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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,124 @@ | ||
| --- | ||
| title: New package released! Epidatr, an R client for Delphi Epidata API | ||
| author: Dmitry Shemetov, David Weber | ||
| date: 2023-09-27 | ||
| tags: | ||
| - r | ||
| - epidata | ||
| - covidcast | ||
| authors: | ||
| - dmitry | ||
| - davidweb | ||
| heroImage: blog-lg-epidatr.jpg | ||
| heroImageThumb: blog-thumb-epidatr.jpg | ||
| summary: | | ||
| `epidatr` is designed to streamline the downloading and usage of data from the [Delphi Epidata 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. | ||
| output: | ||
| blogdown::html_page: | ||
| toc: true | ||
| --- | ||
|
|
||
| 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 from both official government sources such as the [Centers | ||
| for Disease Control and Prevention | ||
| (CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as | ||
| [Facebook (now | ||
| Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) | ||
| and [Change Healthcare](https://www.changehealthcare.com/), and other public | ||
| datasets like [Google | ||
| Trends](https://console.cloud.google.com/marketplace/product/bigquery-public-datasets/covid19-search-trends). | ||
| It is built and maintained by the Carnegie Mellon University [Delphi Research | ||
| Group](https://delphi.cmu.edu/). | ||
|
|
||
| Today we introduce the R package `epidatr`, available [on | ||
| CRAN](https://cloud.r-project.org/web/packages/epidatr/index.html), with the | ||
| source and development [on github](https://github.com/cmu-delphi/epidatr). | ||
|
|
||
| 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](https://github.com/cmu-delphi/epiprocess)) and modeling | ||
| ([epipredict](https://github.com/cmu-delphi/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 | ||
| <chr> <chr> <chr> <fct> <fct> <date> | ||
| 1 us smoothed_cli fb-su… nation day 2021-01-01 | ||
| 2 us smoothed_cli fb-su… nation day 2021-01-02 | ||
| 3 us smoothed_cli fb-su… nation day 2021-01-03 | ||
| 4 us smoothed_cli fb-su… nation day 2021-01-04 | ||
| 5 us smoothed_cli fb-su… nation day 2021-01-05 | ||
| 6 us smoothed_cli fb-su… nation day 2021-01-06 | ||
| 7 us smoothed_cli fb-su… nation day 2021-01-07 | ||
| 8 us smoothed_cli fb-su… nation day 2021-01-08 | ||
| 9 us smoothed_cli fb-su… nation day 2021-01-09 | ||
| 10 us smoothed_cli fb-su… nation day 2021-01-10 | ||
| # ℹ 141 more rows | ||
| # ℹ 9 more variables: direction <dbl>, issue <date>, | ||
| # lag <dbl>, missing_value <dbl>, missing_stderr <dbl>, | ||
| # missing_sample_size <dbl>, value <dbl>, stderr <dbl>, | ||
| # sample_size <dbl> | ||
| # ℹ Use `print(n = ...)` to see more rows | ||
| ``` | ||
|
|
||
| ## 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") | ||
| ``` | ||
|
|
||
| ### API Keys | ||
|
|
||
| The Delphi API requires a (free) API key for full functionality. To generate | ||
| your key, register for a pseudo-anonymous account | ||
| [here](https://api.delphi.cmu.edu/epidata/admin/registration_form) and see more | ||
| discussion on the [general API | ||
| website](https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html). 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](https://cmu-delphi.github.io/covidcast/covidcastR/), 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`](https://cmu-delphi.github.io/epidatr/reference/pub_covidcast.html) | ||
| function in `epidatr`. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| --- | ||
| title: New package released! Epidatr, an R client for Delphi Epidata API | ||
| author: Dmitry Shemetov, David Weber | ||
| date: 2023-09-27 | ||
| tags: | ||
| - r | ||
| - epidata | ||
| - covidcast | ||
| authors: | ||
| - dmitry | ||
| - davidweb | ||
| heroImage: blog-lg-epidatr.jpg | ||
| heroImageThumb: blog-thumb-epidatr.jpg | ||
| summary: | | ||
| `epidatr` is designed to streamline the downloading and usage of data from the [Delphi Epidata 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. | ||
|
|
||
| output: | ||
| blogdown::html_page: | ||
| toc: true | ||
| --- | ||
|
|
||
| <div id="TOC"> | ||
| <ul> | ||
| <li><a href="#usage">Usage</a></li> | ||
| <li><a href="#installation">Installation</a><ul> | ||
| <li><a href="#api-keys">API Keys</a></li> | ||
| </ul></li> | ||
| <li><a href="#for-users-of-the-covidcast-r-package">For users of the covidcast R package</a></li> | ||
| </ul> | ||
| </div> | ||
|
|
||
| <p>The <a href="https://cmu-delphi.github.io/delphi-epidata/">Delphi Epidata API</a> provides | ||
