diff --git a/.github/actions/install-cmdstan/LICENSE b/.github/actions/install-cmdstan/LICENSE new file mode 100644 index 00000000..9dbb9280 --- /dev/null +++ b/.github/actions/install-cmdstan/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2024 Epinowcast + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/.github/actions/install-cmdstan/action.yaml b/.github/actions/install-cmdstan/action.yaml new file mode 100644 index 00000000..31988fdd --- /dev/null +++ b/.github/actions/install-cmdstan/action.yaml @@ -0,0 +1,53 @@ +# MIT Licensed action vendored from +# https://github.com/epinowcast/actions + +name: 'Install CmdStan with caching' +description: 'Install CmdStan with caching' +inputs: + cmdstan-version: + description: 'CmdStan version to install (use "latest" for the latest version)' + required: false + default: 'latest' + num-cores: + description: 'Number of cores to use for building CmdStan' + required: false + default: '1' + +runs: + using: 'composite' + steps: + - name: Determine CmdStan Version (Unix) + if: runner.os != 'Windows' && inputs.cmdstan-version == 'latest' + run: | + chmod +x ${{ github.action_path }}/scripts/get-latest-release.sh + ${{ github.action_path }}/scripts/get-latest-release.sh + shell: bash + + - name: Determine CmdStan Version (Windows) + if: runner.os == 'Windows' && inputs.cmdstan-version == 'latest' + run: ${{ github.action_path }}\scripts\get-latest-release.ps1 + shell: pwsh + + - name: Set CmdStan Version (Specified) + if: inputs.cmdstan-version != 'latest' + run: echo "CMDSTAN_VERSION=${{ inputs.cmdstan-version }}" >> $GITHUB_ENV + shell: bash + + - name: Restore Cache + id: cache-cmdstan + uses: actions/cache@v4 + with: + path: '~/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}' + key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }} + + - name: Check the CmdStan toolchain and repair it if required + if: steps.cache-cmdstan.outputs.cache-hit != 'true' + run: | + Rscript -e 'cmdstanr::check_cmdstan_toolchain(fix = TRUE)' + shell: bash + + - name: Install CmdStan using cmdstanr + if: steps.cache-cmdstan.outputs.cache-hit != 'true' + run: | + Rscript -e 'cmdstanr::install_cmdstan(version = "${{ env.CMDSTAN_VERSION }}", cores = ${{ inputs.num-cores }})' + shell: bash diff --git a/.github/actions/install-cmdstan/scripts/get-latest-release.ps1 b/.github/actions/install-cmdstan/scripts/get-latest-release.ps1 new file mode 100644 index 00000000..8ce0f9c1 --- /dev/null +++ b/.github/actions/install-cmdstan/scripts/get-latest-release.ps1 @@ -0,0 +1,27 @@ +# PowerShell script to fetch the latest CmdStan release version with retry logic + +# Initialize retry parameters +$max_attempts = 5 +$wait_time = 5 # seconds + +for ($attempt = 1; $attempt -le $max_attempts; $attempt++) { + try { + $response = Invoke-RestMethod -Uri "https://api.github.com/repos/stan-dev/cmdstan/releases/latest" -ErrorAction Stop + $version = $response.tag_name -replace '^v', '' + + if (-not [string]::IsNullOrWhiteSpace($version)) { + "CMDSTAN_VERSION=$version" | Out-File -Append -FilePath $env:GITHUB_ENV + Write-Host "CmdStan latest version: $version" + break + } + } catch { + Write-Host "Attempt $attempt of $max_attempts failed. Retrying in $wait_time seconds..." + Start-Sleep -Seconds $wait_time + $wait_time = $wait_time * 2 + } +} + +if ([string]::IsNullOrWhiteSpace($version)) { + Write-Host "Failed to fetch CmdStan version after $max_attempts attempts." + exit 1 +} diff --git a/.github/actions/install-cmdstan/scripts/get-latest-release.sh b/.github/actions/install-cmdstan/scripts/get-latest-release.sh new file mode 100644 index 00000000..284dc434 --- /dev/null +++ b/.github/actions/install-cmdstan/scripts/get-latest-release.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +# Detect the operating system and install jq +if [[ "$OSTYPE" == "linux-gnu"* ]]; then + sudo apt-get update + sudo apt-get install -y jq +elif [[ "$OSTYPE" == "darwin"* ]]; then + brew install jq +else + echo "Unsupported OS for this script" + exit 1 +fi + +# Function to get the latest CmdStan version using GitHub API +get_latest_version() { + local retries=3 + local wait_time=5 + local status=0 + local version="" + + for ((i=0; i> $GITHUB_ENV + +echo "CmdStan latest version: $version" diff --git a/.github/workflows/r-cmd-check.yaml b/.github/workflows/r-cmd-check.yaml new file mode 100644 index 00000000..0e5d8b7e --- /dev/null +++ b/.github/workflows/r-cmd-check.yaml @@ -0,0 +1,27 @@ +name: R CMD check project package + +on: + pull_request: + push: + branches: [main] + +jobs: + build-and-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: r-lib/actions/setup-r@v2 + with: + r-version: 'release' + use-public-rspm: true + extra-repositories: 'https://mc-stan.org/r-packages/' + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + working-directory: cfaforecastrenewalww + needs: check + - name: "Install cmdstan via cmdstanr" + uses: ./.github/actions/install-cmdstan + - uses: r-lib/actions/check-r-package@v2 + with: + working-directory: cfaforecastrenewalww + error-on: '"error"' diff --git a/_targets.R b/_targets.R index 850b5aa2..8e4242d6 100644 --- a/_targets.R +++ b/_targets.R @@ -759,14 +759,22 @@ list( ), # Format data for the hub ---------------------------------------------------- + tar_target( + name = loc_model_map_submission, + command = get_loc_model_map( + df_of_filepaths_id, + hosp_only_states + ), + deployment = "main" + ), tar_target( name = df_of_filepaths, command = get_submission_filepath_df( prod_model_type = prod_model_type, - hosp_only_states = hosp_only_states, + loc_model_map = loc_model_map_submission, df_of_filepaths_inf_dyn = df_of_filepaths_id, df_of_filepaths_agg = df_of_filepaths_us, - df_of_filepaths_hosp_only = df_of_filepaths_ho, + df_of_filepaths_hosp_only = df_of_filepaths_ho ), deployment = "main" ), @@ -797,11 +805,17 @@ list( ), tar_target( name = table_of_state_model_designations, - command = get_summarized_table( - hub_submission_df, - full_diagnostics_df, - hosp_only_states, - repo_file_path + 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 + ) ), deployment = "main" ), @@ -876,14 +890,28 @@ list( ), # Generate "would-be" submissions from each model type ----------------------- + tar_target( + name = is_submitted_forecast, + command = FALSE, + deployment = "main" + ), + tar_target( + name = loc_model_map_ho, + command = get_loc_model_map( + df_of_filepaths_ho |> dplyr::filter(location != "US"), + hosp_only_states, + us_model_type = "hospital admissions only" + ), + deployment = "main" + ), tar_target( name = df_of_filepaths_hosp_only, command = get_submission_filepath_df( prod_model_type = "hospital admissions only", - hosp_only_states = c(), + loc_model_map = loc_model_map_ho, df_of_filepaths_inf_dyn = df_of_filepaths_id, df_of_filepaths_agg = df_of_filepaths_us, - df_of_filepaths_hosp_only = df_of_filepaths_ho, + df_of_filepaths_hosp_only = df_of_filepaths_ho ), deployment = "main" ), @@ -896,8 +924,8 @@ list( submitting_model_name = "cfa-wwrenewal_hosp_only", submission_file_path = submission_file_path, repo_file_path = repo_file_path, # We won't write to the repo - prod_run = FALSE, # This is not what we're submitting, even if it is part of a - # production run + prod_run = is_submitted_forecast, # This is not what we're submitting, + # even if it is part of a production run is_for_public_repo = FALSE ) ), @@ -938,14 +966,21 @@ list( ), deployment = "main" ), + tar_target( + name = loc_model_map_ww, + command = get_loc_model_map(df_of_filepaths_id, + hosp_only_states = c() + ), + deployment = "main" + ), tar_target( name = df_of_filepaths_ww, command = get_submission_filepath_df( prod_model_type = prod_model_type, - hosp_only_states = c(), + loc_model_map = loc_model_map_ww, df_of_filepaths_inf_dyn = df_of_filepaths_id, df_of_filepaths_agg = df_of_filepaths_us, - df_of_filepaths_hosp_only = df_of_filepaths_ho, + df_of_filepaths_hosp_only = df_of_filepaths_ho ), deployment = "main" ), @@ -958,8 +993,8 @@ list( submitting_model_name = "cfa-wwrenewal_all_ww", submission_file_path = submission_file_path, repo_file_path = repo_file_path, # we won't write to the repo - prod_run = FALSE, # This is not what we're submitting, even if it is part of a - # production run + prod_run = is_submitted_forecast, # This is not what we're submitting, + # even if it is part of a production run is_for_public_repo = FALSE ) ), diff --git a/cfaforecastrenewalww/DESCRIPTION b/cfaforecastrenewalww/DESCRIPTION index 323f83ca..37c857df 100644 --- a/cfaforecastrenewalww/DESCRIPTION +++ b/cfaforecastrenewalww/DESCRIPTION @@ -70,10 +70,12 @@ Suggests: covidcast, httr, knitr, - withr + withr, + testthat Additional_repositories: https://mc-stan.org/r-packages/ SystemRequirements: CmdStan (>=2.34.1) RoxygenNote: 7.3.1 Encoding: UTF-8 LazyData: true Config/testthat/edition: 3 +Config/Needs/check: rcmdcheck, testthat diff --git a/cfaforecastrenewalww/NAMESPACE b/cfaforecastrenewalww/NAMESPACE index 74980ed4..14f53be3 100644 --- a/cfaforecastrenewalww/NAMESPACE +++ b/cfaforecastrenewalww/NAMESPACE @@ -33,6 +33,7 @@ export(get_hosp_reporting_delay) export(get_ind_m) export(get_ind_m_cum_sum) export(get_init_fun) +export(get_loc_model_map) export(get_low_case_count_diagnostic) export(get_metadata) export(get_metadata_yaml) diff --git a/cfaforecastrenewalww/R/fit_model.R b/cfaforecastrenewalww/R/fit_model.R index 11555ef1..7ace1769 100644 --- a/cfaforecastrenewalww/R/fit_model.R +++ b/cfaforecastrenewalww/R/fit_model.R @@ -250,6 +250,8 @@ fit_aggregated_model <- function(train_data, params, state_agg_inits(train_data, params, stan_data) } + print(paste0("Model type: ", model_type)) + fit_dynamic_rt <- model_file$sample( data = stan_data, seed = seed, @@ -266,8 +268,21 @@ fit_aggregated_model <- function(train_data, params, all_draws <- fit_dynamic_rt$draws() # Grabs just predicted hospitalizations, WW concentration, and hosp per 100k - gen_quants_draws <- get_generated_quantities_draws(all_draws) + gen_quants_draws <- get_generated_quantities_draws(all_draws, model_type) + + # Time-varying parameters depend on model type + if (model_type == "state-level aggregated wastewater") { + time_varying_pars <- c( + "pred_hosp", "pred_ww", "R(t)", + "p_hosp", "exp_state_ww_conc" + ) + } else { + time_varying_pars <- c( + "pred_hosp", "pred_ww", "R(t)", + "exp_state_ww_conc" + ) + } # First make the dataframe with the generated quantities @@ -279,10 +294,7 @@ fit_aggregated_model <- function(train_data, params, location = location, data_type = "draw" ) %>% - filter(name %in% c( - "pred_hosp", "pred_ww", "R(t)", - "p_hosp", "exp_state_ww_conc" - )) %>% + filter(name %in% time_varying_pars) %>% left_join(date_df, by = "t") %>% left_join(train_data %>% select( t, date, ww, daily_hosp_admits, @@ -324,11 +336,7 @@ fit_aggregated_model <- function(train_data, params, "pred_hosp", "pred_ww", "R(t)", "exp_state_ww_conc" ))) %>% - mutate(model_type = ifelse( - include_ww == 1, - "state-level aggregated wastewater", - "hospital admissions only" - )) + mutate(model_type = model_type) # Get a subset of the draws gen_quants_draws <- gen_quants_draws %>% @@ -339,9 +347,7 @@ fit_aggregated_model <- function(train_data, params, pop, obs_data, period ) %>% mutate( - model_type = ifelse(include_ww == 1, "state-level aggregated wastewater", - "hospital admissions only" - ) + model_type = model_type ) %>% filter(draw %in% c(sample(1:max(draw), n_draws))) @@ -352,7 +358,7 @@ fit_aggregated_model <- function(train_data, params, # Then make the one for the parameter draws - parameter_draws <- get_raw_param_draws(all_draws) + parameter_draws <- get_raw_param_draws(all_draws, model_type) parameter_draws <- parameter_draws %>% mutate( data_type = "draw", @@ -361,9 +367,7 @@ fit_aggregated_model <- function(train_data, params, location = location, hosp_reporting_delay = hosp_reporting_delay, pop = pop, - model_type = ifelse(include_ww == 1, "state-level aggregated wastewater", - "hospital admissions only" - ) + model_type = model_type ) diagnostics <- get_diagnostics( @@ -780,7 +784,7 @@ fit_site_level_model <- function(train_data, filter(draw %in% c(sample(1:max(draw), n_draws))) - parameter_draws <- get_raw_param_draws(all_draws) + parameter_draws <- get_raw_param_draws(all_draws, model_type) parameter_draws <- parameter_draws %>% mutate( data_type = "draw", diff --git a/cfaforecastrenewalww/R/get_config_vals.R b/cfaforecastrenewalww/R/get_config_vals.R index adc68a59..6841ab2f 100644 --- a/cfaforecastrenewalww/R/get_config_vals.R +++ b/cfaforecastrenewalww/R/get_config_vals.R @@ -56,6 +56,7 @@ get_pdf_file_path <- function(output_dir) { #' @param full_diagnostics_df #' @param hosp_only_states #' @param repo_file_path +#' @param prod_run #' #' @return #' @export @@ -64,7 +65,9 @@ get_pdf_file_path <- function(output_dir) { get_summarized_table <- function(hub_submission_df, full_diagnostics_df, hosp_only_states, - repo_file_path) { + repo_file_path, + prod_run, + ...) { diag_df_wide <- full_diagnostics_df %>% dplyr::select(location, diagnostic, value) %>% dplyr::filter(diagnostic %in% c( @@ -101,16 +104,18 @@ get_summarized_table <- function(hub_submission_df, ) %>% dplyr::select(location, additional_notes) - create_dir(repo_file_path) - - readr::write_tsv( - diag_df_wide, - file = fs::path( - repo_file_path, - glue::glue("wastewater_metadata_table.tsv") + 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 ") + cli::cli_inform("Writing forecast additional notes to repo ") + } + (diag_df_wide) @@ -122,6 +127,7 @@ get_summarized_table <- function(hub_submission_df, #' @param full_diagnostics_df #' @param repo_file_path #' @param hosp_only_states +#' @param prod_run #' #' @return #' @export @@ -130,6 +136,7 @@ get_summarized_table <- function(hub_submission_df, get_metadata_yaml <- function(full_diagnostics_df, repo_file_path, hosp_only_states, + prod_run, ...) { summary_list <- get_summary_stats(full_diagnostics_df) @@ -145,11 +152,14 @@ get_metadata_yaml <- function(full_diagnostics_df, "States we chose to use hospital admissions only model on" = ifelse(rlang::is_empty(hosp_only_states), "None", list(hosp_only_states)) ) - create_dir(repo_file_path) - write_yaml(metadata, file = file.path( - repo_file_path, - glue::glue("metadata.yaml") - )) + if (isTRUE(prod_run)) { + create_dir(repo_file_path) + write_yaml(metadata, file = file.path( + repo_file_path, + glue::glue("metadata.yaml") + )) + } + return(metadata) } diff --git a/cfaforecastrenewalww/R/get_data.R b/cfaforecastrenewalww/R/get_data.R index 2f94abd8..3e328201 100644 --- a/cfaforecastrenewalww/R/get_data.R +++ b/cfaforecastrenewalww/R/get_data.R @@ -532,6 +532,7 @@ state_agg_inits <- function(train_data, params, stan_data) { # Estimate of number of initial infections i0 <- mean(train_data$daily_hosp_admits[1:7], na.rm = TRUE) / p_hosp_mean + include_ww <- stan_data$include_ww init_list <- list( w = rnorm(n_weeks - 1, 0, 0.01), @@ -543,8 +544,8 @@ state_agg_inits <- function(train_data, params, stan_data) { inv_sqrt_phi_h = 1 / (sqrt(200)) + rnorm(1, 1 / 10000, 1 / 10000), sigma_ww = abs(rnorm(1, 0, 0.5)), p_hosp_int = rnorm(1, qlogis(p_hosp_mean), 0.01), - p_hosp_w = rnorm(tot_weeks - 1, 0, 0.01), - p_hosp_w_sd = abs(rnorm(1, 0.01, 0.001)), + p_hosp_w = if (include_ww == 1) rnorm(tot_weeks - 1, 0, 0.01) else rep(0, 0), + p_hosp_w_sd = if (include_ww == 1) abs(rnorm(1, 0.01, 0.001)) else rep(0, 0), t_peak = rnorm(1, t_peak_mean, 0.1 * t_peak_sd), viral_peak = rnorm(1, viral_peak_mean, 0.1 * viral_peak_sd), dur_shed = rnorm(1, duration_shedding_mean, 0.1 * duration_shedding_sd), diff --git a/cfaforecastrenewalww/R/model_params.R b/cfaforecastrenewalww/R/model_params.R index a3536a40..0a0970ab 100644 --- a/cfaforecastrenewalww/R/model_params.R +++ b/cfaforecastrenewalww/R/model_params.R @@ -118,7 +118,7 @@ get_model_param_df <- function(x) { "eta_sd", "autoreg_rt", "log_r", "i0_over_n", "initial_growth", "inv_sqrt_phi_h", "sigma_ww", - "p_hosp_w_sd", "t_peak", "dur_shed", + "p_hosp_w_sd[1]", "t_peak", "dur_shed", "infection_feedback" ) daily_params <- c("rt", "new_i", "p_hosp") diff --git a/cfaforecastrenewalww/R/process_model_outputs.R b/cfaforecastrenewalww/R/process_model_outputs.R index 12bab9dd..7d51ed63 100644 --- a/cfaforecastrenewalww/R/process_model_outputs.R +++ b/cfaforecastrenewalww/R/process_model_outputs.R @@ -834,7 +834,9 @@ get_gen_quants_draws <- function(all_draws, #' @export #' #' @examples -get_generated_quantities_draws <- function(all_draws, n_draws = 100) { +get_generated_quantities_draws <- function(all_draws, + model_type, + n_draws = 100) { # Dataframes with ndraws (long format) hosp_draws <- all_draws %>% spread_draws(pred_hosp[t]) %>% @@ -877,20 +879,26 @@ get_generated_quantities_draws <- function(all_draws, n_draws = 100) { ) %>% select(name, t, value, draw) - p_hosp_draws <- all_draws %>% - spread_draws(p_hosp[t]) %>% - # sample_draws(ndraws = n_draws) %>% - rename(value = p_hosp) %>% - mutate( - draw = `.draw`, - name = "p_hosp" - ) %>% - select(name, t, value, draw) - - model_draws <- rbind( - hosp_draws, ww_draws, rt_draws, - exp_state_ww_draws, p_hosp_draws - ) + if (model_type != "hospital admissions only") { + p_hosp_draws <- all_draws %>% + spread_draws(p_hosp[t]) %>% + # sample_draws(ndraws = n_draws) %>% + rename(value = p_hosp) %>% + mutate( + draw = `.draw`, + name = "p_hosp" + ) %>% + select(name, t, value, draw) + model_draws <- rbind( + hosp_draws, ww_draws, rt_draws, + exp_state_ww_draws, p_hosp_draws + ) + } else { + model_draws <- rbind( + hosp_draws, ww_draws, rt_draws, + exp_state_ww_draws + ) + } return(model_draws) } @@ -918,6 +926,7 @@ get_pars <- function() { #' This concatenates all the tidy draws dataframes of each of the parameters #' #' @param stan_output_draws +#' @param model_type #' @param n_draws #' @param ... #' @@ -927,8 +936,9 @@ get_pars <- function() { #' @export #' #' @examples -get_raw_param_draws <- function(stan_output_draws, n_draws = 500, ...) { - # Single parmeter psoterior draws with sumamry stats +get_raw_param_draws <- function(stan_output_draws, model_type, + n_draws = 500, ...) { + # Single parmeter posterior draws with sumamry stats phi_h <- stan_output_draws %>% spread_draws(phi_h) %>% sample_draws(ndraws = n_draws) %>% @@ -974,17 +984,6 @@ get_raw_param_draws <- function(stan_output_draws, n_draws = 500, ...) { rename(value = i0) %>% select(name, t, value, draw) - p_hosp_sd <- stan_output_draws %>% - spread_draws(p_hosp_w_sd) %>% - sample_draws(ndraws = n_draws) %>% - mutate(draw = `.draw`) %>% - mutate( - name = "p_hosp_sd", - t = NA - ) %>% - rename(value = p_hosp_w_sd) %>% - select(name, t, value, draw) - initial_growth <- stan_output_draws %>% spread_draws(initial_growth) %>% sample_draws(ndraws = n_draws) %>% @@ -1018,12 +1017,48 @@ get_raw_param_draws <- function(stan_output_draws, n_draws = 500, ...) { rename(value = autoreg_rt) %>% select(name, t, value, draw) + if (model_type == "state-level aggregated wastewater") { + p_hosp_sd <- stan_output_draws %>% + spread_draws(p_hosp_w_sd[1]) %>% + sample_draws(ndraws = n_draws) %>% + mutate(draw = `.draw`) %>% + mutate( + name = "p_hosp_sd", + t = NA + ) %>% + rename(value = p_hosp_w_sd) %>% + select(name, t, value, draw) + posterior_params <- rbind( + phi_h, eta_sd, log10_g, i0, + infection_feedback, + autoreg_rt, initial_growth, p_hosp_sd + ) + } else if (model_type == "hospital admissions only") { + posterior_params <- rbind( + phi_h, eta_sd, log10_g, i0, + infection_feedback, + autoreg_rt, initial_growth + ) + } else { # case for the site level wastewater models + + p_hosp_sd <- stan_output_draws %>% + spread_draws(p_hosp_w_sd) %>% + sample_draws(ndraws = n_draws) %>% + mutate(draw = `.draw`) %>% + mutate( + name = "p_hosp_sd", + t = NA + ) %>% + rename(value = p_hosp_w_sd) %>% + select(name, t, value, draw) + + posterior_params <- rbind( + phi_h, eta_sd, log10_g, i0, + infection_feedback, + autoreg_rt, initial_growth, p_hosp_sd + ) + } - posterior_params <- rbind( - phi_h, eta_sd, log10_g, i0, - infection_feedback, - autoreg_rt, initial_growth, p_hosp_sd - ) return(posterior_params) } @@ -1081,24 +1116,53 @@ get_parameter_draws <- function(model_draws, pars, train_data) { # Prepare for submission ---------------------------------------------------- + +#' Get location to model map +#' +#' @param df_of_filepaths the dataframe that comes out of fit model with +#' columns indicating the paths to the specified models and the model type +#' of those outputs +#' @param hosp_only_states the states we want to manually replace with the +#' hospital admissions only model for submission +#' @param us_model_type The default model type for the US +#' +#' @return +#' @export +#' +#' @examples +get_loc_model_map <- function(df_of_filepaths, + hosp_only_states, + us_model_type = "state-level aggregated wastewater") { + # Specify the desired model type + loc_model_map_states <- df_of_filepaths |> + dplyr::select(location, model_type) |> + # Modify model type to hospital admissions only if specified + dplyr::mutate( + model_type = dplyr::case_when( + (location %in% hosp_only_states) ~ "hospital admissions only", + TRUE ~ model_type + ) + ) + + us_df <- data.frame(location = "US", model_type = us_model_type) + loc_model_map <- rbind(loc_model_map_states, us_df) + + + return(loc_model_map) +} + #' Get a consolidated dataframe with each location and its corresponding #' file path for the necesary outputs. #' +#' @param prod_model_type the model type we want to submit, default is +#' "site-level infection dynamics" +#' @param loc_model_map two column dataframe with location and desired model type #' @param df_of_filepaths_inf_dyn the output filepaths resulting after running -#' the infection dynamics model targets, default is NA -#' @param df_of_filepaths_site_obs the output filepaths resulting after running -#' the site-level observation error model targets, default is NA +#' the infection dynamics model targets, default is NULL #' @param df_of_filepaths_hosp_only the output filepaths resulting after running -#' the hospital admissions only model targets, default is NA +#' the hospital admissions only model targets, default is NULL #' @param df_of_filepaths_agg the output filepaths resulting after running the -#' national aggreated model target, default is NA -#' @param df_of_filepaths_varying_conc the output filepaths resulting after -#' running the time varying concentration model targets, default is NA -#' @param prod_model_type the model type we want to submit, default is -#' "site-level infection dynamics" -#' @param hosp_only_states the states that we want to manually -#' specify to use the hospital admissions only model instead of the wastewater -#' informed model +#' national aggreated model target, default is NULL #' #' @return a dataframe of length of the number of locations (will message if #' not = 53) containing the model type and filepaths for the model outputs needed @@ -1107,76 +1171,40 @@ get_parameter_draws <- function(model_draws, pars, train_data) { #' #' @examples get_submission_filepath_df <- function(prod_model_type, - hosp_only_states, - df_of_filepaths_inf_dyn = NA, - df_of_filepaths_site_obs = NA, - df_of_filepaths_hosp_only = NA, - df_of_filepaths_agg = NA, - df_of_filepaths_varying_conc = NA) { - if (prod_model_type == "site-level observation error") { + loc_model_map, + df_of_filepaths_inf_dyn = NULL, + df_of_filepaths_hosp_only = NULL, + df_of_filepaths_agg = NULL) { + if (prod_model_type == "site-level infection dynamics") { stopifnot( "Filepaths for production model type not passed in" = - !is.na(df_of_filepaths_site_obs) + !is.null(df_of_filepaths_inf_dyn) ) - df_of_filepaths <- rbind( - df_of_filepaths_site_obs, - df_of_filepaths_agg - ) - } else if (prod_model_type == "site-level infection dynamics") { - stopifnot( - "Filepaths for production model type not passed in" = - !is.na(df_of_filepaths_inf_dyn) - ) - df_of_filepaths <- rbind( + df_of_filepaths_raw <- rbind( df_of_filepaths_inf_dyn, df_of_filepaths_agg ) - } else if (prod_model_type == "site-level time-varying concentration") { - stopifnot( - "Filepaths for production model type not passed in" = - !is.na(df_of_filepaths_varying_conc) - ) - df_of_filepaths <- rbind( - df_of_filepaths_varying_conc, - df_of_filepaths_agg - ) } else if (prod_model_type == "hospital admissions only") { stopifnot( "Filepaths for production model type not passed in" = - !is.na(df_of_filepaths_hosp_only) + !is.null(df_of_filepaths_hosp_only) ) - df_of_filepaths <- df_of_filepaths_hosp_only + df_of_filepaths_raw <- df_of_filepaths_hosp_only } else { message("Production model type not specified properly") } + # Get all the model file paths in one place + all_model_filepaths <- rbind( + df_of_filepaths_inf_dyn, + df_of_filepaths_agg, + df_of_filepaths_hosp_only + ) - if (!is.null(hosp_only_states)) { - # Replace the full file path of the wastewater model with the - # hospital admissions only model - inds_ho <- df_of_filepaths$location %in% c(hosp_only_states) - # This is a hacky very temporary way of ensuring the US is at the end. - # This needs to be refactored with a join by location - df_of_filepaths_ho_ordered <- df_of_filepaths_hosp_only %>% - filter(location != "US") - df_of_filepaths_hosp_only <- rbind( - df_of_filepaths_ho_ordered, - df_of_filepaths_hosp_only %>% - filter(location == "US") - ) - - df_of_filepaths$model_draws_file_path[inds_ho] <- - df_of_filepaths_hosp_only$model_draws_file_path[inds_ho] - df_of_filepaths$quantiles_file_path[inds_ho] <- - df_of_filepaths_hosp_only$quantiles_file_path[inds_ho] - df_of_filepaths$future_hosp_draws_file_path[inds_ho] <- - df_of_filepaths_hosp_only$future_hosp_draws_file_path[inds_ho] - df_of_filepaths$parameters_file_path[inds_ho] <- - df_of_filepaths_hosp_only$parameters_file_path[inds_ho] - df_of_filepaths$diagnostics_file_path[inds_ho] <- - df_of_filepaths_hosp_only$diagnostics_file_path[inds_ho] - # Replace model type - df_of_filepaths$model_type[inds_ho] <- "hospital admissions only" - } + df_of_filepaths <- loc_model_map |> + dplyr::inner_join(all_model_filepaths, + by = c("location", "model_type") + ) |> + distinct() if (any(duplicated(df_of_filepaths$location))) { stop("Multiple model outputs for a single location") @@ -1301,7 +1329,7 @@ get_df_for_hub_submission <- function(df_of_filepaths, )) message("Writing forecast Hub files to csv") - if (isTRUE(is_for_public_repo)) { + if (isTRUE(is_for_public_repo) && isTRUE(prod_run)) { create_dir(repo_file_path) write.table(quant_summary_full, file = diff --git a/cfaforecastrenewalww/R/sysdata.rda b/cfaforecastrenewalww/R/sysdata.rda index 6ab7e03e..efd4e4ba 100644 Binary files a/cfaforecastrenewalww/R/sysdata.rda and b/cfaforecastrenewalww/R/sysdata.rda differ diff --git a/cfaforecastrenewalww/inst/stan/renewal_ww_hosp.stan b/cfaforecastrenewalww/inst/stan/renewal_ww_hosp.stan index 0c0ddd5b..0031ea08 100644 --- a/cfaforecastrenewalww/inst/stan/renewal_ww_hosp.stan +++ b/cfaforecastrenewalww/inst/stan/renewal_ww_hosp.stan @@ -3,6 +3,7 @@ functions { #include functions/biased_rw.stan #include functions/convolve.stan #include functions/infections.stan +#include functions/hospitalization.stan #include functions/observation_model.stan #include functions/utils.stan } @@ -93,8 +94,10 @@ parameters { real inv_sqrt_phi_h; real sigma_ww; real p_hosp_int; // Estimated IHR - vector[tot_weeks -1] p_hosp_w; // weekly random walk for IHR - real p_hosp_w_sd; // Estimated IHR sd + vector[(include_ww==1) ? tot_weeks -1 : 0] p_hosp_w; + array [(include_ww==1) ? 1 : 0] real p_hosp_w_sd; + //vector[tot_weeks -1] p_hosp_w; // weekly random walk for IHR + // real p_hosp_w_sd; // Estimated IHR sd real t_peak; // time to viral load peak in shedding real viral_peak; // log10 peak viral load shed /mL real dur_shed; // duration of detectable viral shedding @@ -106,7 +109,7 @@ parameters { transformed parameters { vector[ot + uot + ht] new_i; // daily incident infections /n - vector[ot + uot + ht] p_hosp; // probability of hospitalization + vector [(include_ww ==1) ? ot + uot + ht: 1] p_hosp; // probability of hospitalization vector[ot + uot + ht] model_hosp; // model estimated hospital admissions vector[oht] exp_obs_hosp; // expected observed hospital admissions vector[ot] exp_obs_hosp_no_wday_effect; // expected observed hospital admissions before weekday effect @@ -142,12 +145,18 @@ transformed parameters { // Expected hospitalizations: // generates all hospitalizations, across unobserved time, observed time, and forecast time - p_hosp = p_hosp_m * append_row(p_hosp_int, p_hosp_w_sd * p_hosp_w); - p_hosp = inv_logit(p_hosp); - - // generates all hospitalizations, across unobserved time, observed time, and forecast time - model_hosp = convolve_dot_product(p_hosp .* new_i, reverse(inf_to_hosp), + if(include_ww==1){ + p_hosp = assemble_p_hosp(p_hosp_m, p_hosp_int, p_hosp_w_sd[1], p_hosp_w); + model_hosp = convolve_dot_product(p_hosp .* new_i, reverse(inf_to_hosp), + ot + uot + ht); + }else{ + p_hosp[1] = inv_logit(p_hosp_int); + // generates all hospitalizations, across unobserved time, observed time, and forecast time + model_hosp = convolve_dot_product(p_hosp[1] * new_i, reverse(inf_to_hosp), ot + uot + ht); + } + + // just get the expected observed hospitalizations exp_obs_hosp_no_wday_effect = model_hosp[uot + 1 : uot + ot]; diff --git a/cfaforecastrenewalww/man/get_generated_quantities_draws.Rd b/cfaforecastrenewalww/man/get_generated_quantities_draws.Rd index fdcff8cb..69ee6d2a 100644 --- a/cfaforecastrenewalww/man/get_generated_quantities_draws.Rd +++ b/cfaforecastrenewalww/man/get_generated_quantities_draws.Rd @@ -4,7 +4,7 @@ \alias{get_generated_quantities_draws} \title{Get generated quantities draws} \usage{ -get_generated_quantities_draws(all_draws, n_draws = 100) +get_generated_quantities_draws(all_draws, model_type, n_draws = 100) } \arguments{ \item{train_data}{} diff --git a/cfaforecastrenewalww/man/get_loc_model_map.Rd b/cfaforecastrenewalww/man/get_loc_model_map.Rd new file mode 100644 index 00000000..e81d0ec4 --- /dev/null +++ b/cfaforecastrenewalww/man/get_loc_model_map.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/process_model_outputs.R +\name{get_loc_model_map} +\alias{get_loc_model_map} +\title{Get location to model map} +\usage{ +get_loc_model_map( + df_of_filepaths, + hosp_only_states, + us_model_type = "state-level aggregated wastewater" +) +} +\arguments{ +\item{df_of_filepaths}{the dataframe that comes out of fit model with +columns indicating the paths to the specified models and the model type +of those outputs} + +\item{hosp_only_states}{the states we want to manually replace with the +hospital admissions only model for submission} + +\item{us_model_type}{The default model type for the US} +} +\description{ +Get location to model map +} diff --git a/cfaforecastrenewalww/man/get_metadata_yaml.Rd b/cfaforecastrenewalww/man/get_metadata_yaml.Rd index 10342b5a..d7795669 100644 --- a/cfaforecastrenewalww/man/get_metadata_yaml.Rd +++ b/cfaforecastrenewalww/man/get_metadata_yaml.Rd @@ -5,10 +5,16 @@ \title{Get metadata to list all states with no wastewater or insufficient wastewater data} \usage{ -get_metadata_yaml(full_diagnostics_df, repo_file_path, hosp_only_states, ...) +get_metadata_yaml( + full_diagnostics_df, + repo_file_path, + hosp_only_states, + prod_run, + ... +) } \arguments{ -\item{hosp_only_states}{} +\item{prod_run}{} } \description{ Get metadata to list all states with no wastewater or insufficient wastewater diff --git a/cfaforecastrenewalww/man/get_raw_param_draws.Rd b/cfaforecastrenewalww/man/get_raw_param_draws.Rd index 733f0276..c128f63e 100644 --- a/cfaforecastrenewalww/man/get_raw_param_draws.Rd +++ b/cfaforecastrenewalww/man/get_raw_param_draws.Rd @@ -4,7 +4,7 @@ \alias{get_raw_param_draws} \title{Get raw parameter draws} \usage{ -get_raw_param_draws(stan_output_draws, n_draws = 500, ...) +get_raw_param_draws(stan_output_draws, model_type, n_draws = 500, ...) } \arguments{ \item{...}{} diff --git a/cfaforecastrenewalww/man/get_submission_file_path.Rd b/cfaforecastrenewalww/man/get_submission_file_path.Rd index da9aa37f..704e46b0 100644 --- a/cfaforecastrenewalww/man/get_submission_file_path.Rd +++ b/cfaforecastrenewalww/man/get_submission_file_path.Rd @@ -1,20 +1,14 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_config_vals.R, R/process_model_outputs.R +% Please edit documentation in R/process_model_outputs.R \name{get_submission_file_path} \alias{get_submission_file_path} -\title{Get the submission file path fior hub csv} +\title{Get the hardcoded submission file path} \usage{ -get_submission_file_path(output_dir, forecast_date, date_run) - -get_submission_file_path(output_dir, forecast_date, date_run) +get_submission_file_path(output_dir) } \arguments{ -\item{date_run}{} - \item{...}{} } \description{ -Get the submission file path fior hub csv - Get the hardcoded submission file path } diff --git a/cfaforecastrenewalww/man/get_submission_filepath_df.Rd b/cfaforecastrenewalww/man/get_submission_filepath_df.Rd index 2b140ee8..96ecf8ad 100644 --- a/cfaforecastrenewalww/man/get_submission_filepath_df.Rd +++ b/cfaforecastrenewalww/man/get_submission_filepath_df.Rd @@ -7,36 +7,26 @@ file path for the necesary outputs.} \usage{ get_submission_filepath_df( prod_model_type, - hosp_only_states, - df_of_filepaths_inf_dyn = NA, - df_of_filepaths_site_obs = NA, - df_of_filepaths_hosp_only = NA, - df_of_filepaths_agg = NA, - df_of_filepaths_varying_conc = NA + loc_model_map, + df_of_filepaths_inf_dyn = NULL, + df_of_filepaths_hosp_only = NULL, + df_of_filepaths_agg = NULL ) } \arguments{ \item{prod_model_type}{the model type we want to submit, default is "site-level infection dynamics"} -\item{hosp_only_states}{the states that we want to manually -specify to use the hospital admissions only model instead of the wastewater -informed model} +\item{loc_model_map}{two column dataframe with location and desired model type} \item{df_of_filepaths_inf_dyn}{the output filepaths resulting after running -the infection dynamics model targets, default is NA} - -\item{df_of_filepaths_site_obs}{the output filepaths resulting after running -the site-level observation error model targets, default is NA} +the infection dynamics model targets, default is NULL} \item{df_of_filepaths_hosp_only}{the output filepaths resulting after running -the hospital admissions only model targets, default is NA} +the hospital admissions only model targets, default is NULL} \item{df_of_filepaths_agg}{the output filepaths resulting after running the -national aggreated model target, default is NA} - -\item{df_of_filepaths_varying_conc}{the output filepaths resulting after -running the time varying concentration model targets, default is NA} +national aggreated model target, default is NULL} } \value{ a dataframe of length of the number of locations (will message if diff --git a/cfaforecastrenewalww/man/get_summarized_table.Rd b/cfaforecastrenewalww/man/get_summarized_table.Rd index d6d6582c..b75acb88 100644 --- a/cfaforecastrenewalww/man/get_summarized_table.Rd +++ b/cfaforecastrenewalww/man/get_summarized_table.Rd @@ -8,11 +8,13 @@ get_summarized_table( hub_submission_df, full_diagnostics_df, hosp_only_states, - repo_file_path + repo_file_path, + prod_run, + ... ) } \arguments{ -\item{repo_file_path}{} +\item{prod_run}{} } \description{ Get summarized table with each location and diff --git a/cfaforecastrenewalww/man/save_to_pdf.Rd b/cfaforecastrenewalww/man/save_to_pdf.Rd index fc8c0f53..02f3f5b3 100644 --- a/cfaforecastrenewalww/man/save_to_pdf.Rd +++ b/cfaforecastrenewalww/man/save_to_pdf.Rd @@ -6,6 +6,7 @@ \usage{ save_to_pdf( list_of_plots, + model_name, type_of_output, pdf_file_path, forecast_date, diff --git a/cfaforecastrenewalww/tests/testthat/test_ho_model.R b/cfaforecastrenewalww/tests/testthat/test_ho_model.R index d1a8b553..9435be8f 100644 --- a/cfaforecastrenewalww/tests/testthat/test_ho_model.R +++ b/cfaforecastrenewalww/tests/testthat/test_ho_model.R @@ -46,7 +46,11 @@ test_that("Test the state-level