Add Function For Generating Forecast Webpage Text

NAMESPACE

@@ -6,7 +6,9 @@ export(excluded_locations)
 export(generate_hub_baseline)
 export(generate_hub_ensemble)
 export(generate_oracle_output)
+export(generate_webtext_block)
 export(get_hub_name)
+export(get_webtext)
 export(included_locations)
 export(summarize_ref_date_forecasts)
 export(update_authorized_users)

R/get_webtext.R

@@ -0,0 +1,357 @@
+#' Check hospital reporting data latency and completeness.
+#'
+#' This function retrieves hospital reporting data from
+#' data.cdc.gov and checks for data latency and reporting
+#' completeness issues. It returns a flag string
+#' describing any reporting issues.
+#'
+#' @param reference_date Date, the reference date for the
+#' forecast.
+#' @param disease Character, disease name ("covid" or
+#' "rsv").
+#' @param excluded_locations Character vector of location
+#' codes to exclude. Default: character(0).
+#'
+#' @return Character string describing reporting issues,
+#' or empty string if no issues.
+check_hospital_reporting_latency <- function(
+  reference_date,
+  disease,
+  excluded_locations = character(0)
+) {
+  desired_weekendingdate <- as.Date(reference_date) - lubridate::dweeks(1)
+
+  disease_abbr <- dplyr::case_match(
+    disease,
+    "covid" ~ "c19",
+    "rsv" ~ "rsv"
+  )
+
+  reporting_column <- glue::glue(
+    "totalconf{disease_abbr}newadmperchosprepabove80pct"
+  )
+
+  percent_hosp_reporting_below80 <- forecasttools::pull_data_cdc_gov_dataset(
+    dataset = "mpgq-jmmr",
+    columns = reporting_column,
+    start_date = "2024-11-09"
+  ) |>
+    dplyr::mutate(
+      weekendingdate = as.Date(.data$weekendingdate),
+      report_above_80_lgl = as.logical(
+        as.numeric(.data[[reporting_column]])
+      ),
+      jurisdiction = dplyr::case_match(
+        .data$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 <- cli::ansi_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 {
+    ""
+  }
+
+  return(reporting_rate_flag)
+}
+
+
+#' Generate forecast hub webpage text block.
+#'
+#' This function creates formatted text content for
+#' forecast hub visualizations. It processes forecast
+#' data, target data, and team metadata to generate a
+#' text description.
+#'
+#' @param reference_date Character, the reference date for
+#' the forecast in YYYY-MM-DD format (ISO-8601).
+#' @param disease Character, disease name ("covid" or
+#' "rsv").
+#' @param base_hub_path Character, path to the forecast
+#' hub directory.
+#' @param hub_reports_path Character, path to forecast
+#' hub reports directory.
+#' @param excluded_locations Character vector of location
+#' codes to exclude. Default: character(0).
+#'
+#' @return Character string containing the formatted
+#' webpage text.
+#' @export
+generate_webtext_block <- function(
+  reference_date,
+  disease,
+  base_hub_path,
+  hub_reports_path,
+  excluded_locations = character(0)
+) {
+  checkmate::assert_choice(disease, choices = c("covid", "rsv"))
+
+  reference_date <- lubridate::as_date(reference_date)
+
+  hub_name <- get_hub_name(disease)
+  disease_name <- dplyr::case_match(
+    disease,
+    "covid" ~ "COVID-19",
+    "rsv" ~ "RSV"
+  )
+
+  weekly_data_path <- fs::path(
+    hub_reports_path,
+    "weekly-summaries",
+    reference_date
+  )
+
+  # could possibly use write_ref_date_summary_ensemble() or
+  # summarize_ref_date_forecasts()?
+  ensemble_us_1wk_ahead <- forecasttools::read_tabular(
+    fs::path(
+      weekly_data_path,
+      glue::glue("{reference_date}_{disease}_map_data"),
+      ext = "csv"
+    )
+  ) |>
+    dplyr::filter(horizon == 1, location_name == "US")
+
+  target_data <- forecasttools::read_tabular(
+    fs::path(
+      weekly_data_path,
+      glue::glue(
+        "{reference_date}_{disease}_target_hospital_admissions_data"
+      ),
+      ext = "csv"
+    )
+  )
+
+  contributing_teams <- forecasttools::read_tabular(
+    fs::path(
+      weekly_data_path,
