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Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change Healthcare. It is built and maintained by the Carnegie Mellon University Delphi research group.
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Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.
The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases for the USA at various geographical resolutions, both from official government sources such as the [Center for Disease Control (CDC)](https://www.cdc.gov/datastatistics/index.html) and [Google Trends](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/google-symptoms.html) and private partners such as [Facebook](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/). It is built and maintained by the Carnegie Mellon University [Delphi research group](https://delphi.cmu.edu/).
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This package is designed to streamline the downloading and usage of data from the [Delphi Epidata
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API](https://cmu-delphi.github.io/delphi-epidata/). 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](https://github.com/cmu-delphi/epiprocess)) and modeling ([epipredict](https://github.com/cmu-delphi/epipredict)).
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## Usage
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```{r}
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library(epidatr)
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# Obtain the smoothed covid-like illness (CLI) signal from the
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# Facebook survey as it was on April 10, 2021 for the US
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epidata <- pub_covidcast(
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source = "fb-survey",
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signals = "smoothed_cli",
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geo_type = "nation",
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time_type = "day",
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geo_values = "us",
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time_values = epirange(20210101, 20210601),
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as_of = "2021-06-01"
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)
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epidata
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```
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```{r fb-cli-signal}
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# Plot this data
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library(ggplot2)
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ggplot(epidata, aes(x = time_value, y = value)) +
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geom_line() +
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labs(
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title = "Smoothed CLI from Facebook Survey",
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subtitle = "US, 2021",
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x = "Date",
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y = "CLI"
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)
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```
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## Installation
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Install from GitHub:
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```R
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# Install the dev version using `pak` or `remotes`
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pak::pkg_install("cmu-delphi/epidatr")
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remotes::install_github("cmu-delphi/epidatr")
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```
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CRAN version coming soon.
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### API Keys
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The Delphi API requires a (free) API key for full functionality. To generate
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your key, register for a pseudo-anonymous account
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[here](https://api.delphi.cmu.edu/epidata/admin/registration_form) and see more
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discussion on the [general API
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website](https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html). The
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`epidatr` client will automatically look for this key in the R option
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`delphi.epidata.key` or in the environment variable
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`DELPHI_EPIDATA_KEY`. We recommend storing your key in `.Renviron` file, which R
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will read by default.
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Note that for the time being, the private endpoints (i.e. those prefixed with
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`pvt`) will require a separate key that needs to be passed as an argument.
You should consider subscribing to the [API mailing list](https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api) to be notified of package updates, new data sources, corrections, and other updates.
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## For users of the `covidcast` R package
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The `epidatr` package is a complete rewrite of the [`covidcast` package](https://cmu-delphi.github.io/covidcast/covidcastR/), with a focus on speed, reliability, and ease of use. The `covidcast` package is deprecated and will no longer be updated.
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