Release v3.2.11

.github/workflows/blog.yaml

@@ -37,7 +37,7 @@ jobs:
         run: |
           Rscript ./dependencies.R
       - name: Restore Blogdown Cache
-        uses: actions/cache@v3.3.2
+        uses: actions/cache@v4.0.0
         with:
           path: |
             ./blogdown

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: 16
-      - uses: actions/cache@v3.3.2
+      - uses: actions/cache@v4.0.0
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node3-${{ hashFiles('**/package-lock.json') }}

.github/workflows/release_main.yml

@@ -47,7 +47,7 @@ jobs:
         with:
           node-version: 16
       - name: Cache Node.js modules
-        uses: actions/cache@v3.3.2
+        uses: actions/cache@v4.0.0
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}

content/_index.md

@@ -5,7 +5,7 @@ layout: landing
 
 carousel:
   - pre: Tools
-    title: Real-time Indicators of COVID-19 Activity
+    title: Real-time Indicators of Infectious Disease Activity
     ref: covidcast
     alt: Explore the COVIDcast Dashboard
     image: covidcast_v2.jpg
@@ -14,16 +14,16 @@ carousel:
     link: https://www.cs.cmu.edu/news/2023/delphi-cdc-center
     alt: Learn More
     image: landing-pg-hero-_cfa_oadm.jpg
+  - pre: Blog
+    title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic
+    ref: 2023-12-20-changepoint_explore
+    alt: View Post
+    image: landing-pg-hero-exploratory_analysis.jpg
   - pre: Tools
-    title: Evaluation of COVID-19 Forecasts
-    link: /forecast-eval
-    alt: Explore the Forecast Evaluation Dashboard
-    image: forecast_evaluation_dashboard.jpg
-  - pre: Tools
-    title: COVID Trends and Impact Survey (CTIS)
-    ref: covidcast/survey-results
-    alt: Explore the CTIS Dashboard
-    image: covidcast_survey.jpg
+    title: Introducing Epidata
+    link: https://delphi.cmu.edu/blog/2022/12/14/introducing-epidata-v4/
+    alt: View Post
+    image: landing-pg-hero-introducing_epidata.jpg
   - pre: Blog
     title: On the Predictability of COVID-19
     ref: 2021-09-30-ensemble-analysis
@@ -40,7 +40,7 @@ carousel:
     alt: View Paper
     image: research-hero-collaborative-hubs.jpg  
   - pre: Research
-    title: An Open Repository of Real-Time COVID-19 Indicators
+    title: Introduction to the Delphi Real-Time Signal Repository
     link: https://www.medrxiv.org/content/10.1101/2021.07.12.21259660v1
     alt: View Paper
     image: landing-pg_hero-img_An Open Repository of Real-Time COVID-19 Indicators.jpg

content/about/publications/index.md

@@ -1,11 +1,18 @@
 ---
 title: Research
 papers:
+  - title: "RtEstim: Effective reproduction number estimation with trend filtering"
+    image: rtestim.jpg
+    authors: Liu, Cai, Gustafson, McDonald
+    link: https://doi.org/10.1101/2023.12.18.23299302
+    journal: medRxiv
+    year: 2023
   - title: "Computationally Assisted Quality Control for Public Health Data Streams"
     image: forecast.png
     authors: Joshi, Mazaitis, Rosenfeld, Wilder
     link: https://arxiv.org/abs/2306.16914
-    journal: International Joint Conference on Artificial Intelligence  
+    year: 2023
+    journal: International Joint Conference on Artificial Intelligence
   - title: "Nowcasting Reported COVID-19 Hospitalizations Using De-Identified, Aggregated Medical Insurance Claims Data"
     image: paper-2023-nowcasting-reported.jpg
     authors: Shen, Rumack, Wilder, Tibshirani
@@ -36,12 +43,6 @@ papers:
     link: https://doi.org/10.2105/AJPH.2022.306831
     journal: American Journal of Public Health
     year: 2022
-  - title: "Smooth Multi-Period Forecasting with Application to Prediction of COVID-19 Cases"
-    image: smoothing-paper-teaser.jpg
-    authors: Tuzhilina, Hastie, McDonald, Tay, Tibshirani
-    link: https://arxiv.org/abs/2202.09723
-    journal: arXiv
-    year: 2022
   - title: "Recalibrating Probabilistic Forecasts of Epidemics"
     image: recalibrating-thumb.jpg
     authors: Rumack, Tibshirani, Rosenfeld

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

@@ -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`.

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

@@ -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&#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;,
+    geo_type = &quot;nation&quot;,
+    time_type = &quot;day&quot;,
+    geo_values = &quot;us&quot;,
+    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
+   &lt;chr&gt;     &lt;chr&gt;        &lt;chr&gt;  &lt;fct&gt;    &lt;fct&gt;     &lt;date&gt;
+ 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 &lt;dbl&gt;, issue &lt;date&gt;,
+#   lag &lt;dbl&gt;, missing_value &lt;dbl&gt;, missing_stderr &lt;dbl&gt;,
+#   missing_sample_size &lt;dbl&gt;, value &lt;dbl&gt;, stderr &lt;dbl&gt;,
+#   sample_size &lt;dbl&gt;
+# 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(&quot;epidatr&quot;)
+
+# 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 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>

content/blog/2023-12-20-changepoint_explore.Rmd

@@ -1,5 +1,5 @@
 ---
-title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic
+title: 'Identifying Changing Variant Behavior during a Pandemic: An Exploratory Analysis'
 author: Tara Lakdawala, Ananya Joshi
 date: 2023-12-20
 tags:
@@ -9,8 +9,8 @@ tags:
 authors:
   - tara
   - ajoshi
-heroImage: changepoint-hero.png
-heroImageThumb: changepoint-blog.png
+heroImage: blog-lg-changepoint.jpeg
+heroImageThumb: blog-thumb-changepoint.jpeg
 
 summary: | 
   We use changepoint detection algorithms to analyze Delphi's indicators and classify them as early, on-time, late, undefined, or undetermined. 

content/blog/2023-12-20-changepoint_explore.html

@@ -1,5 +1,5 @@
 ---
-title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic
+title: 'Identifying Changing Variant Behavior during a Pandemic: An Exploratory Analysis'
 author: Tara Lakdawala, Ananya Joshi
 date: 2023-12-20
 tags:
@@ -9,8 +9,8 @@
 authors:
   - tara
   - ajoshi
-heroImage: changepoint-hero.png
-heroImageThumb: changepoint-blog.png
+heroImage: blog-lg-changepoint.jpeg
+heroImageThumb: blog-thumb-changepoint.jpeg
 
 summary: | 
   We use changepoint detection algorithms to analyze Delphi's indicators and classify them as early, on-time, late, undefined, or undetermined.