hospitalization-only model on simulated data.", ) # Check the parameters we care most about - model_params <- get_model_param_df(fit) %>% dplyr::pull(param_name) + model_params <- get_model_param_df(fit) %>% + filter(!param_name %in% c("p_hosp_w_sd[1]", "p_hosp_w")) %>% + dplyr::pull(param_name) + # hospital admissions only model doesn't + # have time-varying IHR for (param in model_params) { expect_equal( posterior::subset_draws(obs_last_draw, variable = !!param), diff --git a/docs/evaluation_plan.md b/docs/evaluation_plan.md new file mode 100644 index 00000000..076c39aa --- /dev/null +++ b/docs/evaluation_plan.md @@ -0,0 +1,57 @@ +# Evaluation analysis scoping +This is a draft evaluation plan for the wastewater-informed COVID-19 forecasting models in this repo. Our aim is to complete a first analysis and draft a preprint by April 12th, and post the preprint circa April 26th. + +## Key questions this analysis should address: +1. What is the marginal value of incorporating wastewater data into a COVID-19 hospital admission forecasting model? We will quantify the change in forecast performance from incorporating wastewater with standard forecast evaluation metrics: a proper scoring rule and measures of error, bias, and coverage. +a. **The marginal value of wastewater within our model**. How do these metrics change when our model takes in wastewater data in addition to hospital admissions data? We will compare our model's forecast performance when it is fit to wastewater and incident admissions data to its performance when it is fit to admissions data alone. +b. **The real-time performance of our wastewater-informed model in a COVID forecasting challenge**. How did forecasts from our model submitted to the [COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) perform compared to other models submitted to the Hub, and compared to the Hub ensemble forecast? +2. How do the quality and quantity of wastewater data available for a location affect forecast model performance? +a. How much do forecast predictions change as a function of the following wastewater characteristics: (1) reporting lag, (2) sample collection cadence, (3) population coverage etc.? +b. What effect do these data quantity/quality features have on quantifiable forecast model performance? + +## Analysis plans +The below outline the specific analyses intended to answer each of these questions +### Retrospective evaluation of our model's performance with and without wastewater data over the winter 2023-2024 season +- Use time-stamped data sets of hospital admissions and site-level wastewater data under two data lags: + - 9 day hospital data delay: as if submitting on Monday from data available from wastewater as of Monday night, hospital admissions data up until previous Saturday + - 4 day hospital data delay: as if submitting on Wednesday from wastewater data available as of Monday night, hospital admissions data up until most recent Saturday + - **Note: we only have Monday night's NWSS data for the entire duration. If we can get time stamped datasets, we will use Sunday nights and Tuesday nights data** + - Proposed time: October 16, 2023 - May 1, 2024 (28 weeks) +- Generate forecasts from hospital admissions only renewal model and site-level infection dynamics wastewater model for all weeks, all states + DC, PR (excluding the US). Exclude location-weeks that don't have wastewater data OR that fit our criteria for insufficient wastewater (delayed by 21 days or < max of 5 points per site) +- Compare forecast performance on hospital admissions (nowcasts + forecasts) using proper scoring rules: CRPS for the 28 day ahead forecasts of hospital admissions and compare coverage and bias. We will use the [`scoringutils` R package](https://github.com/epiforecasts/scoringutils) to compute these metrics. + +### Real-time evaluation compared to the Hub models +From Feb 5, 2024 - May 4, 2024, use the archived real-time outputs to compare what we would have submitted real-time, for 3 sets of outputs: (i) all wastewater where possible (ii) hospital admissions only (iii) the human judgment filtered wastewater model that we submitted for all locations + - Use WIS for [log-transformed incidence](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011393), starting at the most granular (location and forecast date) and exploring different summary options + - Compare to the ensemble + top 3 performing Hub models by WIS for log transformed incidence over the period we submitted (Feb 5 - May 4). +Potential secondary analysis: hypothetical hub submissions with reduced admissions data latency. + - Use the exact codebase from Monday's run to generate forecasts on Wednesday using Tuesday's wastewater data, compare outputs from target end dates on Monday from Hub models to our Wednesday wastewater + hospital admissions outputs. + - We will set up infrastructure to save these outputs going forward (starting on 2/28), but we are not planning to include a comparative analysis of Monday vs ednesday runs in the first draft of the preprint. + + + ### Empirical evaluation of impact of wastewater characteristics on forecast performance +US states are heterogeneous in their wastewater data quantity, coverage, and reporting lag. We can leverage this heterogeneity to investigate empirically which characteristics are most critical to improving forecast performance. +- Use the results from the head-to-head model performance in each state and forecast date to assess the impact of: + - number of wastewater sites + - proportion of state population covered by the sites combined + - reporting lag across sites + - sample collection cadence across sites +- Capture for each forecast date and location, + - the difference between the two models' outputs: distance metric (which one?) + - the difference in forecast performance between the two models: compare CRPS scores + - We might need to average across forecast dates and locations to get something meaningful/interpretable, but propose we start more granular and go up. Final output could be as simple as avg change in forecasts vs wastewater characteristic avg model performance gain vs wastewater characteristic? + +## Additional questions that we might consider addressing +These are probably not in scope now, but they might be worth thinking about in future work +1. What is the added value of incorporating hospital admissions data AND combining wastewater data across sites using a renewal framework at improving forecasting of wastewater concentrations? + - This would entail coming up with two comparison model for wastewater + - (1) fits to individual sites alone + - (2) fits jointly across sites without wastewater data or renewal framework e.g. using brms + +The goal here would be to assess the added value of integrating multiple data signals (i.e. _multi-signal fusion_), either just from pooling data across sites without mechanism (might be super helpful in and of itself) or by integrating different types of signals using a semi-mechanistic framework with a shared latent process + +2. What is the theoretical impact of the various wastewater characteristics on forecast performance +Since the empirical analysis is subject to a range of biases (for example, states with more sites also probably have better surveillance), follow-up studies to investigate these might be worthwhile. This would entail: +- Simulating data from an underlying process with the ability to vary the number of sites, the proportion of the state population covered by the sites, the average reporting latency, the average collection cadence +- Sub-sampling the observed data to construct datasets with varying lags, number of sites, and population coverage +- Performing a sensitivity analysis across the variables described above, comparing gain in forecast performance across epidemic phases compared to a hospital admissions only model. diff --git a/model_definition.md b/model_definition.md index 5856ca81..938f5c46 100644 --- a/model_definition.md +++ b/model_definition.md @@ -124,8 +124,9 @@ $$H(t) = \omega(t) p_\mathrm{hosp}(t) \sum_{\tau = 0}^{T_d} d(\tau) I(t-\tau)$$ Where $T_d$ is the maximum delay from infection to hospitalization that we consider. We define the discrete hospital admissions delay distribution $d(\tau)$ as a convolution of the incubation period distribution [^Park2023] and a separate estimate of the distribution of time from symptom onset to hospital admission (see [Parameter section](#model-parameters) below for further details). +#### Infection-hospitalization rate +In the models that include fits to wastewater data, we allow the population-level infection-hospitalization rate (IHR) to change over time. An inferred change in the IHR could reflect either a true change in the rate at which infections result in hospital admissions (e.g. the age distribution of cases could shift, a more or less severe variant could emerge, or vaccine coverage could shift) or a change in the relationship between infections and genomes shed in wastewater $G$ (which we currently treat as fixed, but which could change in time if, for example, immunity reduces wastewater shedding without reducing transmission, or a variant emerges with a different per infection wastewater shedding profile). -The population-level infection-hospitalization ratio can change over time due to multiple unmodeled factors. For example, the age distribution of cases could shift, a more or less severe variant could emerge, or vaccine coverage could change. Therefore, we model the hospitalization proportion $p_\mathrm{hosp}(t)$ as a piecewise-constant function with weekly change points. If $t$ and $t'$ are two days in the same week, then $p_\mathrm{hosp}(t) = p_\mathrm{hosp}(t')$. @@ -136,6 +137,9 @@ $$ \mathrm{logit} (p_{\mathrm{hosp}}(t_2)) \sim \mathrm{Normal}(\mathrm{logit}(p The process is initialized at the calibration start time $t_0$ via a prior distribution (see [Prior Distributions](#prior-distributions) below). +In hospital admissions only models, we model the IHR as constant. We assign this constant IHR the same prior distribution we assign to the mean of the time-varying IHR in the wastewater-informed models. + +### Hospital admissions observation model We model the observed hospital admission counts $h_t$ as: $$h_t \sim \mathrm{NegBinom}(n H(t), \phi)$$ diff --git a/output/forecasts/2024-03-04/2024-03-04.tsv b/output/forecasts/2024-03-04/2024-03-04.tsv new file mode 100644 index 00000000..1ce8ef34 --- /dev/null +++ b/output/forecasts/2024-03-04/2024-03-04.tsv @@ -0,0 +1,34133 @@ +"target" "location" "forecast_date" "target_end_date" "quantile" "value" "type" "model_type" +"1 day ahead inc hosp" "02" 2024-03-04 2024-03-05 0.01 0.99 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-04 2024-03-05 0.025 1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-04 2024-03-05 0.05 1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "02" 2024-03-04 2024-03-05 0.1 2 "quantile" "site-level 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"quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.5 7 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.55 8 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.6 8 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.65 8 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.7 9 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.75 10 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.8 10.2 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.85 11 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.9 12.1 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.95 14 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.975 15.525 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "02" 2024-03-04 2024-03-20 0.99 16.01 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.01 0.99 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.025 1.475 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.05 2 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.1 2 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.15 3 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.2 3 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.25 3 "quantile" "site-level infection 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"site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.8 7 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.85 8 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.9 9 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.95 10 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.975 11.525 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "02" 2024-03-04 2024-03-21 0.99 13.01 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.01 1 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.025 2 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.05 2 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.1 3 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.15 3 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.2 3 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.25 4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.3 4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.35 4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.4 4 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.45 5 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.5 5 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "02" 2024-03-04 2024-03-22 0.55 5 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" 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2024-03-25 0.05 2 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.1 2 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.15 3 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.2 3 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.25 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.3 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.35 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.4 5 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.45 5 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "02" 2024-03-04 2024-03-25 0.5 5 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" 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2024-04-01 0.65 81 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.7 83.3 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.75 86.5 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.8 95.8 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.85 103.45 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.9 115.1 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.95 132 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.975 140.825 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "01" 2024-03-04 2024-04-01 0.99 148.26 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.01 17.98 "quantile" "site-level 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29 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.5 30 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.55 31 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.6 32 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.65 33 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.7 34 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.75 36 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.8 37 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.85 37.15 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.9 39.1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.95 41.05 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.975 44.575 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "05" 2024-03-04 2024-03-05 0.99 47 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.01 16.98 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.025 17 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.05 17 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.1 18.9 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.15 20.85 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.2 22 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "05" 2024-03-04 2024-03-06 0.25 23 "quantile" "site-level infection 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inc hosp" "04" 2024-03-04 2024-03-31 0.01 6.99 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.025 8.475 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.05 10.95 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.1 12.9 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.15 13 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.2 15 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.25 19.5 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.3 21.7 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.35 23 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.4 26 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.45 27 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.5 29 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.55 30 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.6 31.4 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.65 33.35 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.7 36 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.75 38 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.8 40.8 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.85 48 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.9 50.1 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.95 54.05 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.975 58.1 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "04" 2024-03-04 2024-03-31 0.99 61.1300000000001 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.01 6 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.025 7.95 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.05 10.9 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.1 13.9 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.15 15.85 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.2 17 