feat: adjust epidatr blog to Logan's feedback

Author: dshemetov

content/blog/2023-09-27-epidatr.Rmd

@@ -19,17 +19,39 @@ output:
     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 [Center for Disease Control (CDC)](https://www.cdc.gov/datastatistics/index.html), 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/), 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)).
+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 the Facebook survey as it was on April 10, 2021 for the US
+# 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",
@@ -66,21 +88,14 @@ epidata
 
 ## Installation
 
-You can install the stable version of this package from CRAN:
+Installing the package is straightforward.
 
 ```
-install.packages("epidatr")
+# Install the CRAN version
 pak::pkg_install("epidatr")
-renv::install("epidatr")
-```
 
-Or if you want the development version, install from GitHub:
-
-```
-# Install the dev version using `pak` or `remotes`
-pak::pkg_install("cmu-delphi/epidatr")
-remotes::install_github("cmu-delphi/epidatr")
-renv::install("cmu-delphi/epidatr")
+# Install the development version from the GitHub dev branch
+pak::pkg_install("cmu-delphi/epidatr@dev")
 ```
 
 ### API Keys
@@ -90,14 +105,20 @@ 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 R option
-`delphi.epidata.key` or in the environment variable
-`DELPHI_EPIDATA_KEY`. We recommend storing your key in `.Renviron` file, which R
-will read by default.
+`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 `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.
+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`.

content/blog/2023-09-27-epidatr.html

@@ -29,13 +29,35 @@
 </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">Center for Disease Control (CDC)</a>, private partners such as <a href="https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/">Facebook</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>
+<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 the Facebook survey as it was on April 10, 2021 for the US
+# Obtain the smoothed covid-like illness (CLI) signal from Delphi&#39;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 &lt;- pub_covidcast(
     source = &quot;fb-survey&quot;,
     signals = &quot;smoothed_cli&quot;,
@@ -68,31 +90,34 @@ <h2>Usage</h2>
 </div>
 <div id="installation" class="section level2">
 <h2>Installation</h2>
-<p>You can install the stable version of this package from CRAN:</p>
-<pre><code>install.packages(&quot;epidatr&quot;)
+<p>Installing the package is straightforward.</p>
+<pre><code># Install the CRAN version
 pak::pkg_install(&quot;epidatr&quot;)
-renv::install(&quot;epidatr&quot;)</code></pre>
-<p>Or if you want the development version, install from GitHub:</p>
-<pre><code># Install the dev version using `pak` or `remotes`
-pak::pkg_install(&quot;cmu-delphi/epidatr&quot;)
-remotes::install_github(&quot;cmu-delphi/epidatr&quot;)
-renv::install(&quot;cmu-delphi/epidatr&quot;)</code></pre>
+
+# Install the development version from the GitHub dev branch
+pak::pkg_install(&quot;cmu-delphi/epidatr@dev&quot;)</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 R option
-<code>delphi.epidata.key</code> or in the environment variable
-<code>DELPHI_EPIDATA_KEY</code>. We recommend storing your key in <code>.Renviron</code> file, which R
-will read by default.</p>
+<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>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. The <code>covidcast</code> package is deprecated and will no longer be updated.</p>
+<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>