add updated webtext script

Author: O957

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ repos:
 #####
 # Basic file cleanliness
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: check-added-large-files
     -   id: check-yaml
@@ -13,7 +13,7 @@ repos:
 #####
 # Python
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.10
+  rev: v0.13.1
   hooks:
     # Sort imports
     - id: ruff
@@ -27,13 +27,13 @@ repos:
 #####
 # R
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9009
+    rev: v0.4.3.9014
     hooks:
     -   id: lintr
 #####
 # Java
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.14.0
+  rev: v2.15.0
   hooks:
   - id: pretty-format-java
     args: [--aosp,--autofix]

R/get_webtext.R

@@ -0,0 +1,264 @@
+#' Generate text content for COVID-19 forecast
+#' visualization webpage.
+#'
+#' This script generates formatted text summaries for the
+#' COVID-19 forecast visualization webpage. It processes
+#' ensemble forecast data, target hospital admissions data,
+#' and contributing team information to create a text
+#' description of the current week's COVID-19
+#' hospitalization forecasts.
+#'
+#' Usage:
+#' Rscript src/get_webtext.R --reference-date "2025-09-19"
+#' --hub-reports-path "../covidhub-reports"
+
+parser <- argparser::arg_parser(
+  "Generate text for the webpage."
+)
+parser <- argparser::add_argument(
+  parser,
+  "--reference-date",
+  type = "character",
+  help = "The reference date for the forecast in YYYY-MM-DD format (ISO-8601)"
+)
+parser <- argparser::add_argument(
+  parser,
+  "--base-hub-path",
+  type = "character",
+  default = ".",
+  help = "Path to the Covid19 forecast hub directory."
+)
+parser <- argparser::add_argument(
+  parser,
+  "--hub-reports-path",
+  type = "character",
+  default = "../covidhub-reports",
+  help = "path to COVIDhub reports directory"
+)
+
+args <- argparser::parse_args(parser)
+reference_date <- args$reference_date
+base_hub_path <- args$base_hub_path
+hub_reports_path <- args$hub_reports_path
+
+weekly_data_path <- file.path(
+  hub_reports_path,
+  "weekly-summaries",
+  reference_date
+)
+
+ensemble_us_1wk_ahead <- readr::read_csv(
+  file.path(weekly_data_path, paste0(reference_date, "_covid_map_data.csv")),
+  show_col_types = FALSE
+) |>
+  dplyr::filter(horizon == 1, location_name == "US")
+
+target_data <- readr::read_csv(
+  file.path(
+    weekly_data_path,
+    paste0(
+      reference_date,
+      "_covid_target_hospital_admissions_data.csv"
+    )
+  ),
+  show_col_types = FALSE
+)
+
+contributing_teams <- readr::read_csv(
+  file.path(
+    weekly_data_path,
+    paste0(reference_date, "_covid_forecasts_data.csv")
+  ),
+  show_col_types = FALSE
+) |>
+  dplyr::filter(model != "CovidHub-ensemble") |>
+  dplyr::pull(model) |>
+  unique()
+
+wkly_submissions <- hubData::load_model_metadata(
+  base_hub_path,
+  model_ids = contributing_teams
+) |>
+  dplyr::distinct(.data$model_id, .data$designated_model, .keep_all = TRUE) |>
+  dplyr::mutate(
+    team_model_url = glue::glue(
+      "[{team_name} (Model: {model_abbr})]({website_url})"
+    )
+  ) |>
+  dplyr::select(
+    model_id,
+    team_abbr,
+    model_abbr,
+    team_model_url,
+    designated_model
+  )
+
+# Generate flag for less than 80 percent of hospitals reporting
+desired_weekendingdate <- as.Date(reference_date) - lubridate::dweeks(1)
+
+exclude_territories_path <- fs::path(
+  base_hub_path,
+  "auxiliary-data",
+  "excluded_territories",
+  ext = "toml"
+)
+stopifnot(fs::file_exists(exclude_territories_path))
+exclude_territories_toml <- RcppTOML::parseTOML(exclude_territories_path)
+excluded_locations <- exclude_territories_toml$locations
+
+percent_hosp_reporting_below80 <- forecasttools::pull_data_cdc_gov_dataset(
+  dataset = "mpgq-jmmr",
+  columns = c("totalconfc19newadmperchosprepabove80pct"),
+  start_date = "2024-11-09"
+) |>
+  dplyr::mutate(
+    weekendingdate = as.Date(.data$weekendingdate),
+    report_above_80_lgl = as.logical(
+      as.numeric(.data$totalconfc19newadmperchosprepabove80pct)
+    ),
+    jurisdiction = dplyr::case_match(
+      .data$jurisdiction,
+      "USA" ~ "US",
+      .default = .data$jurisdiction
+    ),
+    location = forecasttools::us_location_recode(
+      .data$jurisdiction,
+      "abbr",
+      "code"
+    ),
+    location_name = forecasttools::us_location_recode(
+      .data$jurisdiction,
+      "abbr",
+      "name"
+    )
+  ) |>
+  dplyr::filter(!(.data$location %in% !!excluded_locations)) |>
+  dplyr::group_by(.data$jurisdiction) |>
+  dplyr::mutate(max_weekendingdate = max(.data$weekendingdate)) |>
+  dplyr::ungroup()
+
+jurisdiction_w_latency <- percent_hosp_reporting_below80 |>
+  dplyr::filter(.data$max_weekendingdate < !!desired_weekendingdate)
+
+if (nrow(jurisdiction_w_latency) > 0) {