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.25 19 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.3 19.7 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.35 22 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.4 23.6 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.45 25.55 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.5 28 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.55 29.45 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.6 31.4 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.65 33 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.7 34 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.75 35 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.8 39.4 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.85 44 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.9 53 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.95 55 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.975 59.625 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "04" 2024-03-04 2024-04-01 0.99 66.2400000000001 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.01 139.95 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.025 144 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.05 144.95 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.1 149 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.15 153 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.2 158 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.25 159 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.3 164 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.35 167.65 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.4 169 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.45 170 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.5 174 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.55 176.45 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.6 180.4 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.65 182.7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.7 189.3 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.75 194 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.8 198.2 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.85 202.15 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.9 208.1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.95 223 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.975 224.525 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "06" 2024-03-04 2024-03-05 0.99 227.47 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.01 124.94 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.025 130.85 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.05 142.6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.1 147 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.15 153 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.2 155 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.25 158 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.3 162.7 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.35 168.95 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.4 171.6 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.45 172.55 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.5 176.5 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.55 181 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.6 183.4 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.65 186.35 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.7 189.3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.75 193.25 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.8 199 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.85 203.15 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.9 208.1 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.95 218.05 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.975 225.05 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "06" 2024-03-04 2024-03-06 0.99 231.21 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.01 120.96 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.025 122 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.05 137 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.1 139 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.15 145 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.2 150.8 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.25 154.75 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.3 160.1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.35 166 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.4 168 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.45 169.55 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.5 173.5 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.55 176.35 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.6 182.4 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.65 186 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.7 188.3 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.75 191.25 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.8 195 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.85 197.45 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.9 204.3 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.95 227 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.975 236.05 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "06" 2024-03-04 2024-03-07 0.99 238.24 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.01 115.84 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.025 118.475 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.05 119 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.1 131.8 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.15 136.85 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.2 143 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.25 144 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.3 150 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.35 154 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.4 160.6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.45 163.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.5 168 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.55 172 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.6 175 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.65 177.35 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.7 181 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.75 185 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.8 187.6 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.85 192 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.9 197 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.95 210 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.975 214.05 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "06" 2024-03-04 2024-03-08 0.99 238.01 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.01 94.97 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.025 96.9 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.05 106.7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.1 116.8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.15 122.85 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.2 125 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.25 130 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.3 131.4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.35 134 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.4 137 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.45 141.55 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.5 145 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.55 147 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.6 149.8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.65 153 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.7 156 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.75 158 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.8 163.2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.85 167.15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.9 173 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.95 182.15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.975 189.1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "06" 2024-03-04 2024-03-09 0.99 194.23 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.01 96.98 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.025 100.85 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.05 111 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.1 117.9 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.15 122 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.2 124.8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.25 127.75 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.3 132 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.35 139.65 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.4 142 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.45 144 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.5 146.5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.55 149.45 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.6 151 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.65 152.35 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.7 157.3 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.75 159.25 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.8 164 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.85 166.15 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.9 173.9 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.95 193.15 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.975 208 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "06" 2024-03-04 2024-03-10 0.99 214.16 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.01 95.94 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.025 97.95 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.05 105.7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.1 118 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.15 124 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.2 129.8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.25 132.25 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.3 138.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.35 140.65 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.4 143.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.45 145 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.5 151.5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.55 157.45 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.6 161.4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.65 166.35 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.7 172.2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "06" 2024-03-04 2024-03-11 0.75 176 "quantile" "site-level 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286.45 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.01 57.96 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.025 68.475 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.05 75.95 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.1 80 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.15 95.4 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.2 100 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.25 106.75 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.3 114 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.35 120 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.4 125.6 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.45 129 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.5 133 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.55 141 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.6 143.8 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.65 147.7 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.7 153.3 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.75 161.5 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.8 175.4 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "06" 2024-03-04 2024-03-20 0.85 182 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0.65 143.35 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.7 148.3 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.75 152.5 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.8 167.2 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.85 180.45 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.9 192.5 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.95 229.25 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.975 261.875 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "06" 2024-03-04 2024-03-21 0.99 270.03 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "06" 2024-03-04 2024-03-22 0.01 52.97 "quantile" "site-level 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ahead inc hosp" "08" 2024-03-04 2024-03-06 0.45 16.55 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.5 17 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.55 18 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.6 19 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.65 20 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.7 21 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.75 21 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.8 22 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.85 23 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "08" 2024-03-04 2024-03-06 0.9 24.1 "quantile" "site-level 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15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.3 15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.35 16 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.4 17 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.45 17 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.5 18 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.55 18.45 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.6 20.4 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.65 21 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.7 22 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.75 22 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.8 23 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.85 23.15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.9 26 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.95 28.05 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.975 32.625 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "08" 2024-03-04 2024-03-07 0.99 39.06 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.01 6.96 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.025 7 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.05 8 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.1 10 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.15 11 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.2 11 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.25 12 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.3 13 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.35 14 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.4 14 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.45 14 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.5 15 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.55 16 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.6 17 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.65 17 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.7 18 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.75 20 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.8 21 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.85 22.15 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.9 23.