantile_plot( df_of_filepaths_us, - figure_file_path + figure_output_subdirectory ), deployment = "main" ), @@ -677,7 +680,7 @@ list( grouped_df_comb, "pred_hosp", grouping_var = "model_type", - figure_file_path, + figure_output_subdirectory, show_calibration_data = FALSE ), pattern = map(grouped_df_comb), @@ -690,7 +693,10 @@ list( comb_df_filepaths %>% ungroup() %>% filter(model_type == "site-level infection dynamics"), - figure_file_path = file.path(figure_file_path, "combined_outputs") + figure_file_path = file.path( + figure_output_subdirectory, + "combined_outputs" + ) ), deployment = "main" ), @@ -700,13 +706,16 @@ list( comb_df_filepaths %>% ungroup() %>% filter(model_type == "hospital admissions only"), - figure_file_path = file.path(figure_file_path, "combined_outputs") + figure_file_path = file.path( + figure_output_subdirectory, + "combined_outputs" + ) ), deployment = "main" ), tar_target( - name = pdf_file_path, - command = get_pdf_file_path( + name = pdf_output_subdirectory, + command = get_pdf_output_subdirectory( output_dir_id ), deployment = "main" @@ -721,7 +730,10 @@ list( plot_ww_site_level_quantiles_id ), type_of_output = "site_level_inf_dynamics", - pdf_file_path = file.path(pdf_file_path, "internal"), + pdf_file_path = file.path( + pdf_output_subdirectory, + "internal" + ), model_name = config_vars_id$submitting_model_name, n_row = 1, n_col = 1, @@ -740,7 +752,10 @@ list( plot_single_location_comb_quantiles_id ), type_of_output = "hosp_and_ww_forecasts_site_level_inf_dyn", - pdf_file_path = file.path(pdf_file_path, "internal"), + pdf_file_path = file.path( + pdf_output_subdirectory, + "internal" + ), model_name = config_vars_id$submitting_model_name, n_row = 3, n_col = 1, @@ -755,7 +770,10 @@ list( save_to_pdf, c(list(list_of_plots = plot_mult_models), type_of_output = "forecasts_from_mult_model_types", - pdf_file_path = file.path(pdf_file_path, "internal"), + pdf_file_path = file.path( + pdf_output_subdirectory, + "internal" + ), model_name = config_vars_id$submitting_model_name, n_row = 3, n_col = 1, @@ -823,34 +841,31 @@ list( ), tar_target( name = table_of_state_model_designations, - command = do.call( - get_summarized_table, - c( - list( - hub_submission_df = hub_submission_df, - full_diagnostics_df = full_diagnostics_df, - hosp_only_states = hosp_only_states, - repo_file_path = repo_file_path - ), - config_vars_id - ) + command = get_location_notes_table( + full_diagnostics_df, + hosp_only_states, + output_dir = repo_file_path, + prod_run = config_vars_id$prod_run ), deployment = "main" ), tar_target( name = pipeline_ww_metadata, - command = do.call(get_metadata_yaml, c( - list(full_diagnostics_df = full_diagnostics_df), - repo_file_path = repo_file_path, - list(hosp_only_states = hosp_only_states), - config_vars_id - )) + command = get_metadata_yaml( + data_diagnostics_df = full_diagnostics_df, + hosp_only_states = hosp_only_states, + output_dir = repo_file_path, + prod_run = config_vars_id$prod_run + ) ), tar_target( name = rt_box_plot_hub, command = get_rt_boxplot_across_states( df_of_filepaths, - figure_file_path = file.path(pdf_file_path, "internal") + figure_file_path = file.path( + pdf_output_subdirectory, + "internal" + ) ), deployment = "main" ), diff --git a/cfaforecastrenewalww/NAMESPACE b/cfaforecastrenewalww/NAMESPACE index f1d8aace..c89805c6 100644 --- a/cfaforecastrenewalww/NAMESPACE +++ b/cfaforecastrenewalww/NAMESPACE @@ -23,7 +23,7 @@ export(get_config_vals) export(get_df_for_hub_submission) export(get_df_of_filepaths) export(get_diagnostics) -export(get_figure_file_path) +export(get_figure_output_subdirectory) export(get_full_param_distrib) export(get_gen_quants_draws) export(get_generated_quantities_draws) @@ -35,6 +35,7 @@ export(get_ind_m) export(get_ind_m_cum_sum) export(get_init_fun) export(get_loc_model_map) +export(get_location_notes_table) export(get_low_case_count_diagnostic) export(get_metadata) export(get_metadata_yaml) @@ -47,7 +48,7 @@ export(get_param_samples_long_df) export(get_parameter_draws) export(get_params) export(get_pars) -export(get_pdf_file_path) +export(get_pdf_output_subdirectory) export(get_pipeline_metadata) export(get_plot_covidhub_submission) export(get_plot_draws) @@ -55,6 +56,8 @@ export(get_plot_labsite_ww_draws) export(get_plot_metadata) export(get_plot_param_distribs) export(get_ppa_long) +export(get_prior_pred_hosps_df) +export(get_prior_pred_ww_df) export(get_quantiles) export(get_quantiles_on_site_level_ww) export(get_random_string) @@ -73,7 +76,6 @@ export(get_state_level_hosp_data) export(get_state_level_summary) export(get_submission_file_path) export(get_submission_filepath_df) -export(get_summarized_table) export(get_summary_stats) export(get_testing_data) export(get_training_data) @@ -95,6 +97,7 @@ export(pivot_data_for_plotting) export(plot_combined_data) export(plot_quantiles) export(posterior_predictive_analysis) +export(prior_predictive_check) export(pull_nhsn) export(read_diagnostics_df) export(save_timestamped_nwss_data) diff --git a/cfaforecastrenewalww/R/get_config_vals.R b/cfaforecastrenewalww/R/get_config_vals.R index 6841ab2f..8ad4cc9a 100644 --- a/cfaforecastrenewalww/R/get_config_vals.R +++ b/cfaforecastrenewalww/R/get_config_vals.R @@ -1,11 +1,10 @@ -#' Read in the config yaml +#' Read in the config yaml and add run-specific +#' dynamic configuration to it. #' #' @param path_to_config path the config yaml #' -#' @return +#' @return The configuration values, as a list #' @export -#' -#' @examples get_config_vals <- function(path_to_config) { config <- read_yaml(path_to_config) config$forecast_date <- lubridate::ymd(config$forecast_date) @@ -17,232 +16,3 @@ get_config_vals <- function(path_to_config) { return(full_config) } - - -#' Get the figure file path -#' -#' @param output_dir -#' -#' @return -#' @export -#' -#' @examples -get_figure_file_path <- function(output_dir) { - fp <- file.path( - output_dir, "figures" - ) - return(fp) -} - -#' get the cleaned pdf filepath -#' -#' @param output_dir -#' -#' @return -#' @export -#' -#' @examples -get_pdf_file_path <- function(output_dir) { - fp <- file.path( - output_dir, - "cleaned" - ) - return(fp) -} - -#' Get summarized table with each location and -#' -#' @param hub_submission_df -#' @param full_diagnostics_df -#' @param hosp_only_states -#' @param repo_file_path -#' @param prod_run -#' -#' @return -#' @export -#' -#' @examples -get_summarized_table <- function(hub_submission_df, - full_diagnostics_df, - hosp_only_states, - repo_file_path, - prod_run, - ...) { - diag_df_wide <- full_diagnostics_df %>% - dplyr::select(location, diagnostic, value) %>% - dplyr::filter(diagnostic %in% c( - "no_wastewater_data_flag", - "delayed_wastewater_data_flag", - "insufficient_ww_data_flag" - )) %>% - tidyr::pivot_wider( - id_cols = location, - names_from = diagnostic, - values_from = value - ) %>% - dplyr::mutate( - additional_notes = - ifelse(no_wastewater_data_flag == 1, "No wastewater data available", - dplyr::case_when( - insufficient_ww_data_flag == 1 ~ paste0( - "Wastewater data is too sparse, ", - "forecast not likely to be informed ", - "by wastewater" - ), - (delayed_wastewater_data_flag == 1) ~ paste0( - "Wastewater data is unavailable for recent ", - "time-points, forecast not likely to be ", - "informed by wastewater" - ), - location %in% c(hosp_only_states) ~ paste0( - "Hospital admissions only model was run ", - "due to either issues with input data or model" - ), - TRUE ~ "None" - ) - ) - ) %>% - dplyr::select(location, additional_notes) - - if (isTRUE(prod_run)) { - create_dir(repo_file_path) - readr::write_tsv( - diag_df_wide, - file = fs::path( - repo_file_path, - glue::glue("wastewater_metadata_table.tsv") - ) - ) - cli::cli_inform("Writing forecast additional notes to repo ") - } - - - - (diag_df_wide) -} - -#' Get metadata to list all states with no wastewater or insufficient wastewater -#' data -#' -#' @param full_diagnostics_df -#' @param repo_file_path -#' @param hosp_only_states -#' @param prod_run -#' -#' @return -#' @export -#' -#' @examples -get_metadata_yaml <- function(full_diagnostics_df, - repo_file_path, - hosp_only_states, - prod_run, - ...) { - summary_list <- get_summary_stats(full_diagnostics_df) - - metadata <- list( - "States without wastewaster data" = - ifelse(rlang::is_empty(summary_list$states_w_no_ww_data), "None", - list(summary_list$states_w_no_ww_data) - ), - "States with insufficient wastewater data" = - ifelse(rlang::is_empty(summary_list$states_to_flag_for_hub), "None", - list(summary_list$states_to_flag_for_hub) - ), - "States we chose to use hospital admissions only model on" = - ifelse(rlang::is_empty(hosp_only_states), "None", list(hosp_only_states)) - ) - if (isTRUE(prod_run)) { - create_dir(repo_file_path) - write_yaml(metadata, file = file.path( - repo_file_path, - glue::glue("metadata.yaml") - )) - } - - return(metadata) -} - - - -#' @title Write pipeline metadata to a YAML -#' @param us_run US run? -#' @param path_to_save_metadata -#' @param run_id -#' @param date_run -#' @param ww_data_dir -#' @param hosp_data_dir -#' @param forecast_date -#' @param prod_run -#' @param model_type -#' @param location -#' @param output_dir -#' @param root_dir root directory where pipeline is being run, used to make absolute filepaths -#' @param ... -#' @return the metadata -#' @export -get_pipeline_metadata <- function(us_run, - path_to_save_metadata, - run_id, - date_run, - ww_data_path, hosp_data_dir, - forecast_date, - prod_run, - model_type, - location, - output_dir, - root_dir, - ...) { - git_hash <- system("git log --pretty=format:'%h' -n 1", intern = TRUE) - - - prod <- ifelse(isTRUE(prod_run), "prod", "test") - if (isTRUE(us_run)) { - locations_run <- c(location, "US") - } else { - locations_run <- location - } - - relative_hosp_path <- file.path( - hosp_data_dir, - glue::glue( - as.character(forecast_date), - ".csv" - ) - ) - - if (prod_run == TRUE) { - full_file_path <- file.path( - path_to_save_metadata, "prod", - glue::glue("{forecast_date}-run-on-{date_run}") - ) - } else { - full_file_path <- file.path( - path_to_save_metadata, "test", - glue::glue("{forecast_date}-run-on-{date_run}") - ) - } - create_dir(full_file_path) - - pipeline_metadata <- list( - git_hash = git_hash, - relative_output_path = output_dir, - relative_hosp_path = relative_hosp_path, - relative_ww_path = ww_data_path, - full_output_path = fs::path(root_dir, output_dir), - full_ww_path = fs::path(root_dir, ww_data_path), - full_hosp_path = fs::path(root_dir, relative_hosp_path), - date_run = date_run, - prod_run = prod_run, - run_id = run_id, - model_type = model_type, - locations_run = locations_run, - all_locs_run = length(locations_run) == 53 - ) - - write_yaml(pipeline_metadata, file = file.path( - full_file_path, - glue::glue("{run_id}.yaml") - )) - return(pipeline_metadata) -} diff --git a/cfaforecastrenewalww/R/get_output_metadata.R b/cfaforecastrenewalww/R/get_output_metadata.R new file mode 100644 index 00000000..03049a1a --- /dev/null +++ b/cfaforecastrenewalww/R/get_output_metadata.R @@ -0,0 +1,227 @@ +#' Get a table that records notes on data characteristics +#' and model choices for individual locations, +#' e.g. the absence of recent wastewater observations or +#' the decision to publish the hospital admissions only +#' model +#' +#' @param full_diagnostics_df Data frame of data diagnostics +#' by locations. +#' @param hosp_only_states States for which we chose +#' to use the hospitalization only model, as a vector +#' with states coded identically to how they are in +#' the `location` column of `full_diagnostics_df` +#' @param output_dir Path to a directory in which to save +#' the metadata table. Only used if `prod_run = TRUE`. +#' Default `NULL`. +#' @param prod_run Is this a run for publication / +#' production? If so, the output will be saved in an +#' appropriate location as a .tsv. Boolean, default `FALSE` +#' +#' @return The table of information as a [tibble::tibble()]. +#' @export +get_location_notes_table <- function(full_diagnostics_df, + hosp_only_states, + output_dir = NULL, + prod_run = FALSE) { + metadata_df <- full_diagnostics_df %>% + dplyr::select(location, diagnostic, value) %>% + dplyr::filter(diagnostic %in% c( + "no_wastewater_data_flag", + "delayed_wastewater_data_flag", + "insufficient_ww_data_flag" + )) %>% + tidyr::pivot_wider( + id_cols = location, + names_from = diagnostic, + values_from = value + ) %>% + dplyr::mutate(additional_notes = dplyr::case_when( + no_wastewater_data_flag == 1 ~ "No wastewater data available", + insufficient_ww_data_flag == 1 ~ paste0( + "Wastewater data is too sparse, ", + "forecast not likely to be ", + "informed by wastewater" + ), + delayed_wastewater_data_flag == 1 ~ paste0( + "Wastewater data is ", + "unavailable for recent ", + "time-points, ", + "forecast not likely to be ", + "informed by wastewater" + ), + location %in% c(hosp_only_states) ~ paste0( + "Hospital admissions only model was run ", + "due to either issues with input data or model" + ), + TRUE ~ "None" + )) %>% + dplyr::select(location, additional_notes) + + if (isTRUE(prod_run)) { + create_dir(output_dir) + save_path <- fs::path( + output_dir, + glue::glue("wastewater_metadata_table.tsv") + ) + cli::cli_inform( + "Writing forecast additional notes to {save_path}" + ) + readr::write_tsv( + metadata_df, + file = save_path + ) + } + + (metadata_df) +} + +#' Create YAML formatted metadata file +#' listing states without wastewater data, +#' states with insufficient wastewater data, +#' and states for which we used the hospital +#' admissions only model. +#' +#' @param data_diagnostics_df Data frame of data +#' diagnostics by location +#' @param hosp_only_states States for which we chose +#' to use the hospitalization only model, as a vector +#' with states coded identically to how they are in +#' the `location` column of `full_diagnostics_df` +#' @param output_dir Path to a directory in which to save +#' the metadata table. Only used if `prod_run = TRUE`. +#' Default `NULL`. +#' @param prod_run Is this a run for publication / +#' production? If so, the output will be saved in an +#' appropriate location as a .tsv. Boolean, default `FALSE` +#' +#' @return The metadata to be saved, as a `list`. +#' @export +get_metadata_yaml <- function(data_diagnostics_df, + hosp_only_states, + output_dir = NULL, + prod_run = FALSE) { + summary_list <- get_summary_stats(data_diagnostics_df) + + metadata <- list( + "States without wastewaster data" = + ifelse(rlang::is_empty(summary_list$states_w_no_ww_data), "None", + list(summary_list$states_w_no_ww_data) + ), + "States with insufficient wastewater data" = + ifelse(rlang::is_empty(summary_list$states_to_flag_for_hub), + "None", + list(summary_list$states_to_flag_for_hub) + ), + "States we chose to use hospital admissions only model on" = + ifelse(rlang::is_empty(hosp_only_states), + "None", + list(hosp_only_states) + ) + ) + if (isTRUE(prod_run)) { + create_dir(output_dir) + write_yaml(metadata, file = file.path( + output_dir, + glue::glue("metadata.yaml") + )) + } + + return(metadata) +} + + + +#' @title Assemble pipeline metadata for a given +#' run, returning it as a list and +#' writing it to disk as a YAML file. +#' +#' @param us_run Was the model run for the US as a +#' whole in addition to states and territories? +#' If so, this will be recorded. Boolean. +#' @param dir_to_save_metadata Subdirectory in which to +#' save the resultant metadata file. +#' @param run_id Unique ID of the pipeline run (as a +#' hash generated at runtime). +#' @param date_run Date the pipeline was run. +#' @param ww_data_dir Subdirectory in which wastewater +#' data used for the run is stored. +#' @param hosp_data_dir Subdirectory in which hospital +#' admissions data used for the run is stored. +#' @param forecast_date Forecast date targeted by the +#' run. +#' @param prod_run Is this a production run? Boolean. +#' @param model_type What was the model type for this run? +#' @param location What location(s) besides the US as a whole +#' were run? +#' @param output_dir What output directory was used to +#' store run output. +#' @param root_dir root directory where pipeline is being run, used to make absolute filepaths +#' @param ... Other keyword arguments, for compatibility +#' with do.call on a large parameter list. +#' @return the metadata, as a list. +#' @export +get_pipeline_metadata <- function(us_run, + dir_to_save_metadata, + run_id, + date_run, + ww_data_path, hosp_data_dir, + forecast_date, + prod_run, + model_type, + location, + output_dir, + root_dir, + ...) { + git_hash <- system("git log --pretty=format:'%h' -n 1", intern = TRUE) + + + prod <- ifelse(isTRUE(prod_run), "prod", "test") + if (isTRUE(us_run)) { + locations_run <- c(location, "US") + } else { + locations_run <- location + } + + relative_hosp_path <- file.path( + hosp_data_dir, + glue::glue( + as.character(forecast_date), + ".csv" + ) + ) + + if (prod_run == TRUE) { + full_file_path <- file.path( + dir_to_save_metadata, "prod", + glue::glue("{forecast_date}-run-on-{date_run}") + ) + } else { + full_file_path <- file.path( + dir_to_save_metadata, "test", + glue::glue("{forecast_date}-run-on-{date_run}") + ) + } + create_dir(full_file_path) + + pipeline_metadata <- list( + git_hash = git_hash, + relative_output_path = output_dir, + relative_hosp_path = relative_hosp_path, + relative_ww_path = ww_data_path, + full_output_path = fs::path(root_dir, output_dir), + full_ww_path = fs::path(root_dir, ww_data_path), + full_hosp_path = fs::path(root_dir, relative_hosp_path), + date_run = date_run, + prod_run = prod_run, + run_id = run_id, + model_type = model_type, + locations_run = locations_run, + all_locs_run = length(locations_run) == 53 + ) + + write_yaml(pipeline_metadata, file = file.path( + full_file_path, + glue::glue("{run_id}.yaml") + )) + return(pipeline_metadata) +} diff --git a/cfaforecastrenewalww/R/get_output_subdirectory_paths.R b/cfaforecastrenewalww/R/get_output_subdirectory_paths.R new file mode 100644 index 00000000..86eb415b --- /dev/null +++ b/cfaforecastrenewalww/R/get_output_subdirectory_paths.R @@ -0,0 +1,30 @@ +#' Get the path to the subdirectory in which to +#' save figures for a given top-level output directory +#' +#' @param output_dir Path to the output directory +#' +#' @return path to the figure subdirectory +#' @export +get_figure_output_subdirectory <- function(output_dir) { + subdir <- file.path( + output_dir, "figures" + ) + return(subdir) +} + +#' Get the path to the subdirectory in which +#' to save summary output for a given top-level +#' output directory. +#' +#' @param output_dir Path to the output directory +#' +#' @return The path to the subdirectory in which +#' to save the summary PDFs +#' @export +get_pdf_output_subdirectory <- function(output_dir) { + subdir <- file.path( + output_dir, + "cleaned" + ) + return(subdir) +} diff --git a/cfaforecastrenewalww/R/make_pps_data.R b/cfaforecastrenewalww/R/make_pps_data.R index 0351a532..ecd175a6 100644 --- a/cfaforecastrenewalww/R/make_pps_data.R +++ b/cfaforecastrenewalww/R/make_pps_data.R @@ -68,25 +68,25 @@ make_pps_data <- function(mcmc_fit, config) { stan_data <- real_data - y_df <- bind_rows( + y_df <- dplyr::bind_rows( pps_hosp_data, pps_ww_data ) hosp_reporting_delay <- config$hosp_reporting_delay length_generated_hosp <- y_df %>% - filter(name == "pred_hosp") %>% + dplyr::filter(name == "pred_hosp") %>% nrow() calibration_time <- config$calibration_time length_input_hosp <- calibration_time # Reallocate hosp vector to be the same length as input hosp vector hosp <- y_df %>% - filter( + dplyr::filter( name == "pred_hosp", day <= calibration_time ) %>% - pull(value) + dplyr::pull(value) # Reallocate wastewater vector to be the same parameter as # the input wastewater vector @@ -96,13 +96,13 @@ make_pps_data <- function(mcmc_fit, # Make into a matrix with each row a ww_lab_site and each column a time ww_conc_matrix <- y_df %>% - filter(name == "pred_ww") %>% - select(value, ww_lab_site, day) %>% - pivot_wider( + dplyr::filter(name == "pred_ww") %>% + dplyr::select(value, ww_lab_site, day) %>% + tidyr::pivot_wider( names_from = "day", values_from = "value" ) %>% - select(-ww_lab_site) + dplyr::select(-ww_lab_site) ww_conc_matrix <- data.matrix(ww_conc_matrix) # Get the vector of generated wastewater concentrations using the same diff --git a/cfaforecastrenewalww/R/posterior_predictive_analysis.R b/cfaforecastrenewalww/R/posterior_predictive_analysis.R index 27a1ad33..5cf74728 100644 --- a/cfaforecastrenewalww/R/posterior_predictive_analysis.R +++ b/cfaforecastrenewalww/R/posterior_predictive_analysis.R @@ -1,9 +1,17 @@ -#' Runs posterior-predictive analyses and returns summaries of performance +#' Runs posterior- and prior--predictive analyses and returns summaries of performance +#' #' @description #' This function takes in a model object, the observed data, and the configuration file used to -#' produce the real-data stan data object. It then fits the model, extracts generated quantities -#' from some number of those fits, and runs new analyses on the simulated data. It then returns -#' summaries of estimation performance. +#' produce the real-data stan data object. +#' +#' If running a posterior-predictive analysis, it then fits the model, extracts generated +#' quantities from some number of those fits, and runs new analyses on the simulated data. +#' Lastly it returns summaries of estimation performance. +#' +#' If running prior-predictive analyses, it runs under the prior to get the joint prior +#' distribution. Then it extracts generated quantities from some number of those fits, +#' and runs new analyses on the simulated data. Lastly it returns summaries of +#' estimation performance. #' #' @param model a CmdStanModel object defining the model #' @param real_data observed data, formated for stan @@ -16,6 +24,7 @@ #' previously-run pps analyses (for re-summarizing) #' @param mclapply_cores integer specifying number of threads to use for #' posterior-predictive-analysis-level parallelization, separate from stan parallelization +#' @param under_prior boolean, if TRUE prior-predictive analysis is run, not posterior #' #' @param ... further arguments passed to model$sample(), e.g. # chains #' @@ -28,6 +37,7 @@ posterior_predictive_analysis <- function(model, real_data_fit = NA, ci_width = 0.89, mclapply_cores = NA, + under_prior = FALSE, ...) { alpha <- 1 - ci_width ci <- c(alpha / 2, 1 - alpha / 2) diff --git a/cfaforecastrenewalww/R/prior_predictive_check.R b/cfaforecastrenewalww/R/prior_predictive_check.R new file mode 100644 index 00000000..5e2122f2 --- /dev/null +++ b/cfaforecastrenewalww/R/prior_predictive_check.R @@ -0,0 +1,77 @@ +#' Draws data under the model's prior. +#' +#' @description +#' This function takes in a model object, observed data, and the configuration file used to +#' produce the real-data stan data object. It then runs the model under the prior and +#' returns the observable (generated quantities) for some number of draws. +#' +#' @param model a CmdStanModel object defining the model +#' @param real_data observed data, formated for stan, needed to match, for example, the number +#' of wastewater sites +#' @param config the output of get_config_vals() +#' @param ndraws integer, number of draws from the prior predictive distribution to return +#' @param mclapply_cores integer specifying number of threads to use for +#' posterior-predictive-analysis-level parallelization, separate from stan parallelization +#' +#' @param ... further arguments passed to model$sample(), e.g. # chains +#' +#' @return a list, each of which is a list of formatted stan data +#' @export +prior_predictive_check <- function(model, + real_data, + config, + ndraws, + ...) { + real_data$compute_likelihood <- FALSE + prior_fit <- model$sample(data = real_data, ...) + + par_df <- get_model_param_df(model) + + prior_draws <- posterior::as_draws_list(prior_fit$draws()) + n_prior_samples <- length(prior_draws[[1]][[1]]) * length(prior_draws) + draw <- round(seq(1, n_prior_samples, length.out = ndraws)) + + prior_predictive_data <- make_pps_data( + prior_fit, + real_data, + config, + draw + ) + + return(prior_predictive_data) +} + +#' Observables extraction from prior predictive samples +#' +#' @param prior_pred output of prior_predictive_check, stan data object +#' +#' @return a tibble, with columns time (the time), +#' hosp (the hospitalization count), and +#' draw (the draw this came from) +#' @export +get_prior_pred_hosps_df <- function(prior_pred) { + lapply(seq_along(prior_pred), function(i) { + pp <- prior_pred[[i]] + dplyr::bind_cols(time = pp$hosp_times, hosp = pp$hosp, draw = i) + }) |> + dplyr::bind_rows() +} + +#' Observables extraction from prior predictive samples +#' +#' @param prior_pred output of prior_predictive_check, stan data object +#' @param site_index which site to extract +#' +#' @return a tibble, with columns time (the time), +#' log_conc (the ww log-concentration), and +#' draw (the draw this came from) +#' @export +get_prior_pred_ww_df <- function(prior_pred, site_index) { + lapply(seq_along(prior_pred), function(i) { + pp <- prior_pred[[i]] + ww <- pp$log_conc[pp$ww_sampled_sites == site_index] + times <- pp$ww_sampled_times[pp$ww_sampled_sites == site_index] + dplyr::bind_cols(time = times, log_conc = ww, draw = i) + }) |> + dplyr::bind_rows() +} diff --git a/cfaforecastrenewalww/R/sysdata.rda b/cfaforecastrenewalww/R/sysdata.rda old mode 100644 new mode 100755 index c0cafd7c..d489b77b Binary files a/cfaforecastrenewalww/R/sysdata.rda and b/cfaforecastrenewalww/R/sysdata.rda differ diff --git a/cfaforecastrenewalww/inst/stan/functions/ar1.stan b/cfaforecastrenewalww/inst/stan/functions/ar1.stan index 7d6c1712..82f4e9ce 100644 --- a/cfaforecastrenewalww/inst/stan/functions/ar1.stan +++ b/cfaforecastrenewalww/inst/stan/functions/ar1.stan @@ -4,6 +4,8 @@ * @param ac The autocorrelation coefficient. * @param sd The sd for the white noise/IID normal terms. * @param z vector of IID Normal(0,1) variables, the white noise/increment terms. + * @param is_stat int serving as logical, should process be initialized at + * stationary variance (1) or not (0)? Not valid for |ac| >= 1. * @return A vector, the values of the mean-preserving AR(1) process: * x[1] = x0, * x[i > 1] = mu + tvd[[i], where @@ -11,17 +13,25 @@ * Formally x(t) = mu(t) + delta(t) where * delta(t) = psi*delta(t-1) + eta(t) */ -vector ar1(vector mu, real ac, real sd, vector z) { +vector ar1(vector mu, real ac, real sd, vector z, int is_stat) { int n = num_elements(z); vector[n] x; vector[n] tvd; - tvd[1] = sd * z[1]; + real adj = 1.0; + if(is_stat) { + if (ac >= 1.0) { + reject("AR(1) process is not stationary if ac >= 1."); + } + adj = 1.0 / sqrt(1.0 - ac^2); + } + + tvd[1] = sd * adj * z[1]; x[1] = mu[1] + tvd[1]; - for (i in 2:n) { - tvd[i] = ac * tvd[i - 1] + sd * z[i]; - x[i] = mu[i] + tvd[i]; + for (t in 2:n) { + tvd[t] = ac * tvd[t - 1] + sd * z[t]; + x[t] = mu[t] + tvd[t]; } return x; diff --git a/cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_inf_dynamics.stan b/cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_inf_dynamics.stan index 36fade9c..82744ed3 100644 --- a/cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_inf_dynamics.stan +++ b/cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_inf_dynamics.stan @@ -215,7 +215,8 @@ transformed parameters { // log(R(t)site) ~ log(R(t)state) + log(R(t)state-log(R(t)site)) + eta_site log_r_site_t_in_weeks = ar1(log_r_mu_t_in_weeks, autoreg_rt_site, sigma_rt, - to_vector(error_site[i])); + to_vector(error_site[i]), + 1); //convert from weekly to daily unadj_r_site_t = exp(to_row_vector(ind_m*(log_r_site_t_in_weeks))); diff --git a/cfaforecastrenewalww/man/get_config_vals.Rd b/cfaforecastrenewalww/man/get_config_vals.Rd index e7c09f16..7f863bff 100644 --- a/cfaforecastrenewalww/man/get_config_vals.Rd +++ b/cfaforecastrenewalww/man/get_config_vals.Rd @@ -2,13 +2,18 @@ % Please edit documentation in R/get_config_vals.R \name{get_config_vals} \alias{get_config_vals} -\title{Read in the config yaml} +\title{Read in the config yaml and add run-specific +dynamic configuration to it.