+      glue::glue("{reference_date}_{disease}_forecasts_data"),
+      ext = "csv"
+    )
+  ) |>
+    dplyr::filter(model != glue::glue("{hub_name}-ensemble")) |>
+    dplyr::pull(model) |>
+    unique()
+
+  wkly_submissions <- hubData::load_model_metadata(
+    base_hub_path,
+    model_ids = contributing_teams
+  ) |>
+    dplyr::distinct(.data$model_id, .data$designated_model, .keep_all = TRUE) |>
+    dplyr::mutate(
+      team_model_url = glue::glue(
+        "[{team_name} (Model: {model_abbr})]({website_url})"
+      )
+    ) |>
+    dplyr::select(
+      model_id,
+      team_abbr,
+      model_abbr,
+      team_model_url,
+      designated_model
+    )
+
+  reporting_rate_flag <- check_hospital_reporting_latency(
+    reference_date = reference_date,
+    disease = disease,
+    excluded_locations = excluded_locations
+  )
+
+  round_to_place <- function(value) {
+    if (value >= 1000) {
+      rounded_val <- round(value, -2)
+    } else if (value >= 10) {
+      rounded_val <- round(value, -1)
+    } else {
+      rounded_val <- round(value, 0)
+    }
+    return(rounded_val)
+  }
+
+  # generate variables used in the web text
+
+  median_forecast_1wk_ahead <- round_to_place(
+    ensemble_us_1wk_ahead$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 {hub_name} ensemble's one-week-ahead forecast predicts that the number ",
+    "of new weekly laboratory-confirmed {disease_name} hospital admissions will be ",
+    "approximately {median_forecast_1wk_ahead} nationally, with ",
+    "{lower_95ci_forecast_1wk_ahead} to {upper_95ci_forecast_1wk_ahead} ",
+    "laboratory confirmed {disease_name} 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 {disease_name} 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 {disease_name} hospital ",
+    "admissions reported in the United States each week from ",
+    "{first_target_data_date} through {last_target_data_date} and forecasted ",
+    "new {disease_name} 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 {hub_name} ensemble:\n",
+    "{paste(model_incl_in_hub_ensemble, collapse = '\n')}\n\n",
+    "Models not included in the {hub_name} ensemble:\n",
+    "{paste(model_not_incl_in_hub_ensemble, collapse = '\n')}"
+  )
+
+  return(web_text)
+}
+
+
+#' Generate and save text content for forecast hub
+#' visualization webpage.
+#'
+#' Light wrapper function that generates formatted text
+#' summaries and saves them to disk.
+#'
+#' @param reference_date Character, the reference date for
+#' the forecast in YYYY-MM-DD format (ISO-8601).
+#' @param disease Character, disease name ("covid" or
+#' "rsv"). Used to derive hub name, file prefix, and
+#' disease display name.
+#' @param base_hub_path Character, path to the forecast hub
+#' directory.
+#' @param hub_reports_path Character, path to forecast hub
+#' reports directory.
+#' @param excluded_locations Character vector of location
+#' codes to exclude from reporting calculations. Default:
+#' character(0).
+#'
+#' @export
+get_webtext <- function(
+  reference_date,
+  disease,
+  base_hub_path,
+  hub_reports_path,
+  excluded_locations = character(0)
+) {
+  reference_date <- lubridate::as_date(reference_date)
+
+  web_text <- generate_webtext_block(
+    reference_date = reference_date,
+    disease = disease,
+    base_hub_path = base_hub_path,
+    hub_reports_path = hub_reports_path,
+    excluded_locations = excluded_locations
+  )
+
+  weekly_data_path <- fs::path(
+    hub_reports_path,
+    "weekly-summaries",
+    reference_date
+  )
+
+  output_filepath <- fs::path(
+    weekly_data_path,
+    glue::glue("{reference_date}_webtext"),
+    ext = "md"
+  )
+
+  fs::dir_create(weekly_data_path)
+
+  if (!fs::file_exists(output_filepath)) {
+    writeLines(web_text, output_filepath)
+    cli::cli_inform("Webtext saved as: {output_filepath}")
+  } else {
+    cli::cli_abort("File already exists: {output_filepath}")
+  }
+
+  return(invisible())
+}