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_nhsn = NULL,
start_date_nssp = NULL,
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_nhsn
Earliest week-ending date to include in the NHSN (admissions) target dataset. Default
NULL(include all available data).- start_date_nssp
Earliest week-ending date to include in the NSSP (ED visit) target dataset. Default
NULL(include all available 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).
- 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.