} \usage{ get_config_vals(path_to_config) } \arguments{ \item{path_to_config}{path the config yaml} } +\value{ +The configuration values, as a list +} \description{ -Read in the config yaml +Read in the config yaml and add run-specific +dynamic configuration to it. } diff --git a/cfaforecastrenewalww/man/get_figure_output_subdirectory.Rd b/cfaforecastrenewalww/man/get_figure_output_subdirectory.Rd new file mode 100644 index 00000000..fcb7d40a --- /dev/null +++ b/cfaforecastrenewalww/man/get_figure_output_subdirectory.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/get_output_subdirectory_paths.R +\name{get_figure_output_subdirectory} +\alias{get_figure_output_subdirectory} +\title{Get the path to the subdirectory in which to +save figures for a given top-level output directory} +\usage{ +get_figure_output_subdirectory(output_dir) +} +\arguments{ +\item{output_dir}{Path to the output directory} +} +\value{ +path to the figure subdirectory +} +\description{ +Get the path to the subdirectory in which to +save figures for a given top-level output directory +} diff --git a/cfaforecastrenewalww/man/get_location_notes_table.Rd b/cfaforecastrenewalww/man/get_location_notes_table.Rd new file mode 100644 index 00000000..9dc7f201 --- /dev/null +++ b/cfaforecastrenewalww/man/get_location_notes_table.Rd @@ -0,0 +1,44 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/get_output_metadata.R +\name{get_location_notes_table} +\alias{get_location_notes_table} +\title{Get a table that records notes on data characteristics +and model choices for individual locations, +e.g. the absence of recent wastewater observations or +the decision to publish the hospital admissions only +model} +\usage{ +get_location_notes_table( + full_diagnostics_df, + hosp_only_states, + output_dir = NULL, + prod_run = FALSE +) +} +\arguments{ +\item{full_diagnostics_df}{Data frame of data diagnostics +by locations.} + +\item{hosp_only_states}{States for which we chose +to use the hospitalization only model, as a vector +with states coded identically to how they are in +the `location` column of `full_diagnostics_df`} + +\item{output_dir}{Path to a directory in which to save +the metadata table. Only used if `prod_run = TRUE`. +Default `NULL`.} + +\item{prod_run}{Is this a run for publication / +production? If so, the output will be saved in an +appropriate location as a .tsv. Boolean, default `FALSE`} +} +\value{ +The table of information as a [tibble::tibble()]. +} +\description{ +Get a table that records notes on data characteristics +and model choices for individual locations, +e.g. the absence of recent wastewater observations or +the decision to publish the hospital admissions only +model +} diff --git a/cfaforecastrenewalww/man/get_metadata_yaml.Rd b/cfaforecastrenewalww/man/get_metadata_yaml.Rd index d7795669..eea4924d 100644 --- a/cfaforecastrenewalww/man/get_metadata_yaml.Rd +++ b/cfaforecastrenewalww/man/get_metadata_yaml.Rd @@ -1,22 +1,44 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_config_vals.R +% Please edit documentation in R/get_output_metadata.R \name{get_metadata_yaml} \alias{get_metadata_yaml} -\title{Get metadata to list all states with no wastewater or insufficient wastewater -data} +\title{Create YAML formatted metadata file +listing states without wastewater data, +states with insufficient wastewater data, +and states for which we used the hospital +admissions only model.} \usage{ get_metadata_yaml( - full_diagnostics_df, - repo_file_path, + data_diagnostics_df, hosp_only_states, - prod_run, - ... + output_dir = NULL, + prod_run = FALSE ) } \arguments{ -\item{prod_run}{} +\item{data_diagnostics_df}{Data frame of data +diagnostics by location} + +\item{hosp_only_states}{States for which we chose +to use the hospitalization only model, as a vector +with states coded identically to how they are in +the `location` column of `full_diagnostics_df`} + +\item{output_dir}{Path to a directory in which to save +the metadata table. Only used if `prod_run = TRUE`. +Default `NULL`.} + +\item{prod_run}{Is this a run for publication / +production? If so, the output will be saved in an +appropriate location as a .tsv. Boolean, default `FALSE`} +} +\value{ +The metadata to be saved, as a `list`. } \description{ -Get metadata to list all states with no wastewater or insufficient wastewater -data +Create YAML formatted metadata file +listing states without wastewater data, +states with insufficient wastewater data, +and states for which we used the hospital +admissions only model. } diff --git a/cfaforecastrenewalww/man/get_pdf_output_subdirectory.Rd b/cfaforecastrenewalww/man/get_pdf_output_subdirectory.Rd new file mode 100644 index 00000000..0d9b1077 --- /dev/null +++ b/cfaforecastrenewalww/man/get_pdf_output_subdirectory.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/get_output_subdirectory_paths.R +\name{get_pdf_output_subdirectory} +\alias{get_pdf_output_subdirectory} +\title{Get the path to the subdirectory in which +to save summary output for a given top-level +output directory.} +\usage{ +get_pdf_output_subdirectory(output_dir) +} +\arguments{ +\item{output_dir}{Path to the output directory} +} +\value{ +The path to the subdirectory in which +to save the summary PDFs +} +\description{ +Get the path to the subdirectory in which +to save summary output for a given top-level +output directory. +} diff --git a/cfaforecastrenewalww/man/get_pipeline_metadata.Rd b/cfaforecastrenewalww/man/get_pipeline_metadata.Rd index 48fe3e82..ce736dec 100644 --- a/cfaforecastrenewalww/man/get_pipeline_metadata.Rd +++ b/cfaforecastrenewalww/man/get_pipeline_metadata.Rd @@ -1,12 +1,14 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_config_vals.R +% Please edit documentation in R/get_output_metadata.R \name{get_pipeline_metadata} \alias{get_pipeline_metadata} -\title{Write pipeline metadata to a YAML} +\title{Assemble pipeline metadata for a given +run, returning it as a list and +writing it to disk as a YAML file.} \usage{ get_pipeline_metadata( us_run, - path_to_save_metadata, + dir_to_save_metadata, run_id, date_run, ww_data_path, @@ -21,13 +23,47 @@ get_pipeline_metadata( ) } \arguments{ -\item{us_run}{US run?} +\item{us_run}{Was the model run for the US as a +whole in addition to states and territories? +If so, this will be recorded. Boolean.} + +\item{dir_to_save_metadata}{Subdirectory in which to +save the resultant metadata file.} + +\item{run_id}{Unique ID of the pipeline run (as a +hash generated at runtime).} + +\item{date_run}{Date the pipeline was run.} + +\item{hosp_data_dir}{Subdirectory in which hospital +admissions data used for the run is stored.} + +\item{forecast_date}{Forecast date targeted by the +run.} + +\item{prod_run}{Is this a production run? Boolean.} + +\item{model_type}{What was the model type for this run?} + +\item{location}{What location(s) besides the US as a whole +were run?} + +\item{output_dir}{What output directory was used to +store run output.} \item{root_dir}{root directory where pipeline is being run, used to make absolute filepaths} + +\item{...}{Other keyword arguments, for compatibility +with do.call on a large parameter list.} + +\item{ww_data_dir}{Subdirectory in which wastewater +data used for the run is stored.} } \value{ -the metadata +the metadata, as a list. } \description{ -Write pipeline metadata to a YAML +Assemble pipeline metadata for a given +run, returning it as a list and +writing it to disk as a YAML file. } diff --git a/cfaforecastrenewalww/man/get_prior_pred_hosps_df.Rd b/cfaforecastrenewalww/man/get_prior_pred_hosps_df.Rd new file mode 100644 index 00000000..a0b9eda8 --- /dev/null +++ b/cfaforecastrenewalww/man/get_prior_pred_hosps_df.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prior_predictive_check.R +\name{get_prior_pred_hosps_df} +\alias{get_prior_pred_hosps_df} +\title{Observables extraction from prior predictive samples} +\usage{ +get_prior_pred_hosps_df(prior_pred) +} +\arguments{ +\item{prior_pred}{output of prior_predictive_check, stan data object} +} +\value{ +a tibble, with columns time (the time), +hosp (the hospitalization count), and +draw (the draw this came from) +} +\description{ +Observables extraction from prior predictive samples +} diff --git a/cfaforecastrenewalww/man/get_prior_pred_ww_df.Rd b/cfaforecastrenewalww/man/get_prior_pred_ww_df.Rd new file mode 100644 index 00000000..e8ec8b3d --- /dev/null +++ b/cfaforecastrenewalww/man/get_prior_pred_ww_df.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prior_predictive_check.R +\name{get_prior_pred_ww_df} +\alias{get_prior_pred_ww_df} +\title{Observables extraction from prior predictive samples} +\usage{ +get_prior_pred_ww_df(prior_pred, site_index) +} +\arguments{ +\item{prior_pred}{output of prior_predictive_check, stan data object} + +\item{site_index}{which site to extract} +} +\value{ +a tibble, with columns time (the time), +log_conc (the ww log-concentration), and +draw (the draw this came from) +} +\description{ +Observables extraction from prior predictive samples +} diff --git a/cfaforecastrenewalww/man/posterior_predictive_analysis.Rd b/cfaforecastrenewalww/man/posterior_predictive_analysis.Rd index 2e7b3bf4..f2950d73 100644 --- a/cfaforecastrenewalww/man/posterior_predictive_analysis.Rd +++ b/cfaforecastrenewalww/man/posterior_predictive_analysis.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/posterior_predictive_analysis.R \name{posterior_predictive_analysis} \alias{posterior_predictive_analysis} -\title{Runs posterior-predictive analyses and returns summaries of performance} +\title{Runs posterior- and prior--predictive analyses and returns summaries of performance} \usage{ posterior_predictive_analysis( model, @@ -12,6 +12,7 @@ posterior_predictive_analysis( real_data_fit = NA, ci_width = 0.89, mclapply_cores = NA, + under_prior = FALSE, ... ) } @@ -31,6 +32,8 @@ previous real-data model fit} \item{mclapply_cores}{integer specifying number of threads to use for posterior-predictive-analysis-level parallelization, separate from stan parallelization} +\item{under_prior}{boolean, if TRUE prior-predictive analysis is run, not posterior} + \item{...}{further arguments passed to model$sample(), e.g. # chains} \item{pps_mcmc_fits}{list of CmdStanMCMC objects, optional argument providing @@ -41,7 +44,14 @@ a list, each of which is a list of formatted stan data } \description{ This function takes in a model object, the observed data, and the configuration file used to -produce the real-data stan data object. It then fits the model, extracts generated quantities -from some number of those fits, and runs new analyses on the simulated data. It then returns -summaries of estimation performance. +produce the real-data stan data object. + +If running a posterior-predictive analysis, it then fits the model, extracts generated +quantities from some number of those fits, and runs new analyses on the simulated data. +Lastly it returns summaries of estimation performance. + +If running prior-predictive analyses, it runs under the prior to get the joint prior +distribution. Then it extracts generated quantities from some number of those fits, +and runs new analyses on the simulated data. Lastly it returns summaries of +estimation performance. } diff --git a/cfaforecastrenewalww/man/prior_predictive_check.Rd b/cfaforecastrenewalww/man/prior_predictive_check.Rd new file mode 100644 index 00000000..24074e2c --- /dev/null +++ b/cfaforecastrenewalww/man/prior_predictive_check.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prior_predictive_check.R +\name{prior_predictive_check} +\alias{prior_predictive_check} +\title{Draws data under the model's prior.} +\usage{ +prior_predictive_check(model, real_data, config, ndraws, ...) +} +\arguments{ +\item{model}{a CmdStanModel object defining the model} + +\item{real_data}{observed data, formated for stan, needed to match, for example, the number +of wastewater sites} + +\item{config}{the output of get_config_vals()} + +\item{ndraws}{integer, number of draws from the prior predictive distribution to return} + +\item{...