This function retrieves hospital utilization time series data distributed through healthdata.gov. Data are aggregated to the state granularity from facility level reports via HHS TeleTracking, HHS Protect, and the National Healthcare Safety Network (historically). Users can optionally filter to include all fields or restrict to a prespecified set of fields relevant to COVID and influenza hospital utilization. The results are returned as a tibble.
Usage
get_hdgov_hosp(
endpoint = "https://healthdata.gov/api/views/g62h-syeh/rows.csv",
app_token = Sys.getenv("HEALTHDATA_APP_TOKEN"),
limitcols = FALSE,
shift_back = TRUE
)Arguments
- endpoint
URL to healthdata.gov endpoint
- app_token
App token from healthdata.gov; default is to look for environment variable called
"HEALTHDATA_APP_TOKEN"and if a token is not supplied to proceed with possibility of rate limitation (see "Details" for more information)- limitcols
Logical as to whether or not to limit to prespecified set of columns (see "Value" section for more details); default
FALSE- shift_back
Logical as to whether or not the dates for the retrieved data should be shifted back to reflect previous day; default is
TRUE
Value
A tibble with at least the following columns:
state: Abbreviation of the state
date: Date of report
flu.admits: Count of flu cases among admitted patients on previous day
flu.admits.cov: Coverage (number of hospitals reporting) for incident flu cases
flu.deaths: Count of flu deaths on previous day
flu.deaths.cov: Coverage (number of hospitals reporting) for flu deaths
flu.icu: Count of flu cases among ICU patients on previous day
flu.icu.cov: Coverage (number of hospitals reporting) for flu ICU cases
flu.tot: Count of total flu cases among admitted patients
flu.tot.cov: Coverage (number of hospitals reporting) for total flu cases
cov.admits: Count of COVID cases among admitted patients on previous day
cov.admits.cov: Coverage (number of hospitals reporting) for incident COVID cases
cov.deaths: Count of COVID deaths on previous day
cov.deaths.cov: Coverage (number of hospitals reporting) for COVID deaths
If limitcols=TRUE then the only columns returned will be those listed above. However, if limitcols=FALSE then the function will additionally return all other fields in the state-aggregated hospitalization data.
Details
The data retrieval will proceed whether or not an API token has been supplied via the app_token argument. However, to avoid possible rate limits it is recommended to retrieve a token for the healthdata.gov API (https://healthdata.gov/profile/edit/developer_settings), and add that token as an entry to .Renviron with HEALTHDATA_APP_TOKEN="yourtokenhere".