| real-time access to epidemiological surveillance data for influenza, COVID-19, | ||
| and other diseases from both official government sources such as the <a href="https://www.cdc.gov/datastatistics/index.html">Centers | ||
| for Disease Control and Prevention | ||
| (CDC)</a>, private partners such as | ||
| <a href="https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/">Facebook (now | ||
| Meta)</a> | ||
| and <a href="https://www.changehealthcare.com/">Change Healthcare</a>, and other public | ||
| datasets like <a href="https://console.cloud.google.com/marketplace/product/bigquery-public-datasets/covid19-search-trends">Google | ||
| Trends</a>. | ||
| It is built and maintained by the Carnegie Mellon University <a href="https://delphi.cmu.edu/">Delphi Research | ||
| Group</a>.</p> | ||
| <p>Today we introduce the R package <code>epidatr</code>, available <a href="https://cloud.r-project.org/web/packages/epidatr/index.html">on | ||
| CRAN</a>, with the | ||
| source and development <a href="https://github.com/cmu-delphi/epidatr">on github</a>.</p> | ||
| <p>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 | ||
| (<a href="https://github.com/cmu-delphi/epiprocess">epiprocess</a>) and modeling | ||
| (<a href="https://github.com/cmu-delphi/epipredict">epipredict</a>).</p> | ||
| <div id="usage" class="section level2"> | ||
| <h2>Usage</h2> | ||
| <pre><code>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</code></pre> | ||
| <pre><code># A tibble: 151 × 15 | ||
| geo_value signal source geo_type time_type time_value | ||
| <chr> <chr> <chr> <fct> <fct> <date> | ||
| 1 us smoothed_cli fb-su… nation day 2021-01-01 | ||
| 2 us smoothed_cli fb-su… nation day 2021-01-02 | ||
| 3 us smoothed_cli fb-su… nation day 2021-01-03 | ||
| 4 us smoothed_cli fb-su… nation day 2021-01-04 | ||
| 5 us smoothed_cli fb-su… nation day 2021-01-05 | ||
| 6 us smoothed_cli fb-su… nation day 2021-01-06 | ||
| 7 us smoothed_cli fb-su… nation day 2021-01-07 | ||
| 8 us smoothed_cli fb-su… nation day 2021-01-08 | ||
| 9 us smoothed_cli fb-su… nation day 2021-01-09 | ||
| 10 us smoothed_cli fb-su… nation day 2021-01-10 | ||
| # ℹ 141 more rows | ||
| # ℹ 9 more variables: direction <dbl>, issue <date>, | ||
| # lag <dbl>, missing_value <dbl>, missing_stderr <dbl>, | ||
| # missing_sample_size <dbl>, value <dbl>, stderr <dbl>, | ||
| # sample_size <dbl> | ||
| # ℹ Use `print(n = ...)` to see more rows</code></pre> | ||
| </div> | ||
| <div id="installation" class="section level2"> | ||
| <h2>Installation</h2> | ||
| <p>Installing the package is straightforward.</p> | ||
| <pre><code># Install the CRAN version | ||
| pak::pkg_install("epidatr") | ||
|
|
||
| # Install the development version from the GitHub dev branch | ||
| pak::pkg_install("cmu-delphi/epidatr@dev")</code></pre> | ||
| <div id="api-keys" class="section level3"> | ||
| <h3>API Keys</h3> | ||
| <p>The Delphi API requires a (free) API key for full functionality. To generate | ||
| your key, register for a pseudo-anonymous account | ||
| <a href="https://api.delphi.cmu.edu/epidata/admin/registration_form">here</a> and see more | ||
| discussion on the <a href="https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html">general API | ||
| website</a>. The | ||
| <code>epidatr</code> client will automatically look for this key in the environment | ||
| variable <code>DELPHI_EPIDATA_KEY</code>. We recommend storing your key in your <code>.Renviron</code> | ||
| file, which R will read by default.</p> | ||
| <p>Note that for the time being, the private endpoints (i.e. those prefixed with | ||
| <code>pvt</code>) will require a separate key that needs to be passed as an argument.</p> | ||
| </div> | ||
| </div> | ||
| <div id="for-users-of-the-covidcast-r-package" class="section level2"> | ||
| <h2>For users of the covidcast R package</h2> | ||
| <p>The <code>covidcast</code> package is deprecated and will no longer be updated. The | ||
| <code>epidatr</code> package is a complete rewrite of the <a href="https://cmu-delphi.github.io/covidcast/covidcastR/"><code>covidcast</code> | ||
| package</a>, with a focus on | ||
| speed, reliability, and ease of use. It also supports more endpoints and data | ||
| sources than <code>covidcast</code>. When migrating from that package, you will need to use | ||
| the | ||
| <a href="https://cmu-delphi.github.io/epidatr/reference/pub_covidcast.html"><code>pub_covidcast</code></a> | ||
| function in <code>epidatr</code>.</p> | ||
| </div> |
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