}{further arguments passed to model$sample(), e.g. # chains} + +\item{mclapply_cores}{integer specifying number of threads to use for +posterior-predictive-analysis-level parallelization, separate from stan parallelization} +} +\value{ +a list, each of which is a list of formatted stan data +} +\description{ +This function takes in a model object, observed data, and the configuration file used to +produce the real-data stan data object. It then runs the model under the prior and +returns the observable (generated quantities) for some number of draws. +} diff --git a/cfaforecastrenewalww/tests/testthat/test_ar1.R b/cfaforecastrenewalww/tests/testthat/test_ar1.R new file mode 100644 index 00000000..5181ce0a --- /dev/null +++ b/cfaforecastrenewalww/tests/testthat/test_ar1.R @@ -0,0 +1,56 @@ +test_that("Test AR(1) function in stan.", { + model <- compiled_site_inf_model + + ar1ify <- function(z, sd, ac, stationary = FALSE) { + x <- rep(NA, length(z)) + + x[1] <- z[1] * sd + if (stationary) { + stat_sd <- sd / sqrt(1 - ac * ac) + x[1] <- z[1] * stat_sd + } + + for (i in 2:length(z)) { + x[i] <- ac * x[i - 1] + z[i] * sd + } + + return(x) + } + + withr::with_seed(42, { + z <- rnorm(10) + + stan_ar <- model$functions$ar1( + mu = rep(0, length(z)), + ac = 0.73, + sd = 1.26, + z = z, + is_stat = TRUE + ) + r_ar <- ar1ify(z, 1.26, 0.73, TRUE) + + testthat::expect_equal( + stan_ar, + r_ar + ) + + stan_ar_nonstat <- model$functions$ar1( + mu = rep(0, length(z)), + ac = 0.73, + sd = 1.26, + z = z, + is_stat = FALSE + ) + + testthat::expect_true( + all(abs(stan_ar - stan_ar_nonstat) > testthat::testthat_tolerance()) + ) + + r_ar_nonstat <- ar1ify(z, 1.26, 0.73, FALSE) + + testthat::expect_equal( + stan_ar_nonstat, + r_ar_nonstat + ) + }) +}) diff --git a/cfaforecastrenewalww/tests/testthat/test_ar1_marginal_variance.R b/cfaforecastrenewalww/tests/testthat/test_ar1_marginal_variance.R new file mode 100644 index 00000000..bffe8c82 --- /dev/null +++ b/cfaforecastrenewalww/tests/testthat/test_ar1_marginal_variance.R @@ -0,0 +1,40 @@ +test_explanation <- paste0( + "When running a stationary AR(1) process initialized from the stationary variance, ", + "the marginal variances should be larger than when compared to an AR(1) process ", + "initialized from the (smaller) variance of the residuals. (At least, until stationarity ", + "is reached.)" +) + +test_that(test_explanation, { + model <- compiled_site_inf_model + + withr::with_seed(42, { + stationary <- sapply(1:1e3, function(i) { + z <- rnorm(10) + + model$functions$ar1( + mu = rep(0, length(z)), + ac = 0.95, + sd = 0.15, + z = z, + is_stat = TRUE + ) + }) + + nonstationary <- sapply(1:1e3, function(i) { + z <- rnorm(10) + + model$functions$ar1( + mu = rep(0, length(z)), + ac = 0.95, + sd = 0.15, + z = z, + is_stat = FALSE + ) + }) + + testthat::expect_true( + all(apply(stationary, 1, var) > apply(nonstationary, 1, var)) + ) + }) +}) diff --git a/model_definition.md b/model_definition.md index d20bddda..c66d20e6 100644 --- a/model_definition.md +++ b/model_definition.md @@ -111,7 +111,7 @@ The damping term we use is based on Asher et al. 2018[^Asher2018] but extended t $$ \mathcal{R}(t) = \mathcal{R}^\mathrm{u}(t) \exp \left( -\gamma \sum_{\tau = 1}^{T_f}I(t-\tau)g(\tau) \right) $$ -where $\gamma$ is the _infection feedback term_ controlling the strength of the damping on $\mathcal{R}(t)$, and the summation is analogous to the "force of infection." +where $\gamma$ is the _infection feedback term_ controlling the strength of the damping on $\mathcal{R}(t)$, and the summation is analogous to the "force of infection." See [Prior Distributions](#prior-distributions) below for description of prior choice on $\gamma$. ### Hospital admissions component @@ -137,7 +137,7 @@ $$ \mathrm{logit} (p_{\mathrm{hosp}}(t_2)) \sim \mathrm{Normal}(\mathrm{logit}(p The process is initialized at the calibration start time $t_0$ via a prior distribution (see [Prior Distributions](#prior-distributions) below). -In hospital admissions only models, we model the IHR as constant. We assign this constant IHR the same prior distribution we assign to the mean of the time-varying IHR in the wastewater-informed models. +In hospital admissions only models, we model the IHR as constant. We assign this constant IHR the same prior distribution we assign to the intercept of the time-varying IHR in the wastewater-informed models. ### Hospital admissions observation model We model the observed hospital admission counts $h_t$ as: @@ -296,6 +296,7 @@ We use informative priors for parameters that have been well characterized in th | Total genomes shed per infected individual | $\log_{10}[G] \sim \mathrm{Normal}(9, 2)$ | Watson et al 2023[^Watson] | | Initial infections per capita $I_0$ | $I_0 \sim \mathrm{Beta}(1 + k i_\mathrm{est}, 1 + k (1-i_\mathrm{est}))$ | where $i_\mathrm{est}$ is the sum of the last 7 days of hospital admissions, divided by state population, and divided by the prior mode for $p_\mathrm{hosp}$, and $k = 5$ is a parameter governing the informativeness ("certainty") of the Beta distribution | | Initial exponential growth rate | $r \sim \mathrm{Normal}(0, 0.01)$ | Chosen to assume flat dynamics prior to observations | +| Infection feedback term | $\gamma \sim \mathrm{logNormal}(6.37, 0.4)$ | Weakly informative prior chosen to have a mode of 500 in natural scale, based on posterior estimates of peaks from prior seasons in a few locations| ### Scalar parameters diff --git a/output/forecasts/2024-03-18/2024-03-18.tsv b/output/forecasts/2024-03-18/2024-03-18.tsv new file mode 100644 index 00000000..b8aa52d5 --- /dev/null +++ b/output/forecasts/2024-03-18/2024-03-18.tsv @@ -0,0 +1,34133 @@ +"target" "location" "forecast_date" "target_end_date" "quantile" "value" "type" "model_type" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.01 0 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.025 0 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.05 1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.1 2 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.15 2.85 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.2 3 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.25 3 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.3 3.7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.35 4 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.4 4 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.45 5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.5 5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.55 5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.6 5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.65 6 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.7 6 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.75 7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.8 7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.85 8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.9 8.10000000000001 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.95 9.05 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.975 10 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-18 2024-03-19 0.99 10.01 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.01 1.99 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.025 2 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.05 2 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.1 2 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.15 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.2 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.25 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.3 4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.35 4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.4 4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.45 5 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.5 5 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.55 6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.6 6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.65 7 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.7 7 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.75 8 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.8 8 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.85 9 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.9 10 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.95 11 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.975 12.525 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "02" 2024-03-18 2024-03-20 0.99 15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.01 0.99 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.025 1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.05 1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.1 2 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.15 2 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.2 3 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.25 3 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.3 4 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.35 4 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.4 4 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.45 5 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.5 5 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.55 5 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.6 6 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.65 6 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.7 6.30000000000001 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.75 7 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.8 8 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.85 8.15000000000001 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.9 10 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.95 11 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.975 11.525 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "02" 2024-03-18 2024-03-21 0.99 14.07 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.01 0.99 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.025 1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.05 1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.1 1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.15 2 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.2 2 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.25 2 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.3 3 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.35 3 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.4 3 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.45 3.55 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.5 4 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.55 5 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.6 5 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.65 6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.7 6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.75 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.8 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.85 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.9 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.95 9 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.975 9.52499999999999 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "02" 2024-03-18 2024-03-22 0.99 10 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.01 0 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.025 0 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.05 0 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.1 1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.15 1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.2 1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.25 2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.3 2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.35 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.4 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.45 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.5 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.55 3.45 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.6 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.65 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.7 4.30000000000001 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.75 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.8 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.85 6 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 2024-03-23 0.9 7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "02" 2024-03-18 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67.02 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.01 18.98 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.025 22.475 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.05 24 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.1 27.9 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.15 30 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.2 31.8 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.25 34 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.3 35 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "01" 2024-03-18 2024-03-28 0.35 37 "quantile" "site-level infection dynamics" +"10 day ahead 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"04" 2024-03-18 2024-04-04 0.65 20.35 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.7 22 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.75 24.25 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.8 26 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.85 28.15 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.9 30 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.95 35.1 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.975 38.05 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "04" 2024-03-18 2024-04-04 0.99 45.09 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.01 4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.025 6 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.05 6.95 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.1 8 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.15 9 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.2 10 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.25 11 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.3 13 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.35 14 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.4 15 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.45 16 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.5 16 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.55 17 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.6 18.4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.65 19.35 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.7 21 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.75 21 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.8 23 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.85 26 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.9 28.1 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.95 30 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.975 33 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "04" 2024-03-18 2024-04-05 0.99 36.1400000000001 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.01 3 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.025 4.425 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.05 6 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.1 8 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.15 9.85 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.2 11 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.25 12 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.3 