Release v3.0.1

.github/workflows/blog.yaml

@@ -17,7 +17,7 @@ jobs:
           # submodules: true  # Fetch Hugo themes (true OR recursive)
           fetch-depth: 3
       - name: Cache Conda
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }}
@@ -45,7 +45,7 @@ jobs:
         run: |
           Rscript ./dependencies.R
       - name: Restore Blogdown Cache
-        uses: actions/cache@v2
+        uses: actions/cache@v2.1.7
         with:
           path: |
             ./blogdown
@@ -68,7 +68,7 @@ jobs:
       - uses: actions/setup-node@v2
         with:
           node-version: 16
-      - uses: actions/cache@v2
+      - uses: actions/cache@v2.1.7
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/setup-node@v2
         with:
           node-version: 16
-      - uses: actions/cache@v2
+      - uses: actions/cache@v2.1.7
         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@v2
+        uses: actions/cache@v2.1.7
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}

content/about/_index.md

@@ -39,26 +39,30 @@ Public health authorities (federal, state, local), the healthcare industry, the
 
 In reverse chronological order.
 
-- **April 2020.** We began supporting and advising the U.S. CDC in their community-driven COVID-19 forecasting effort. This work (collaborative with the [Reich Lab](https://reichlab.io) at UMass) includes:
-
-    * Creating and evaluating an ensemble forecast from the 70+ forecasts in the [COVID-19 Forecast Hub](https://covid19forecasthub.org), which serves as the basis of the [CDC's official communications](https://www.cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html) on COVID-19 forecasting.
-
-    * Creating a [forecast evaluation dashboard](https://delphi.cmu.edu/forecast-eval/), which provides an interactive analysis of the performance of Hub forecasters.
-
-- **March 2020.** We launched [COVIDcast]({{< relref "covidcast" >}}), the nation's largest public repository of diverse, real-time indicators of COVID-19 activity.
-    * Our indicators are freely available through a [public API]({{< apiref "api/covidcast.html" >}}), which is updated daily with the latest data.
-
-    * Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes:
-
-        *  A massive [national daily survey]({{< relref "ctis">}}) we're running in [partnership with Facebook](https://covid-survey.dataforgood.fb.com/survey_and_map_data.html). Over 20 million Americans have answered the survey since April 2020, providing real-time insights into, e.g., self-reported symptoms, mask wearing, testing, contacts, and vaccination.
-
-        *  An enormous database of medical insurance claims that have been de-identified in accordance with HIPAA privacy regulations, covering more than half the U.S. population. This data is made available by health system partners including Change Healthcare, and provides insights into disease activity through outpatient visits and hospitalizations.
-
-
-- **2019.** We became a CDC National Center of Excellence for Influenza Forecasting, one of two nationally (and a 5-year designation).
-
-- **2016.** We developed and deployed [influenza nowcasts](https://delphi.cmu.edu/nowcast/) for the CDC, state departments of public health, and the public.
-
-- **2016.** We developed and deployed the [Epidata API]({{< apiref "/" >}}), which provides real-time access to epidemiological surveillance data.
-
-- **2013.** We began supporting the U.S. CDC's Influenza Division in advancing and growing a [scientific community around influenza forecasting](https://www.cdc.gov/flu/weekly/flusight/index.html). We've been [perennial leaders in forecasting accuracy](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202014-2018%20Results.pdf) ever since.
+- **April 2020.** We began supporting and advising the U.S. CDC's
+  community-driven COVID-19 forecasting effort, including creating and
+  maintaining an ensemble forecast from the models submitted to the 
+  [COVID-19 Forecast Hub](https://covid19forecasthub.org), and a [forecast 
+  evaluation dashboard](https://delphi.cmu.edu/forecast-eval/).
+
+- **March 2020.** We launched [COVIDcast]({{< relref "covidcast" >}}), the
+  nation's largest public repository of diverse, real-time indicators of
+  COVID-19 activity, freely accessible through the [Epidata API]({{< apiref 
+  "api/covidcast.html" >}}), which is updated daily with the latest data.
+
+- **2019.** We became a CDC National Center of Excellence for Influenza
+  Forecasting, one of two nationally (and a 5-year designation). 
+
+- **2016.** We developed and deployed
+  [influenza nowcasts](https://delphi.cmu.edu/nowcast/) for the CDC, state
+  departments of public health, and the public. 
+
+- **2016.** We developed and deployed the [Epidata API]({{< apiref "/" >}}),
+  which provides real-time access to epidemiological surveillance data. 
+
+- **2013.** We began supporting the U.S. CDC's Influenza Division in advancing
+  and growing a [scientific community around influenza
+  forecasting](https://www.cdc.gov/flu/weekly/flusight/index.html). We've been 
+  [perennial leaders in forecasting
+  accuracy](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202014-2018%20Results.pdf)
+  ever since. 

