Update hub target data. — update_hub_target

This function pulls, formats and saves NHSN and NSSP data for use in the Hub. It combines both data sources with any existing data and writes to the target-data directory.

Usage

update_hub_target_data(
  base_hub_path,
  disease,
  as_of = lubridate::today(),
  start_date = lubridate::as_date("2024-11-09"),
  excluded_locations = NULL,
  legacy_file = FALSE,
  nssp_update_local = FALSE,
  overwrite_existing = FALSE
)

Arguments

base_hub_path: Path to the base hub directory.
disease: Disease name ("covid" or "rsv").
as_of: As-of date of the data pull. Default is the system date as determined by lubridate::today().
start_date: First week-ending date to include for the NHSN dataset. Default value is "2024-11-09".
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).
legacy_file: Logical. Whether to write legacy CSV output (default: FALSE).
nssp_update_local: Logical. Whether to update NSSP data from local hub file auxiliary-data/latest.parquet (default: FALSE).
overwrite_existing: Logical. If TRUE, overwrite existing rows that share key columns (target_end_date, location, as_of, target) with the new data. If FALSE (default), error if any conflicts are found.

Value

Writes time-series.parquet and optionally legacy CSV target data files to the target-data directory in the hub.