Pull NHSN data from data.cdc.gov — pull

Pull relevant epidemiological data from NHSN, defaulting to the data.cdc.gov public API endpoint.

Usage

pull_nhsn(
  api_endpoint = "https://data.cdc.gov/resource/mpgq-jmmr.json",
  api_key_id = Sys.getenv("NHSN_API_KEY_ID"),
  api_key_secret = Sys.getenv("NHSN_API_KEY_SECRET"),
  start_date = NULL,
  end_date = NULL,
  columns = NULL,
  jurisdictions = NULL,
  order_by = c("jurisdiction", "weekendingdate"),
  desc = FALSE,
  limit = 1e+05,
  error_on_limit = TRUE,
  ...
)

Arguments

api_endpoint: API endpoint to use. Defaults to the https:/.json Socrata endpoint for NHSN COVID, Influenza, and RSV Wednesday release of data on data.cdc.gov, namely data.cdc.gov/resource/mpgq-jmmr.json
api_key_id: Key ID of an API key to use when querying the dataset. Not required, but polite and reduces throttling. You can create one at data.cdc.gov/profile/edit/developer_settings . Defaults to the value of the environment variable NHSN_API_KEY_ID, if any.
api_key_secret: Associated key secret for the API key given in api_key_id. Defaults to the value of the environment variable NHSN_API_KEY_SECRET, if any.
start_date: Pull only rows with dates greater than or equal to this date. If NULL, no minimum date. Default NULL.
end_date: Pull only rows with dates less than or equal to this date. If NULL, no maximum date. Default NULL.
columns: Vector of columns to retrieve, in addition to weekendingdate and jurisdiction, which are always retrieved. If NULL, retrieve all columns. Default NULL.
jurisdictions: value or values to filter on for the jurisdiction column of the NHSN dataset. If NULL, do not filter on that column. Default NULL.
order_by: column or columns to order (sort) by. Default c("jurisdiction", "weekendingdate") (sort first by jurisdiction, then by date).
desc: Boolean. Whether to order descending instead of ascending. Default FALSE (order ascending).
limit: maximum number of rows to return. Default 1e5 (100000)
error_on_limit: Boolean. Raise an error if the number of rows returned is equal to the maximum? Default TRUE. This ensures that one does not silently end up with a subset of the total set of rows matching the query. If a subset is desired, one can set error_on_limit = FALSE.
...: other arguments passed to nhsn_soda_query()

Value

the pulled data, as a tibble.