13 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.35 14 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.4 15 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.45 15 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.5 17 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.55 18 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.6 19 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.65 20 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.7 22 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.75 22 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.8 23.4 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.85 26 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.9 28.1 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.95 34.05 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.975 36 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "04" 2024-03-18 2024-04-06 0.99 44.04 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "04" 2024-03-18 2024-04-07 0.01 6 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "04" 2024-03-18 2024-04-07 0.025 7 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "04" 2024-03-18 2024-04-07 0.05 7 "quantile" "site-level infection dynamics" +"20 day ahead inc 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48.01 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.01 4.99 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.025 6 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.05 7 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.1 8 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.15 9 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.2 10 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.25 11 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.3 12 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "04" 2024-03-18 2024-04-08 0.35 13 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" 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2024-04-09 0.2 11.8 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.25 12 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.3 13 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.35 14 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.4 15.6 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.45 17 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.5 17.5 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.55 20 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.6 21 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "04" 2024-03-18 2024-04-09 0.65 23 "quantile" "site-level infection dynamics" +"22 day 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2024-04-11 0.3 11.7 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.35 12.65 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.4 14 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.45 16 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.5 16 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.55 17 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.6 17.4 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.65 19 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.7 20.3 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.75 21 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.8 22 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.85 24 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.9 26 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.95 33.05 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.975 37.1 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "04" 2024-03-18 2024-04-11 0.99 50.2000000000001 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.01 1.99 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.025 2.475 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.05 3.95 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.1 6 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.15 7.85 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.2 9.8 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.25 10.75 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.3 12 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.35 12 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.4 13 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.45 13.55 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.5 14 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.55 15 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.6 17 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.65 20 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.7 22 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.75 23 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.8 23.2 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.85 27.15 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.9 30 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.95 36 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.975 38.575 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "04" 2024-03-18 2024-04-12 0.99 44.1700000000001 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.01 1.99 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.025 3 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.05 5 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.1 7 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.15 8 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.2 10 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.25 10 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.3 11 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.35 12 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.4 13 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.45 14 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.5 15 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.55 16 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.6 18.4 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.65 19.35 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.7 21.3 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.75 24 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.8 25 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.85 28 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.9 30.1 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.95 33 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.975 39 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "04" 2024-03-18 2024-04-13 0.99 41.1100000000001 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.01 3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.025 3.475 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.05 5.95 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.1 6.9 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.15 7 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.2 8 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.25 9.75 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.3 11.7 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.35 13 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.4 14 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.45 16 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.5 16.5 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.55 18 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.6 19 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.65 20 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.7 21.3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.75 22 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.8 24.2 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.85 29 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.9 32 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.95 37.1 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.975 40 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-18 2024-04-14 0.99 42.1900000000001 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.01 4 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.025 4 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.05 5 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.1 6.9 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.15 7.85 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.2 10 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.25 10.75 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.3 12 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.35 13 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.4 14 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.45 15.55 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.5 16 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.55 18 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.6 19 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.65 21 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.7 22 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.75 24 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.8 26 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.85 27 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.9 31 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-18 2024-04-15 0.95 35.05 "quantile" "site-level infection dynamics" 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2024-03-18 2024-03-19 0.3 118 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.35 120 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.4 122 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.45 124 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.5 127 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.55 128 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.6 131 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.65 134.05 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.7 138.3 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.75 141.5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.8 145.2 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.85 147.15 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.9 151.1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.95 156.05 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.975 162.575 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-18 2024-03-19 0.99 167.02 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.01 84.99 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.025 87.375 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.05 98.8 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.1 108 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.15 113 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.2 116.6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.25 120 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.3 120.7 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.35 121 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.4 124 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.45 125.55 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.5 127.5 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.55 131 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.6 132.4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.65 134 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.7 137.6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.75 140 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.8 142.4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.85 146.15 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.9 151 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.95 155.05 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.975 164 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-18 2024-03-20 0.99 165.05 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.01 90.89 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.025 93 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.05 96.9 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.1 102.9 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.15 105 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.2 110.2 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.25 113.75 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.3 115.7 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.35 118.65 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.4 121.6 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.45 123.55 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.5 125 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.55 128.45 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.6 132 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.65 133.7 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.7 136.3 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.75 138 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.8 141 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.85 146 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.9 150 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.95 152.1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.975 156.525 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-18 2024-03-21 0.99 162.01 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.01 90.75 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.025 92 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.05 92.95 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.1 97.6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.15 100 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.2 101 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.25 105 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.3 108.7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.35 111 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.4 112 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.45 115 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.5 118 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.55 120.45 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.6 122.4 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.65 125 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.7 128 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.75 132.25 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.8 134 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.85 136 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.9 141.3 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.95 150.