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.95 29.05 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.975 31.525 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "08" 2024-03-04 2024-03-08 0.99 33.03 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.01 6 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.025 7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.05 7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.1 8.9 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.15 10 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.2 11 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.25 12 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.3 12 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.35 13 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.4 13 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.45 14 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.5 15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.55 15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.6 16 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.65 17 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.7 17.3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.75 18 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.8 19 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "08" 2024-03-04 2024-03-09 0.85 20 "quantile" "site-level infection dynamics" 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"quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.25 12.75 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.3 13 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.35 14 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.4 14 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.45 15 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.5 16 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.55 16.45 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.6 17 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.65 18 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.7 18.3 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.75 19.25 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.8 20.2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.85 22 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.9 23.2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.95 26 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.975 27.525 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "08" 2024-03-04 2024-03-10 0.99 31.04 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-04 2024-03-11 0.01 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-04 2024-03-11 0.025 7.475 "quantile" "site-level infection 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0.975 31.525 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "08" 2024-03-04 2024-03-11 0.99 35.01 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.01 5.96 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.025 7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.05 7 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.1 9 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.15 10 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.2 11 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.25 12 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.3 12 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.35 13 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.4 13.6 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.45 15 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.5 16 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.55 18 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.6 18 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.65 19 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.7 20 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.75 20.25 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.8 22 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.85 24 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.9 24.1 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.95 27.05 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.975 28 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "08" 2024-03-04 2024-03-12 0.99 30.05 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.01 6.98 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.025 8 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.05 9 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.1 9.9 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.15 10.85 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.2 12 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.25 12.75 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.3 13 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.35 14 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.4 14 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.45 14 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.5 15 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.55 16 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.6 17 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.65 17.35 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.7 18 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.75 19 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.8 20 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.85 21 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.9 23 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.95 29 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.975 33.1 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "08" 2024-03-04 2024-03-13 0.99 43 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "08" 2024-03-04 2024-03-14 0.01 6.98 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" 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"site-level infection dynamics" +"18 day ahead inc hosp" "08" 2024-03-04 2024-03-22 0.95 31.05 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "08" 2024-03-04 2024-03-22 0.975 37.575 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "08" 2024-03-04 2024-03-22 0.99 41.01 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.01 1.99 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.025 3 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.05 3 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.1 5 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.15 7 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.2 8 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.25 9 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.3 10 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.35 10 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.4 11 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.45 11 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.5 12 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.55 12.45 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.6 14 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.65 15 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "08" 2024-03-04 2024-03-23 0.7 16 "quantile" "site-level infection dynamics" 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"quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.1 6 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.15 7 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.2 8 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.25 8.75 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.3 9 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.35 9.65000000000001 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.4 10 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.45 11 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.5 12 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.55 13 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.6 14 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.65 15 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.7 15.3 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.75 16.25 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.8 19 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.85 20.15 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.9 21 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.95 26.15 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.975 31.575 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "08" 2024-03-04 2024-03-24 0.99 34 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.01 1.99 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.025 2.475 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.05 4 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.1 6.9 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.15 7 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.2 9 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.25 10 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.3 10 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.35 11 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.4 12 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.45 12.55 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.5 13 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.55 14 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.6 16 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.65 16 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.7 17.3 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.75 19 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.8 21 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.85 22 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.9 23.1 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.95 30 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.975 34.1499999999999 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "08" 2024-03-04 2024-03-25 0.99 41.01 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.01 4 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.025 5 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.05 6 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.1 7 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.15 8 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.2 9 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.25 9 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.3 10 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.35 11 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.4 12 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.45 13 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.5 14 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.55 14.45 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.6 15 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.65 15.35 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.7 16.3 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.75 18 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.8 20 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.85 23 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.9 26.1 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.95 31.05 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.975 42.575 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "08" 2024-03-04 2024-03-26 0.99 48.06 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.01 2.99 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.025 3.475 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.05 5 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.1 5.9 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.15 7 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.2 8 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.25 8 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.3 9 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.35 9 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.4 10 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.45 11 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.5 12 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.55 13 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.6 14 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.65 15 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.7 16 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.75 18 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.8 19 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.85 19 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.9 21 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.95 26.05 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.975 30.05 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "08" 2024-03-04 2024-03-27 0.99 46.08 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.01 3.98 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.025 4 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.05 4 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.1 6.9 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.15 7 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.2 8 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.25 8.75 "quantile" "site-level infection 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"quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.8 21 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.85 25.15 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.9 27.1 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.95 35 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.975 40.1 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "08" 2024-03-04 2024-03-28 0.99 44.1100000000001 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "08" 2024-03-04 2024-03-29 0.01 1.99 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "08" 2024-03-04 2024-03-29 0.025 2 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "08" 2024-03-04 2024-03-29 0.05 2 "quantile" "site-level infection dynamics" +"25 day 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2024-03-04 2024-03-29 0.99 42.06 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.01 0.99 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.025 2.475 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.05 3.95 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.1 4 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.15 6 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.2 7 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.25 8 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.3 8 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "08" 2024-03-04 2024-03-30 0.35 9 "quantile" "site-level infection 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"quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.2 14.8 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.25 15 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.3 18 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.35 19.65 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.4 21 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.45 23 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.5 24 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.55 25 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 2024-03-04 2024-03-19 0.6 27 "quantile" "site-level infection dynamics" +"15 day ahead inc hosp" "09" 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2024-03-20 0.45 22 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.5 24.5 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.55 26 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.6 27 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.65 29 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.7 30.3 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.75 32.25 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.8 34 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.85 35 "quantile" "site-level infection dynamics" +"16 day ahead inc hosp" "09" 2024-03-04 2024-03-20 0.9 37 "quantile" "site-level infection dynamics" +"16 day 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2024-03-04 2024-03-15 0.1 4.9 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.15 6 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.2 7 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.25 7 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.3 7 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.35 8 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.4 8 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.45 9 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.5 9 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "11" 2024-03-04 2024-03-15 0.55 10 "quantile" "site-level infection dynamics" +"11 day 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2024-03-27 0.15 9 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.2 9 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.25 10 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.3 10 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.35 11 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.4 12 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.45 12 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.5 13 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.55 13 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "10" 2024-03-04 2024-03-27 0.6 14.4 "quantile" "site-level infection dynamics" +"23 day ahead 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"quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.8 17.2 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.85 19 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.9 20 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.95 22.05 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.975 24.525 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "10" 2024-03-04 2024-03-29 0.99 25.04 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "10" 2024-03-04 2024-03-30 0.01 3.99 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "10" 2024-03-04 2024-03-30 0.025 4 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "10" 2024-03-04 2024-03-30 0.05 4.95 "quantile" "site-level infection dynamics" +"26 day ahead 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131.175 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.05 142.8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.1 146.8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.15 149.85 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.2 153.8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.25 157.75 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.3 161 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.35 166.3 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.4 170 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "12" 2024-03-04 2024-03-05 0.45 172.55 "quantile" "site-level infection dynamics" +"1 day 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2024-03-11 0.01 78 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.025 80.475 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.05 83.9 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.1 92.