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Delphi Epidata R client

License: MIT Github Actions codecov

The Delphi Epidata API provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the Centers for Disease Control and Prevention (CDC), private partners such as Facebook (now Meta) and Change Healthcare, and other public datasets like Google Trends. It is built and maintained by the Carnegie Mellon University Delphi Research Group.

This package is designed to streamline the downloading and usage of data from the Delphi Epidata API. It provides a simple R interface to the API, including functions for downloading data, parsing the results, and converting the data into a tidy format. The API stores a historical record of all data, including corrections and updates, which is particularly useful for accurately backtesting forecasting models. We also provide packages for downstream data processing (epiprocess) and modeling (epipredict).

Usage

library(epidatr)
# Obtain the smoothed covid-like illness (CLI) signal from Delphi's US COVID-19
# Trends and Impact Survey (CTIS), in partnership with Facebook, as it was on
# April 10, 2021 for the US at the national level
epidata <- pub_covidcast(
  source = "fb-survey",
  signals = "smoothed_cli",
  geo_type = "nation",
  time_type = "day",
  geo_values = "us",
  time_values = epirange(20210101, 20210601),
  as_of = 20210601
)
epidata
#> # A tibble: 151 × 15
#>    geo_value signal    source geo_type time_type time_value direction issue     
#>    <chr>     <chr>     <chr>  <fct>    <fct>     <date>         <dbl> <date>    
#>  1 us        smoothed… fb-su… nation   day       2021-01-01        NA 2021-01-06
#>  2 us        smoothed… fb-su… nation   day       2021-01-02        NA 2021-01-07
#>  3 us        smoothed… fb-su… nation   day       2021-01-03        NA 2021-01-08
#>  4 us        smoothed… fb-su… nation   day       2021-01-04        NA 2021-01-09
#>  5 us        smoothed… fb-su… nation   day       2021-01-05        NA 2021-01-10
#>  6 us        smoothed… fb-su… nation   day       2021-01-06        NA 2021-01-29
#>  7 us        smoothed… fb-su… nation   day       2021-01-07        NA 2021-01-29
#>  8 us        smoothed… fb-su… nation   day       2021-01-08        NA 2021-01-29
#>  9 us        smoothed… fb-su… nation   day       2021-01-09        NA 2021-01-29
#> 10 us        smoothed… fb-su… nation   day       2021-01-10        NA 2021-01-29
#> # ℹ 141 more rows
#> # ℹ 7 more variables: lag <dbl>, missing_value <dbl>, missing_stderr <dbl>,
#> #   missing_sample_size <dbl>, value <dbl>, stderr <dbl>, sample_size <dbl>

Installation

Installing the package is straightforward.

# Install the CRAN version
pak::pkg_install("epidatr")
# Install the development version from the GitHub dev branch
pak::pkg_install("cmu-delphi/epidatr@dev")

Our CRAN listing is here.

API Keys

The Delphi API requires a (free) API key for full functionality. To generate your key, register for a pseudo-anonymous account here and see more discussion on the general API website. The epidatr client will automatically look for this key in the environment variable DELPHI_EPIDATA_KEY. We recommend storing your key in your .Renviron file, which R will read by default.

Note that for the time being, the private endpoints (i.e. those prefixed with pvt) will require a separate key that needs to be passed as an argument.

For users of the covidcast R package

The covidcast package is deprecated and will no longer be updated. The epidatr package is a complete rewrite of the covidcast package, with a focus on speed, reliability, and ease of use. It also supports more endpoints and data sources than covidcast. When migrating from that package, you will need to use the pub_covidcast function in epidatr.

Get updates

You should consider subscribing to the API mailing list to be notified of package updates, new data sources, corrections, and other updates.

Usage terms and citation

We request that if you use the epidatr package in your work, or use any of the data provided by the Delphi Epidata API through non-covidcast endpoints, that you cite us using the citation given by citation("epidatr"). If you use any of the data from the covidcast endpoint, please use the COVIDcast citation as well. See the COVIDcast licensing documentation and the licensing documentation for other endpoints for information about citing the datasets provided by the API.

Warning: If you use data from the Epidata API to power a product, dashboard, app, or other service, please download the data you need and store it centrally rather than making API requests for every user. Our server resources are limited and cannot support high-volume interactive use.

See also the Terms of Use, noting that the data is a research product and not warranted for a particular purpose.