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.975 154.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-18 2024-03-22 0.99 159.07 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.01 66.96 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.025 69 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.05 72.85 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.1 81.8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.15 85.85 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.2 88 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.25 89.75 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.3 92 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.35 94 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.4 96 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.45 98 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.5 99.5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.55 102.45 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.6 106 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.65 109 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.7 112 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.75 113 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.8 117.4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.85 120.15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.9 124.1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-18 2024-03-23 0.95 129.05 "quantile" "site-level infection 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2024-03-18 2024-03-24 0.8 118 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-18 2024-03-24 0.85 121 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-18 2024-03-24 0.9 124.1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-18 2024-03-24 0.95 134.1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-18 2024-03-24 0.975 138.575 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-18 2024-03-24 0.99 141.13 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.01 71 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.025 73.475 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.05 76 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.1 83.9 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.15 86.85 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.2 90.8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.25 93 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.3 96.7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.35 99.65 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.4 102.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.45 104 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.5 106 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.55 109 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.6 112 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.65 115 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.7 118 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.75 121 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.8 124.2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.85 127 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.9 135 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.95 141.05 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.975 147.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-18 2024-03-25 0.99 149.16 "quantile" "site-level infection dynamics" +"8 day ahead 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2024-03-18 2024-03-26 0.9 142.4 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "06" 2024-03-18 2024-03-26 0.95 157.2 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "06" 2024-03-18 2024-03-26 0.975 166.05 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "06" 2024-03-18 2024-03-26 0.99 171.06 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.01 69.96 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.025 81.475 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.05 82 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.1 85.9 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.15 90.85 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.2 92.8 "quantile" "site-level 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2024-03-27 0.7 122.3 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.75 127.25 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.8 132 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.85 135.15 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.9 142 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.95 149 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.975 157.05 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "06" 2024-03-18 2024-03-27 0.99 160.15 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "06" 2024-03-18 2024-03-28 0.01 66.97 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "06" 2024-03-18 2024-03-28 0.025 77.85 "quantile" "site-level infection 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2024-03-29 0.3 91 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.35 95 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.4 97.6 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.45 100.55 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.5 103 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.55 106 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.6 109.4 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.65 112.35 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.7 116.3 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "06" 2024-03-18 2024-03-29 0.75 120.25 "quantile" "site-level infection 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2024-03-18 2024-03-30 0.1 64.8 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.15 69.85 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.2 73.8 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.25 75 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.3 77.7 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.35 80 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.4 82.6 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.45 84 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.5 88.5 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "06" 2024-03-18 2024-03-30 0.55 91.9 "quantile" "site-level infection 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2024-03-18 2024-03-19 0.05 21.95 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.1 24.9 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.15 25 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.2 26.8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.25 28 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.3 30 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.35 30.65 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.4 32 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.45 33 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.5 34 "quantile" "site-level infection dynamics" +"1 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"site-level infection dynamics" +"1 day ahead inc hosp" "08" 2024-03-18 2024-03-19 0.99 56.03 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.01 14.97 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.025 18.475 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.05 19 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.1 21 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.15 21 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.2 22 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.25 24.75 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.3 26.7 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.35 29 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.4 30 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.45 32 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.5 32.5 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.55 34 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.6 34.4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.65 36 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.7 37 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.75 39 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-18 2024-03-20 0.8 39.2 "quantile" "site-level infection dynamics" +"2 day 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0.65 40 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.7 41 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.75 42.25 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.8 44 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.85 46 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.9 50 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.95 58 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.975 60.575 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-18 2024-03-21 0.99 64.1500000000001 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-18 2024-03-22 0.01 16.96 "quantile" "site-level infection dynamics" +"4 day 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2024-03-18 2024-03-24 0.1 21 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.15 23 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.2 26 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.25 27 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.3 29 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.35 30 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.4 31 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.45 31.55 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.5 32.5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-18 2024-03-24 0.55 34 "quantile" "site-level infection dynamics" +"6 day 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2024-03-25 0.4 33 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.45 34 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.5 35 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.55 36 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.6 39.4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.65 41.35 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.7 43.3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.75 44 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.8 46 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-18 2024-03-25 0.85 47.3 "quantile" "site-level infection dynamics" +"7 day ahead 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"site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.75 12.25 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.8 14 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.85 15 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.9 16.1 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.95 20 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.975 22.05 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "11" 2024-03-18 2024-03-27 0.99 23.01 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "11" 2024-03-18 2024-03-28 0.01 2.98 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "11" 2024-03-18 2024-03-28 0.025 3.475 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "11" 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"quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.3 7 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.35 8 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.4 8 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.45 9 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.5 9 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.55 9 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.6 10 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.65 10 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 2024-04-12 0.7 10 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "11" 2024-03-18 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day ahead inc hosp" "10" 2024-03-18 2024-03-30 0.99 13.01 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.01 0 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.025 1 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.05 1 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.1 1.9 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.15 2 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.2 3 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.25 3 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.3 3 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "10" 2024-03-18 2024-03-31 0.35 3 "quantile" "site-level 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"quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.3 6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.35 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.4 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.45 8 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.5 8 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.55 8 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.6 9 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.65 9 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.7 10 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.75 11 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.8 11 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.85 12 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.9 12.