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.15 95 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.2 98 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.25 104 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.3 107.4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.35 109 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "13" 2024-03-04 2024-03-11 0.4 111 "quantile" "site-level infection dynamics" +"7 day 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day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.01 55.97 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.025 69 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.05 73.85 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.1 84.5 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.15 90.55 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.2 92.8 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.25 95.75 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.3 99.7 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.35 102 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "13" 2024-03-04 2024-03-28 0.4 105.6 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2024-03-06 0.5 50 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.55 51.45 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.6 54 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.65 54 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.7 56.3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.75 57 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.8 59 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.85 63.3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.9 67 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "21" 2024-03-04 2024-03-06 0.95 70 "quantile" "site-level infection dynamics" +"2 day ahead inc 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60.2 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "21" 2024-03-04 2024-03-07 0.85 62 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "21" 2024-03-04 2024-03-07 0.9 64.1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "21" 2024-03-04 2024-03-07 0.95 75.2 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "21" 2024-03-04 2024-03-07 0.975 79 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "21" 2024-03-04 2024-03-07 0.99 81.05 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "21" 2024-03-04 2024-03-08 0.01 23 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "21" 2024-03-04 2024-03-08 0.025 25.95 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "21" 2024-03-04 2024-03-08 0.05 27 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "21" 2024-03-04 2024-03-08 0.1 29.9 "quantile" "site-level infection dynamics" +"4 day ahead inc 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2024-03-30 0.2 29 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.25 30.75 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.3 33 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.35 35.3 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.4 37.6 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.45 38 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.5 40 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.55 44 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.6 45.4 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.65 48 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.7 51.2 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.75 57.25 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.8 62 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.85 65 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.9 75 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.95 91.2 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.975 106.35 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "21" 2024-03-04 2024-03-30 0.99 126.17 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.01 10.96 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.025 13.95 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.05 18.85 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.1 20.9 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.15 25 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.2 26.8 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.25 29.75 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.3 31.7 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.35 34 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.4 35.6 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "21" 2024-03-04 2024-03-31 0.45 38 "quantile" "site-level infection dynamics" +"27 day ahead 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2024-03-04 2024-03-07 0.7 57 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.75 58 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.8 60 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.85 62.15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.9 64.1 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.95 67 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.975 69.525 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "22" 2024-03-04 2024-03-07 0.99 73.1100000000001 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.01 29.99 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.025 31 "quantile" "site-level 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46 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.55 48 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.6 49.4 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.65 51 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.7 52 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.75 52.25 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.8 55 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.85 57 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.9 60.1 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.95 64.05 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.975 66.525 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "22" 2024-03-04 2024-03-08 0.99 69.06 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.01 21.96 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.025 26.475 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.05 29.95 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.1 31 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.15 34.85 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.2 36 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.25 36.75 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.3 38.7 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.35 40 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.4 41 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.45 42 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.5 44.5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.55 45 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.6 46 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.65 47 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.7 49 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.75 50.25 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "22" 2024-03-04 2024-03-09 0.8 53 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hosp" "22" 2024-03-04 2024-03-10 0.15 32.85 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.2 34 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.25 35.75 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.3 37 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.35 37.65 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.4 39 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.45 40 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.5 40.5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.55 41.45 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "22" 2024-03-04 2024-03-10 0.6 44 "quantile" "site-level infection 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0.01 26.99 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.025 29.95 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.05 32 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.1 35 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.15 37 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.2 38 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.25 39 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.3 40 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.35 42 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.4 44.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.45 46 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.5 47.5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.55 49 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.6 50.4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.65 51 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.7 53.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.75 55.25 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.8 58.2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.85 60 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "22" 2024-03-04 2024-03-11 0.9 63 "quantile" "site-level infection 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2024-03-04 2024-03-12 0.75 56 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.8 60 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.85 60 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.9 64 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.95 67.05 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.975 70 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "22" 2024-03-04 2024-03-12 0.99 74 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "22" 2024-03-04 2024-03-13 0.01 25.98 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "22" 2024-03-04 2024-03-13 0.025 30.95 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "22" 2024-03-04 2024-03-13 0.05 33.9 "quantile" "site-level infection 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2024-03-13 0.99 78.06 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.01 29.96 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.025 33 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.05 34.95 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.1 38 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.15 40 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.2 42 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.25 43 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.3 45.7 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "22" 2024-03-04 2024-03-14 0.35 47 "quantile" "site-level infection dynamics" 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2024-03-04 2024-03-16 0.025 25.95 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.05 29 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.1 33 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.15 36 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.2 37 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.25 38 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.3 39 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.35 40.65 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.4 41.6 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.45 42 "quantile" "site-level infection 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58.5 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.975 72 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "22" 2024-03-04 2024-03-16 0.99 73.06 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.01 19.96 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.025 23.95 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.05 25.95 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.1 30 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.15 33 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.2 35 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.25 35.75 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.3 38 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.35 39 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.4 39 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.45 40 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.5 41 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.55 42 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.6 43 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.65 44 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.7 45 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "22" 2024-03-04 2024-03-17 0.75 47 "quantile" "site-level 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2024-03-04 2024-03-18 0.1 35.9 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.15 38 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.2 40 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.25 40.75 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.3 42 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.35 43 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.4 45 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.45 46 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.5 48 "quantile" "site-level infection dynamics" +"14 day ahead inc hosp" "22" 2024-03-04 2024-03-18 0.55 49 "quantile" "site-level infection dynamics" 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0.025 33.95 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.05 36 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.1 40.8 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.15 42.85 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.2 45.8 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.25 46 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.3 48 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.35 50 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.4 51 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "22" 2024-03-04 2024-03-21 0.45 52 "quantile" "site-level infection dynamics" +"17 day ahead 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2024-03-09 0.85 33.15 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "24" 2024-03-04 2024-03-09 0.9 36.1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "24" 2024-03-04 2024-03-09 0.95 42.05 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "24" 2024-03-04 2024-03-09 0.975 45.05 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "24" 2024-03-04 2024-03-09 0.99 52.08 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "24" 2024-03-04 2024-03-10 0.01 12.99 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "24" 2024-03-04 2024-03-10 0.025 14.95 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "24" 2024-03-04 2024-03-10 0.05 16.95 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "24" 2024-03-04 2024-03-10 0.1 19 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "24" 2024-03-04 2024-03-10 0.15 21 "quantile" "site-level infection 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2024-03-11 0.025 15 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.05 17.9 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.1 20 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.15 20.85 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.2 22 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.25 23 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.3 23.7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.35 24.65 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.4 25.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "24" 2024-03-04 2024-03-11 0.45 27 "quantile" "site-level infection dynamics" +"7 day 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23.4 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.35 25 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.4 26 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.45 27 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.5 29.5 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.55 30 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.6 32 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.65 33.35 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.7 35.3 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.75 37.25 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.8 40 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.85 45 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.9 49.1 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.95 52 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.975 52.525 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "24" 2024-03-04 2024-03-12 0.99 63.2000000000001 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "24" 2024-03-04 2024-03-13 0.01 14.99 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "24" 2024-03-04 2024-03-13 0.025 15 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "24" 2024-03-04 2024-03-13 0.05 16 "quantile" "site-level infection dynamics" +"9 day ahead inc hosp" "24" 2024-03-04 2024-03-13 0.1 17 "quantile" "site-level 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2024-03-14 0.9 41.1 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "24" 2024-03-04 2024-03-14 0.95 48.05 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "24" 2024-03-04 2024-03-14 0.975 49 "quantile" "site-level infection dynamics" +"10 day ahead inc hosp" "24" 2024-03-04 2024-03-14 0.99 58.07 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.01 13.98 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.025 16 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.05 17.95 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.1 19 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.15 20 "quantile" "site-level infection dynamics" +"11 day ahead inc hosp" "24" 2024-03-04 2024-03-15 0.2 21 "quantile" "site-level infection 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2024-03-30 0.95 13.05 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "23" 2024-03-04 2024-03-30 0.975 16.525 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "23" 2024-03-04 2024-03-30 0.99 20.02 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.01 0 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.025 0.475 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.05 1.95 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.1 2 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.15 3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.2 3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "23" 2024-03-04 2024-03-31 0.25 4 "quantile" "site-level infection dynamics" 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"quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.25 26.75 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.3 28 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.35 29 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.4 31.6 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.45 33 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.5 36 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.55 38 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.6 41 