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Generate a full report for a disease and reference date with sensible, consistent configuration.

Source: R/generate_hub_report.R
generate_hub_report.Rd

Wrapper function for write_ref_date_summary_ens(), write_ref_date_summary_all(), write_viz_target_data(), and write_webtext().

Usage

generate_hub_report(
  reference_date,
  disease,
  hub_reports_path,
  base_hub_path = NULL,
  horizons = c(0, 1, 2),
  population_data = hubhelpr::population_data,
  excluded_locations = NULL,
  targets = NULL,
  n_models_for_ens_reporting = NULL,
  output_format = "csv",
  overwrite_existing = FALSE,
  observed_data_use_hub = FALSE,
  observed_data_as_of = "latest",
  observed_data_start_date = NULL,
  observed_data_end_date = NULL,
  verbose = TRUE
)

Arguments

reference_date

character, the reference date for the forecast in YYYY-MM-DD format (ISO-8601).

disease

character, disease name ("covid" or "rsv").

hub_reports_path

character, path to forecast hub reports directory.

base_hub_path

character, path to the forecast hub directory.

horizons

integer vector, forecast horizons to include in the output. Default: c(0, 1, 2).

population_data

data frame with columns "location" and "population". Used to compute per-population metrics such as rates per 100k from rate counts. Default: population_data.

excluded_locations

NULL, character vector, or named list of US state/territory abbreviations to exclude. If a character vector, locations are excluded across all targets. If a named list, names should be target names (or "all" for global exclusions) mapping to character vectors of abbreviations. Default: NULL (no exclusions).

targets

character vector, target name(s) to filter forecasts for reporting. If NULL (default), does not filter out targets.

n_models_for_ens_reporting

integer, minimum number of designated model submissions required to include an ensemble forecast in the report. Default: NULL, which uses the minimum designated for reference_date, so that regenerating an older report applies the rule it was published under rather than today's. See get_reference_date_ens_minimum().

output_format

character, output file format. One of "csv", "tsv", or "parquet". Default: "csv".

overwrite_existing

logical. If TRUE, overwrite existing files. Default: FALSE.

observed_data_use_hub

Logical, whether to read data from the hub's time-series file (TRUE) or pull fresh data from raw sources (FALSE) when creating observed data files. Default: FALSE.

observed_data_as_of

As of date for the observed data shown in the report. Either an object coercible by as.Date() or "latest" to use the most recent available vintage. Default "latest". Used only when observed_data_use_hub = TRUE.

observed_data_start_date

Date, earliest date to include in observed data shown in the report. Default: NULL (no filtering). Used only when observed_data_use_hub = FALSE.

observed_data_end_date

Date, latest date to include in observed data shown in the report. Default: NULL (no filtering). Used only when observed_data_use_hub = FALSE.

verbose

Report progress to the terminal? Default TRUE.

Value

NULL, invisibly