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.95 14.05 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.975 15 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "19" 2024-03-18 2024-03-22 0.99 16.04 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.01 1.99 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.025 2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.05 2.95 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.1 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.15 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.2 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.25 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.3 6 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.35 6 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.4 7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.45 7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.5 8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.55 8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.6 9 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.65 9 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.7 9.30000000000001 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.75 10 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.8 10.2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.85 11 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.9 12 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.95 13 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.975 14.05 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "19" 2024-03-18 2024-03-23 0.99 15.06 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.01 0.99 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.025 2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.05 3 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.1 4 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.15 4 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.2 5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.25 5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.3 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.35 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.4 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.45 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.5 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.55 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.6 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.65 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.7 9 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.75 9 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.8 10 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.85 10 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.9 11 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.95 13 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.975 15.575 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "19" 2024-03-18 2024-03-24 0.99 17.03 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.01 2.99 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.025 3.475 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.05 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.1 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.15 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.2 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.25 7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.3 8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.35 8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.4 8.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.45 9 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.5 10 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.55 10 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.6 10 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.65 11 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "19" 2024-03-18 2024-03-25 0.7 12 "quantile" "site-level infection dynamics" +"7 day 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"site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.1 4 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.15 5 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.2 5 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.25 6 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.3 6.7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.35 7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.4 7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.45 8 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.5 8 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.55 9 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.6 9 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.65 10 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.7 10 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.75 11 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.8 12 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.85 13 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.9 14.1 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.95 16 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.975 17 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "19" 2024-03-18 2024-03-26 0.99 19.01 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.01 1.99 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.025 3 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.05 3.95 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.1 4 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.15 5 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.2 5 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.25 5.75 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.3 6 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.35 7 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.4 8 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.45 8 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.5 8 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.55 9 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.6 9 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.65 10 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.7 10 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.75 11 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.8 11 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "19" 2024-03-18 2024-03-27 0.85 12 "quantile" "site-level infection dynamics" +"9 day 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"site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.25 5 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.3 6 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.35 6 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.4 7 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.45 7 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.5 8 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.55 8 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.6 9 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 0.65 10 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "19" 2024-03-18 2024-03-28 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2024-03-18 2024-04-07 0.35 4 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.4 5 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.45 5 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.5 5.5 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.55 6 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.6 6 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.65 7 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.7 7.30000000000001 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.75 8 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "19" 2024-03-18 2024-04-07 0.8 8.2 "quantile" "site-level infection 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0.15 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.2 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.25 5 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.3 5 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.35 6 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.4 6 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.45 7 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.5 7 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.55 7.45 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.6 8 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.65 9 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.7 9 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.75 9.25000000000001 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.8 10 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.85 12 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.9 13 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.95 16.1 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.975 18.525 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "19" 2024-03-18 2024-04-08 0.99 24.04 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "19" 2024-03-18 2024-04-09 0.01 0.99 "quantile" "site-level 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2024-03-18 2024-04-14 0.975 47 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-18 2024-04-14 0.99 50.2700000000001 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.01 6.99 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.025 8 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.05 9.95 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.1 14 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.15 15.85 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.2 17 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.25 20 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.3 22 "quantile" "site-level 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0.8 37 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.85 40.15 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.9 47.2 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.95 55.15 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.975 60.05 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "21" 2024-03-18 2024-04-15 0.99 65.1400000000001 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.01 23.98 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.025 24.95 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.05 26 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.1 29 "quantile" "hospital admissions only" +"1 day ahead 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2024-03-19 0.65 45 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.7 46 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.75 47 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.8 48.2 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.85 51 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.9 53.1 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.95 56 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.975 56 "quantile" "hospital admissions only" +"1 day ahead inc hosp" "22" 2024-03-18 2024-03-19 0.99 59 "quantile" "hospital admissions only" +"2 day ahead inc hosp" "22" 2024-03-18 2024-03-20 0.01 24.98 "quantile" "hospital admissions only" +"2 day ahead inc hosp" "22" 2024-03-18 2024-03-20 0.025 26.475 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hosp" "22" 2024-03-18 2024-03-21 0.4 37 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.45 38.55 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.5 40 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.55 41.45 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.6 42.4 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.65 43.35 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.7 45.3 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.75 47.25 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.8 49.2 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.85 51 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.9 54 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.95 59 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.975 60.525 "quantile" "hospital admissions only" +"3 day ahead inc hosp" "22" 2024-03-18 2024-03-21 0.99 61.06 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.01 20.99 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.025 21 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.05 23.9 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.1 26 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.15 28 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.2 29.8 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.25 31 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.3 31.7 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.35 33 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.4 34 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.45 36 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.5 37 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.55 38 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.6 39.4 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.65 41 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.7 42.3 "quantile" "hospital admissions only" +"4 day ahead inc hosp" "22" 2024-03-18 2024-03-22 0.75 44 "quantile" 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2024-03-18 2024-04-11 0.55 28.45 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.6 30.4 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.65 33 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.7 35 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.75 37.25 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.8 41 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.85 43 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.9 47.2 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.95 53.1 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "24" 2024-03-18 2024-04-11 0.975 57 "quantile" "site-level infection 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2024-03-18 2024-03-19 0.9 13.1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "30" 2024-03-18 2024-03-19 0.95 14.05 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "30" 2024-03-18 2024-03-19 0.975 15 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "30" 2024-03-18 