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" "27" 2024-03-04 2024-03-21 0.65 42.35 "quantile" "site-level infection dynamics" +"17 day ahead inc hosp" 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2024-03-22 0.5 34 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.55 36.45 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.6 39 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.65 41.35 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.7 44 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.75 45 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.8 50 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.85 54.15 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.9 58.2 "quantile" "site-level infection dynamics" +"18 day ahead inc hosp" "27" 2024-03-04 2024-03-22 0.95 70.15 "quantile" "site-level infection dynamics" 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"quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.35 23 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.4 24 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.45 25 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.5 28.5 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.55 30.45 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.6 32.4 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.65 34 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.7 36.3 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "27" 2024-03-04 2024-03-23 0.75 39 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" 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2024-03-30 0.85 51.15 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "27" 2024-03-04 2024-03-30 0.9 59.1 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "27" 2024-03-04 2024-03-30 0.95 64.05 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "27" 2024-03-04 2024-03-30 0.975 67 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "27" 2024-03-04 2024-03-30 0.99 73.07 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "27" 2024-03-04 2024-03-31 0.01 5.98 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "27" 2024-03-04 2024-03-31 0.025 10 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "27" 2024-03-04 2024-03-31 0.05 11 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "27" 2024-03-04 2024-03-31 0.1 14 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "27" 2024-03-04 2024-03-31 0.15 19 "quantile" "site-level infection 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"site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.55 5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.6 5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.65 5 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.7 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.75 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.8 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.85 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.9 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.95 10 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.975 11.05 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "30" 2024-03-04 2024-03-10 0.99 13 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.01 0.99 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.025 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.05 1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.1 1.9 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.15 2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.2 2.8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.25 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.3 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.35 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.4 3.6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.45 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.5 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.55 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.6 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.65 5.35000000000001 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.7 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.75 7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "30" 2024-03-04 2024-03-11 0.8 7 "quantile" "site-level infection dynamics" +"7 day ahead inc 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0.95 115.3 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "37" 2024-03-04 2024-03-29 0.975 123.05 "quantile" "site-level infection dynamics" +"25 day ahead inc hosp" "37" 2024-03-04 2024-03-29 0.99 132.59 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.01 20.9 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.025 22 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.05 22 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.1 27.8 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.15 32.85 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.2 40.6 "quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "37" 2024-03-04 2024-03-30 0.25 43 "quantile" "site-level infection dynamics" 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0.3 11 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.35 13 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.4 14 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.45 15 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.5 16 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.55 17 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.6 18 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.65 19 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.7 20 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.75 21 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.8 22.2 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.85 24 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.9 25 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.95 27 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.975 31.525 "quantile" "site-level infection dynamics" +"19 day ahead inc hosp" "31" 2024-03-04 2024-03-23 0.99 35.07 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "31" 2024-03-04 2024-03-24 0.01 4.98 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "31" 2024-03-04 2024-03-24 0.025 5 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "31" 2024-03-04 2024-03-24 0.05 6 "quantile" "site-level infection dynamics" +"20 day ahead inc hosp" "31" 2024-03-04 2024-03-24 0.1 8.9 "quantile" "site-level 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2024-03-25 0.9 29.1 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "31" 2024-03-04 2024-03-25 0.95 32.05 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "31" 2024-03-04 2024-03-25 0.975 36.1 "quantile" "site-level infection dynamics" +"21 day ahead inc hosp" "31" 2024-03-04 2024-03-25 0.99 39.1300000000001 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.01 3 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.025 5.475 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.05 6.95 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.1 9 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.15 10 "quantile" "site-level infection dynamics" +"22 day ahead inc hosp" "31" 2024-03-04 2024-03-26 0.2 11 "quantile" "site-level 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2024-03-04 2024-03-27 0.975 33.525 "quantile" "site-level infection dynamics" +"23 day ahead inc hosp" "31" 2024-03-04 2024-03-27 0.99 36.05 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.01 4.98 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.025 6 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.05 7.95 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.1 9 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.15 9.85 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.2 10.8 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.25 11.75 "quantile" "site-level infection dynamics" +"24 day ahead inc hosp" "31" 2024-03-04 2024-03-28 0.3 12.7 "quantile" "site-level 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"quantile" "site-level infection dynamics" +"26 day ahead inc hosp" "32" 2024-03-04 2024-03-30 0.99 18.06 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.01 1 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.025 1.475 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.05 2 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.1 3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.15 3 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.2 4 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.25 4.75 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 2024-03-04 2024-03-31 0.3 5 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "32" 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0.65 10 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.7 10.3 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.75 12 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.8 13 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.85 14 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.9 16 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.95 18.05 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.975 20.525 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "32" 2024-03-04 2024-04-01 0.99 21 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "36" 2024-03-04 2024-03-05 0.01 63.91 "quantile" "site-level infection dynamics" +"1 day ahead 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0.8 67.6 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "45" 2024-03-04 2024-03-31 0.85 75.6 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "45" 2024-03-04 2024-03-31 0.9 90.5 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "45" 2024-03-04 2024-03-31 0.95 101.2 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "45" 2024-03-04 2024-03-31 0.975 105.525 "quantile" "site-level infection dynamics" +"27 day ahead inc hosp" "45" 2024-03-04 2024-03-31 0.99 161.670000000001 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.01 13.94 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.025 17.95 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.05 21.95 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.1 25.9 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.15 33.85 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.2 41 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.25 43 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.3 46.7 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.35 48 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.4 51.6 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.45 54 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.5 56.5 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.55 60.45 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.6 65 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.65 66.35 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.7 68.3 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.75 74.25 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.8 79.6 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.85 85.15 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.9 96.3 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.95 108.3 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.975 123.825 "quantile" "site-level infection dynamics" +"28 day ahead inc hosp" "45" 2024-03-04 2024-04-01 0.99 184.120000000001 "quantile" 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5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.45 5 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.5 6 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.55 6 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.6 7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.65 7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.7 7 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.75 8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.8 9 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.85 9 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.9 10 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.95 11 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.975 14 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "46" 2024-03-04 2024-03-05 0.99 15 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.01 0.99 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.025 1 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.05 1.95 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.1 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.15 3 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 2024-03-04 2024-03-06 0.2 3.8 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "46" 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"46" 2024-03-04 2024-03-08 0.9 11 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "46" 2024-03-04 2024-03-08 0.95 13 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "46" 2024-03-04 2024-03-08 0.975 14.525 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "46" 2024-03-04 2024-03-08 0.99 16.01 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.01 0 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.025 1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.05 1 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.1 2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.15 2 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "46" 2024-03-04 2024-03-09 0.2 3 "quantile" "site-level infection dynamics" +"5 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2024-03-10 0.55 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.6 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.65 6 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.7 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.75 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.8 7 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.85 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.9 8 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.95 10 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 2024-03-04 2024-03-10 0.975 11 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "46" 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2024-03-11 0.5 130 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.55 132.45 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.6 136 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.65 140.7 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.7 145 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.75 148 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.8 152 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.85 155 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.9 165.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "48" 2024-03-04 2024-03-11 0.95 178.05 "quantile" "site-level infection dynamics" +"7 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0.5 3 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.55 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.6 4 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.65 4.35000000000001 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.7 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.75 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.8 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.85 5 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.9 6 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.95 8 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.975 8.52499999999999 "quantile" "site-level infection dynamics" +"5 day ahead inc hosp" "50" 2024-03-04 2024-03-09 0.99 10.02 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.01 0.99 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.025 1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.05 1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.1 1 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.15 2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.2 2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.25 2 "quantile" "site-level infection dynamics" +"6 day ahead inc hosp" "50" 2024-03-04 2024-03-10 0.3 2 "quantile" "site-level infection 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0.15 2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.2 2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.25 2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.3 2 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.35 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.4 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.45 3 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.5 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.55 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.6 4 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.65 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.7 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.75 5 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.8 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.85 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.9 6 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.95 8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.975 8 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "50" 2024-03-04 2024-03-11 0.99 9 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.01 0 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.025 0.475 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.05 1 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.1 1 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.15 1.85 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.2 2 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.25 2 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.3 3 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.35 3 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.4 3 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "50" 2024-03-04 2024-03-12 0.45 4 "quantile" "site-level infection dynamics" +"8 day ahead 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0.75 4.25000000000001 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.8 5 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.85 5 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.9 6 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.95 6.05 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.975 7.52499999999999 "quantile" "site-level infection dynamics" +"12 day ahead inc hosp" "50" 2024-03-04 2024-03-16 0.99 10.01 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.01 0 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.025 0 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.05 1 "quantile" "site-level infection 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"site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.6 4.40000000000001 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.65 5 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.7 5 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.75 5 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.8 6 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.85 6 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.9 7 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.95 7.05 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 2024-03-04 2024-03-17 0.975 8 "quantile" "site-level infection dynamics" +"13 day ahead inc hosp" "50" 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2024-03-04 2024-03-05 0.025 6 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.05 6.95 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.1 8 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.15 9 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.2 10 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.25 11 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.3 12 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.35 12 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.4 13 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.45 13 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.5 14 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.55 14 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.6 15 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.65 16 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.7 18 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.75 19 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.8 19.2 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.85 21 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.9 22.1 "quantile" "site-level infection dynamics" +"1 day ahead inc hosp" "54" 2024-03-04 2024-03-05 0.95 24.05 "quantile" "site-level infection 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"quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.35 14 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.4 14 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.45 15 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.5 16 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.55 17 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.6 17 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.65 18 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.7 19 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.75 19 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.8 21 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.85 22 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.9 23 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.95 25.05 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.975 27 "quantile" "site-level infection dynamics" +"2 day ahead inc hosp" "54" 2024-03-04 2024-03-06 0.99 29.04 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.01 5.97 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.025 6 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.05 7 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.1 8 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.15 9 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.2 10 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.25 10.75 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.3 11 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.35 12 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.4 13 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.45 13 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.5 14 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.55 15 "quantile" "site-level infection dynamics" +"3 day ahead inc hosp" "54" 2024-03-04 2024-03-07 0.6 15.4 "quantile" "site-level infection 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2024-03-08 0.45 12 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.5 13 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.55 14 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.6 15 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.65 15 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.7 16 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.75 17 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.8 18 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.85 20 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" "54" 2024-03-04 2024-03-08 0.9 21 "quantile" "site-level infection dynamics" +"4 day ahead inc hosp" 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0.9 24.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "54" 2024-03-04 2024-03-11 0.95 27 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "54" 2024-03-04 2024-03-11 0.975 30.1 "quantile" "site-level infection dynamics" +"7 day ahead inc hosp" "54" 2024-03-04 2024-03-11 0.99 35.06 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.01 5 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.025 6 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.05 6.95 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.1 8 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.15 8.85 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" "54" 2024-03-04 2024-03-12 0.2 9.8 "quantile" "site-level infection dynamics" +"8 day ahead inc hosp" 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day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.75 1801.5 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.8 1983.2 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.85 2263.4 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.9 2474.6 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.95 2742.4 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.975 3216.92499999999 "quantile" "state-level aggregated wastewater" +"24 day ahead inc hosp" "US" 2024-03-04 2024-03-28 0.99 3738.73 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.01 242.56 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.025 436.325 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.05 521.45 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.1 657.8 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.15 706.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.2 785.4 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.25 902.25 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.3 1014.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.35 1066.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.4 1138.6 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.45 1186.1 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.5 1246 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.55 1343.85 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.6 1418 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.65 1511 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.7 1554.4 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.75 1772.5 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.8 1970.4 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.85 2173.45 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.9 2318.9 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.95 2654.05 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.975 3055.375 "quantile" "state-level aggregated wastewater" +"25 day ahead inc hosp" "US" 2024-03-04 2024-03-29 0.99 3294.17 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.01 235.23 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.025 408 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.05 435.65 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.1 563.8 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.15 629.1 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.2 690.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.25 808.75 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.3 911.8 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.35 982.5 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.4 1021.4 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.45 1063.65 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.5 1135 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.55 1180.8 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.6 1284.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.65 1343.85 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.7 1437.9 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.75 1560.75 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.8 1746.2 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.85 1953.2 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.9 2091.6 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.95 2382.15 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.975 2852.2 "quantile" "state-level aggregated wastewater" +"26 day ahead inc hosp" "US" 2024-03-04 2024-03-30 0.99 3317.12 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.01 212.55 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.025 381.5 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.05 461.2 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.1 554.1 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.15 622.7 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.2 677 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.25 800.25 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.3 919.4 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.35 974.85 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.4 1019.6 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.45 1084.85 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.5 1141 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.55 1234.9 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.6 1279.6 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.65 1389.35 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.7 1464.8 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.75 1597 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.8 1774.8 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.85 1981.85 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.9 2220.7 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.95 2492.4 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.975 2987.94999999999 "quantile" "state-level aggregated wastewater" +"27 day ahead inc hosp" "US" 2024-03-04 2024-03-31 0.99 3559.28 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.01 208.53 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.025 392.875 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.05 498.5 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.1 618.7 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.15 679.7 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.2 729.6 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.25 847.75 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.3 1007.3 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.35 1065.8 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.4 1124.8 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.45 1192.9 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.5 1248 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.55 1332.75 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.6 1384.2 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.65 1566.7 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.7 1725.9 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.75 1791.75 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.8 2105.8 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.85 2359.65 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.9 2518 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.95 2855.75 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.975 3441.47499999999 "quantile" "state-level aggregated wastewater" +"28 day ahead inc hosp" "US" 2024-03-04 2024-04-01 0.99 3824.14 "quantile" "state-level aggregated wastewater" diff --git a/output/forecasts/2024-03-04/metadata.yaml b/output/forecasts/2024-03-04/metadata.yaml new file mode 100644 index 00000000..286e5d43 --- /dev/null +++ b/output/forecasts/2024-03-04/metadata.yaml @@ -0,0 +1,13 @@ +States without wastewaster data: +- - MS + - ND + - PR +States with insufficient wastewater data: +- - KY + - DC + - ID +States we chose to use hospital admissions only model on: +- - ID + - OH + - UT + - VA diff --git a/output/forecasts/2024-03-04/wastewater_metadata_table.tsv b/output/forecasts/2024-03-04/wastewater_metadata_table.tsv new file mode 100644 index 00000000..9d894953 --- /dev/null +++ b/output/forecasts/2024-03-04/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 Hospital admissions only model was run due to either issues with input data or model +IL None +IN None +KS None +KY None +LA None +MA None +MD None +ME None +MI None +MN None +MO None +MS None +MT None +NC None +ND None +NE None +NH None +NJ None +NM None +NV None +NY None +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 Hospital admissions only model was run due to either issues with input data or model +VT None +WA None +WI None +WV None +WY None diff --git a/src/test_pipeline.R b/src/test_pipeline.R new file mode 100644 index 00000000..9a3ead1c --- /dev/null +++ b/src/test_pipeline.R @@ -0,0 +1,6 @@ +e2e_result <- testthat::test_file(here::here("src", "tests", "test_end_to_end.R")) + +if ("error" %in% class(e2e_result[[1]]$results[[1]])) { + message("test failure") + quit(save = "no", status = 1) +} diff --git a/src/tests/test_end_to_end.R b/src/tests/test_end_to_end.R new file mode 100644 index 00000000..d543210b --- /dev/null +++ b/src/tests/test_end_to_end.R @@ -0,0 +1,86 @@ +testthat::test_that("End to end test of the pipeline. Should run without error.", { + repo_path <- here::here() + + tmp_dir <- tempfile() + fs::dir_create(tmp_dir) + + ####### + # input + ####### + repo_input <- fs::path(repo_path, "input") + tmp_input <- fs::path(tmp_dir, "input") + fs::dir_create(tmp_input) + + repo_locations <- fs::path(repo_input, "locations.csv") + tmp_locations <- fs::path(tmp_input, "locations.csv") + fs::file_copy(repo_locations, tmp_locations) + + repo_pmfs <- fs::path(repo_input, "saved_pmfs") + tmp_pmfs <- fs::path(tmp_input, "saved_pmfs") + fs::dir_copy(repo_pmfs, tmp_pmfs) + + repo_toml <- fs::path(repo_input, "params.toml") + tmp_toml <- fs::path(tmp_input, "params.toml") + fs::file_copy(repo_toml, tmp_toml) + + ####### + # src + ####### + repo_src <- fs::path(repo_path, "src") + tmp_src <- fs::path(tmp_dir, "src") + fs::dir_copy(repo_src, tmp_src) + + ####### + # secrets + ####### + repo_secrets <- fs::path(repo_path, "secrets.yaml") + cfaforecastrenewalww::setup_secrets(repo_secrets) + + ####### + # diagnostic report + ####### + repo_diag <- fs::path(repo_path, "model_diagnostics", "diagnostic_report.Rmd") + tmp_diag <- fs::path(tmp_dir, "model_diagnostics", "diagnostic_report.Rmd") + fs::dir_create(dirname(tmp_diag)) + fs::file_copy(repo_diag, tmp_diag) + + ####### + # targets file + ####### + repo_targets <- fs::path(repo_path, "_targets.R") + tmp_targets <- fs::path(tmp_dir, "_targets.R") + targets_txt <- scan( + repo_targets, + what = character(), + sep = "\n", + blank.lines.skip = FALSE + ) + + targets_txt <- targets_txt[!grepl("setup_secrets", targets_txt)] |> + paste0(collapse = "\n") + stopifnot( + "Cannot find NULL location in _targets.R to replace with 2-state test." = + grepl("location = NULL,", targets_txt) + ) + stopifnot( + "Cannot find prod_run = FALSE in _targets.R to prod_run = TRUE." = + grepl("prod_run = FALSE,", targets_txt) + ) + targets_txt <- gsub("location = NULL,", "location = c(\"AK\", \"AL\"),", targets_txt) + targets_txt <- gsub("prod_run = FALSE,", "prod_run = TRUE,", targets_txt) + cat(targets_txt, file = tmp_targets) + + ####### + # try running pipeline + ####### + testthat::expect_no_error(!!{ + withr::with_dir(tmp_dir, { + targets::tar_make() + }) + }) + + ####### + # cleanup + ####### + fs::dir_delete(tmp_dir) +}) diff --git a/src/write_config.R b/src/write_config.R index 408e2b25..db0d187e 100644 --- a/src/write_config.R +++ b/src/write_config.R @@ -100,16 +100,40 @@ write_config <- function(run_id, # Assign the dates and locations for hospital admissions to be manually # removed - dates_for_hosp_removal <- c(seq( - from = lubridate::ymd("2024-01-30"), - to = lubridate::ymd("2024-02-02"), + last_3 <- seq( + from = lubridate::ymd("2024-02-21"), + to = lubridate::ymd("2024-02-23"), by = "days" - )) + ) + last_2 <- seq( + from = lubridate::ymd("2024-02-22"), + to = lubridate::ymd("2024-02-23"), + by = "days" + ) + last_1 <- lubridate::ymd("2024-02-23") + dates_for_hosp_removal <- c( + last_2, # AZ + last_3, # CT + last_1, # IL + last_2, # ME + last_3, # MD + last_3, # NJ + last_3, # NM + last_1, # PA + last_3 # DC + ) - states_for_hosp_removal <- c(rep( - "TX", - 4 - )) + states_for_hosp_removal <- c( + rep("AZ", 2), + rep("CT", 3), + rep("IL", 1), + rep("ME", 2), + rep("MD", 3), + rep("NJ", 3), + rep("NM", 3), + rep("PA", 1), + rep("DC", 3) + ) # Assign the dates and locations for wastewater data to be removed manually first_date <- forecast_date - lubridate::days(calibration_time) - hosp_reporting_delay