+  cli::cli_warn(
+    "
+    Some locations have missing reported data for the most recent week.
+    The reference date is {reference_date}, we expect data at least
+    through {desired_weekendingdate}. However, {nrow(jurisdiction_w_latency)}
+    location{?s} did not have reporting through that date:
+    {jurisdiction_w_latency$location_name}.
+  "
+  )
+}
+
+latest_reporting_below80 <- percent_hosp_reporting_below80 |>
+  dplyr::filter(
+    .data$weekendingdate == max(.data$weekendingdate),
+    !.data$report_above_80_lgl
+  )
+
+reporting_rate_flag <- if (length(latest_reporting_below80$location_name) > 0) {
+  location_list <- if (length(latest_reporting_below80$location_name) < 3) {
+    glue::glue_collapse(latest_reporting_below80$location_name, sep = " and ")
+  } else {
+    glue::glue_collapse(
+      latest_reporting_below80$location_name,
+      sep = ", ",
+      last = ", and "
+    )
+  }
+
+  glue::glue(
+    "The following jurisdictions had <80% of hospitals reporting for ",
+    "the most recent week: {location_list}. ",
+    "Lower reporting rates could impact forecast validity. Percent ",
+    "of hospitals reporting is calculated based on the number of active ",
+    "hospitals reporting complete data to NHSN for a given reporting week.\n\n"
+  )
+} else {
+  ""
+}
+
+round_to_place <- function(value) {
+  if (value >= 1000) {
+    rounded_val <- round(value, -2)
+  } else if (value >= 10) {
+    rounded_val <- round(value, -1)
+  } else {
+    rounded_val <- round(value, 0)
+  }
+  return(rounded_val)
+}
+
+# generate variables used in the web text
+
+median_forecast_1wk_ahead <- round_to_place(
+  ensemble_us_1wk_ahead$quantile_0.5_count
+)
+lower_95ci_forecast_1wk_ahead <- round_to_place(
+  ensemble_us_1wk_ahead$quantile_0.025_count
+)
+upper_95ci_forecast_1wk_ahead <- round_to_place(
+  ensemble_us_1wk_ahead$quantile_0.975_count
+)
+
+designated <- wkly_submissions[wkly_submissions$designated_model, ]
+not_designated <- wkly_submissions[!wkly_submissions$designated_model, ]
+weekly_num_teams <- length(unique(designated$team_abbr))
+weekly_num_models <- length(unique(designated$model_abbr))
+model_incl_in_hub_ensemble <- designated$team_model_url
+model_not_incl_in_hub_ensemble <- not_designated$team_model_url
+
+first_target_data_date <- format(
+  as.Date(min(target_data$week_ending_date)),
+  "%B %d, %Y"
+)
+last_target_data_date <- format(
+  as.Date(max(target_data$week_ending_date)),
+  "%B %d, %Y"
+)
+forecast_due_date <- ensemble_us_1wk_ahead$forecast_due_date_formatted
+target_end_date_1wk_ahead <- ensemble_us_1wk_ahead$target_end_date_formatted
+target_end_date_2wk_ahead <- format(
+  ensemble_us_1wk_ahead$target_end_date + lubridate::weeks(1),
+  "%B %d, %Y"
+)
+
+last_reported_target_data <- target_data |>
+  dplyr::filter(week_ending_date == max(week_ending_date), location == "US") |>
+  dplyr::mutate(week_end_date_formatted = format(week_ending_date, "%B %d, %Y"))
+
+last_reported_admissions <- round(last_reported_target_data$value, -2)
+
+web_text <- glue::glue(
+  "The CovidHub ensemble's one-week-ahead forecast predicts that the number ",
+  "of new weekly laboratory-confirmed COVID-19 hospital admissions will be ",
+  "approximately {median_forecast_1wk_ahead} nationally, with ",
+  "{lower_95ci_forecast_1wk_ahead} to {upper_95ci_forecast_1wk_ahead} ",
+  "laboratory confirmed COVID-19 hospital admissions likely reported in the ",
+  "week ending {target_end_date_1wk_ahead}. This is compared to the ",
+  "{last_reported_admissions} admissions reported for the week ",
+  "ending {last_reported_target_data$week_end_date_formatted}, the most ",
+  "recent week of reporting from U.S. hospitals.\n\n",
+  "Reported and forecasted new COVID-19 hospital admissions as of ",
+  "{forecast_due_date}. This week, {weekly_num_teams} modeling groups ",
+  "contributed {weekly_num_models} forecasts that were eligible for inclusion ",
+  "in the ensemble forecasts for at least one jurisdiction.\n\n",
+  "The figure shows the number of new laboratory-confirmed COVID-19 hospital ",
+  "admissions reported in the United States each week from ",
+  "{first_target_data_date} through {last_target_data_date} and forecasted ",
+  "new COVID-19 hospital admissions per week for this week and the next ",
+  "2 weeks through {target_end_date_2wk_ahead}.\n\n",
+  "{reporting_rate_flag}\n",
+  "Contributing teams and models:\n\n",
+  "Models included in the CovidHub ensemble:\n",
+  "{paste(model_incl_in_hub_ensemble, collapse = '\n')}\n\n",
+  "Models not included in the CovidHub ensemble:\n",
+  "{paste(model_not_incl_in_hub_ensemble, collapse = '\n')}"
+)
+
+writeLines(
+  web_text,
+  file.path(weekly_data_path, paste0(reference_date, "_webtext.md"))
+)