2024-03-19 0.99 15.02 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.01 1.99 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.025 2 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.05 2 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.1 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.15 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "30" 2024-03-18 2024-03-20 0.2 4 "quantile" "site-level infection dynamics" +"2 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8.02000000000001 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.01 0 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.025 0 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.05 0 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.1 0 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.15 0 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.2 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.25 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.3 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-18 2024-03-25 0.35 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 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2024-03-28 0.85 4 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "50" 2024-03-18 2024-03-28 0.9 4 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "50" 2024-03-18 2024-03-28 0.95 6 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "50" 2024-03-18 2024-03-28 0.975 6.52499999999999 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "50" 2024-03-18 2024-03-28 0.99 7 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "50" 2024-03-18 2024-03-29 0.01 0 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "50" 2024-03-18 2024-03-29 0.025 0 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "50" 2024-03-18 2024-03-29 0.05 0 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "50" 2024-03-18 2024-03-29 0.1 0.9 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "50" 2024-03-18 2024-03-29 0.15 1 "quantile" "site-level infection dynamics" +"11 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0.1 10 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.15 11 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.2 12 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.25 13 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.3 13 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.35 14 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.4 14 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.45 15 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.5 15 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.55 16 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.6 18 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.65 18.35 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.7 19.3 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.75 20 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.8 22.2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.85 24 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.9 25.1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.95 29.1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.975 32 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "55" 2024-03-18 2024-03-24 0.99 34.02 "quantile" "site-level infection 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2024-03-25 0.9 28.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "55" 2024-03-18 2024-03-25 0.95 31.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "55" 2024-03-18 2024-03-25 0.975 33.525 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "55" 2024-03-18 2024-03-25 0.99 34.03 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.01 7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.025 7.475 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.05 8.95 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.1 10 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.15 10.85 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "55" 2024-03-18 2024-03-26 0.2 11 "quantile" "site-level infection dynamics" +"8 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2024-03-27 0.55 16 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.6 17 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.65 18 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.7 19.3 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.75 21 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.8 22.2 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.85 24 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.9 26 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.95 27.05 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "55" 2024-03-18 2024-03-27 0.975 29.05 "quantile" "site-level infection dynamics" +"9 day ahead 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0.05 286.65 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.1 371.1 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.15 465.3 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.2 540.2 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.25 607.5 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.3 653.2 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.35 674.55 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.4 754.2 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.45 827.1 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.5 892 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.55 912.8 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.6 933.8 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.65 1005.8 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.7 1064 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.75 1150.25 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.8 1245.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.85 1327.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.9 1408.4 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.95 1629.4 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.975 1981.875 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-18 2024-04-12 0.99 2711.48 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.01 162.62 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.025 202.55 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.05 271.1 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.1 299.7 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.15 386.35 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.2 454.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.25 507.75 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.3 573.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.35 620.95 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.4 662.2 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.45 716.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.5 774 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.55 836 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.6 850.4 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.65 899.9 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.7 953.8 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.75 1055.25 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.8 1120 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.85 1190.35 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.9 1387.2 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.95 1468.55 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.975 1886.75 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-18 2024-04-13 0.99 2623.36 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.01 174.66 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.025 197.825 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.05 251.1 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.1 303.7 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.15 395.05 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.2 429 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.25 522.75 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.3 569.6 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.35 632.95 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.4 677.2 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.45 716 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.5 777 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.55 834.05 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.6 864.4 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.65 956.9 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.7 1023.9 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.75 1065.5 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.8 1141 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.85 1182.8 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.9 1367.7 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.95 1540.35 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.975 1947.225 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-18 2024-04-14 0.99 2526.47 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.01 161.62 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.025 187.8 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.05 258.85 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.1 336.6 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.15 427 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.2 490.6 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.25 579 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.3 629.3 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.35 657.65 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.4 743.8 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.45 798.7 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.5 885.5 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.55 947.45 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.6 984.2 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.65 1073.1 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.7 1166.1 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.75 1226.75 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.8 1292.6 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.85 1384.35 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.9 1531.3 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.95 1834.25 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.975 2412.475 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-18 2024-04-15 0.99 2485.26000000001 "quantile" "state-level aggregated wastewater" diff --git a/output/forecasts/2024-03-18/metadata.yaml b/output/forecasts/2024-03-18/metadata.yaml new file mode 100644 index 00000000..8dda4ccb --- /dev/null +++ b/output/forecasts/2024-03-18/metadata.yaml @@ -0,0 +1,16 @@ +States without wastewaster data: +- - MS + - ND + - PR +States with insufficient wastewater data: +- DC +States we chose to use hospital admissions only model on: +- - KS + - NY + - OH + - LA + - IL + - ME + - NC + - NH + - UT diff --git a/output/forecasts/2024-03-18/wastewater_metadata_table.tsv b/output/forecasts/2024-03-18/wastewater_metadata_table.tsv new file mode 100644 index 00000000..92090adb --- /dev/null +++ b/output/forecasts/2024-03-18/wastewater_metadata_table.tsv @@ -0,0 +1,53 @@ +location additional_notes +AK None +AL None +AR None +AZ None +CA None +CO None +CT None +DC None +DE None +FL None +GA None +HI None +IA None +ID None +IL Hospital admissions only model was run due to either issues with input data or model +IN None +KS Hospital admissions only model was run due to either issues with input data or model +KY None +LA Hospital admissions only model was run due to either issues with input data or model +MA None +MD None +ME Hospital admissions only model was run due to either issues with input data or model +MI None +MN None +MO None +MS None +MT None +NC Hospital admissions only model was run due to either issues with input data or model +ND None +NE None +NH Hospital admissions only model was run due to either issues with input data or model +NJ None +NM None +NV None +NY Hospital admissions only model was run due to either issues with input data or model +OH Hospital admissions only model was run due to either issues with input data or model +OK None +OR None +PA None +PR None +RI None +SC None +SD None +TN None +TX None +UT Hospital admissions only model was run due to either issues with input data or model +VA None +VT None +WA None +WI None +WV None +WY None diff --git a/src/write_config.R b/src/write_config.R index 059d0b41..e9e8b21f 100644 --- a/src/write_config.R +++ b/src/write_config.R @@ -83,7 +83,7 @@ write_config <- function(run_id, "output", forecast_date, stringr::str_glue("run-on-{date_run}-{run_id}") ) # nolint - path_to_save_metadata <- + dir_to_save_metadata <- file.path(output_dir, "pipeline_run_metadata") # Pre-specified delay distributions @@ -100,31 +100,22 @@ write_config <- function(run_id, # Assign the dates and locations for hospital admissions to be manually # removed - last_1 <- lubridate::ymd("2024-03-01") + + last_1 <- lubridate::ymd("2024-03-08") dates_for_hosp_removal <- c( - lubridate::ymd("2024-02-27"), # CA 4th to last - last_1, # NE last data point + lubridate::ymd("2024-03-07"), # IA 2nd to last seq( from = lubridate::ymd("2024-02-27"), to = lubridate::ymd("2024-02-29"), by = "days" ), # NM 4th to last to second to last repeated data points - last_1, # OK - last_1, # OR - seq( - from = lubridate::ymd("2024-02-29"), - to = lubridate::ymd("2024-03-01"), - by = "days" - ) # WI last two + last_1 # SC ) states_for_hosp_removal <- c( - rep("CA", 1), - rep("NE", 1), + rep("IA", 1), rep("NM", 3), - rep("OK", 1), - rep("OR", 1), - rep("WI", 2) + rep("SC", 1) ) @@ -205,7 +196,7 @@ write_config <- function(run_id, inf_to_hosp = inf_to_hosp, submitting_model_name = submitting_model_name, prod_run = prod_run, - path_to_save_metadata = path_to_save_metadata, + dir_to_save_metadata = dir_to_save_metadata, config_file_path = fp )