content/about/careers/headless/2021_06_research_programmer_analyst.md → content/about/careers/headless/2021_11_research_programmer_analyst.md

@@ -1,5 +1,5 @@
 ---
-date: 2021-06-22
+date: 2021-11-01
 title: Research Programmer/Analyst
 ---
 

content/about/careers/headless/2021_12_developer_in_residence.md

@@ -0,0 +1,8 @@
+---
+date: 2021-12-14
+title: Developer in Residence
+---
+
+We are looking for a talented senior software developer to take the reins in designing and developing R and Python software packages. These packages support model development and evaluation in predictive tasks in epidemiology such as COVID forecasting, flu forecasting, or hotspot detection for these two pathogens.  This software is important both for Delphi's own internal modeling work, and for a community of modelers that works with the CDC on COVID and flu forecasting.
+
+[Apply to the Developer in Residence position at CMU Careers](https://cmu.wd5.myworkdayjobs.com/CMU/job/Pittsburgh-PA/Developer-in-Residence---School-of-Computer-Sciences_2017318).

content/about/careers/headless/2021_12_project_manager.md

@@ -0,0 +1,8 @@
+---
+date: 2021-12-14
+title: Project Manager
+---
+
+We are looking for a talented project manager to coordinate between and manage the group's continually diverse set of ongoing projects, and assist the Delphi leadership team in translating the group's strategy into concrete deliverables.
+
+[Apply to the Project Manager position at CMU Careers](https://cmu.wd5.myworkdayjobs.com/CMU/job/Pittsburgh-PA/Project-Manager---School-of-Computer-Sciences_2017319).

content/about/careers/headless/2022_11_open_rank_faculty.md

@@ -0,0 +1,8 @@
+---
+date: 2022-01-11
+title: Open Rank Faculty
+---
+
+We would like to welcome new faculty at any rank and any track to join us in leading the Delphi group in the coming decade to develop and test the technology and science that are urgently needed for national epidemic tracking and forecasting, and that we believe we are in a position to do well.
+
+[Apply to the Open Rank Faculty positions at Interfolio](https://apply.interfolio.com/101207).

content/about/news/headless/2016_12.md

@@ -2,6 +2,7 @@
 date: 2016-12-01
 title: Delphi Wins 2015-2016 Forecasting Challenge
 category: accomplishment
+image: placeholder-thumb.jpg
 ---
 
 Our system took the [top spot in the flu forecasting challenge of 2015-2016](https://www.cdc.gov/flu/spotlights/flu-activity-forecasts-2016-2017.htm), out of 14 submissions. ([Results summary](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202015-2016%20Results.pdf).)

content/about/news/headless/2017_10.md

@@ -2,6 +2,7 @@
 date: 2017-10-01
 title: Delphi Wins 2016-2017 Forecasting Challenge
 category: accomplishment
+image: placeholder-thumb.jpg
 ---
 
 We did it again! Our two systems took the [top two spots in the flu forecasting challenge of 2016-2017](https://www.cmu.edu/news/stories/archives/2017/september/flu-forecasts.html), out of 28 submissions. ([Results summary](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202016-2017%20Results.pdf).)

content/about/news/headless/2018_11.md

@@ -2,6 +2,7 @@
 date: 2018-10-01
 title: Delphi Wins 2017-2018 Forecasting Challenge
 category: accomplishment
+image: placeholder-thumb.jpg
 ---
 
 And yet again! Our forecasting systems took the top spot in each of the three separate flu forecasting challenges of 2017-2018, out of up to 30 submissions. ([Results summary](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202017-2018%20Results.pdf).)

content/about/news/headless/2019_10_CenterOfExcellence.md

@@ -1,7 +1,8 @@
 ---
 date: 2019-10-01
-title: Delphi named a Center of Excellence 
+title: Delphi named a Center of Excellence
 category: accomplishment
+image: placeholder-thumb.jpg
 ---
 
 We were just named a national [Center of Excellence for Influenza Forecasting](https://www.cmu.edu/news/stories/archives/2019/october/cdc-funds-carnegie-mellons-flu-forecasting-center.html) by the CDC, one of two nationally. This is a 5 year designation.

content/about/news/headless/2020_03_covid.md

@@ -2,6 +2,7 @@
 date: 2020-03-01
 title: Delphi Shifts Focus to COVID-19
 category: update
+image: placeholder-thumb.jpg
 ---
 
 We are focusing our efforts at this point on COVID-19 tracking and forecasting. We are adapting our existing systems, and developing new ones. Some of our regular activities may be halted as a result.

content/about/news/headless/2020_04_covidcast.md

@@ -2,6 +2,7 @@
 date: 2020-04-01
 title: Delphi Launches COVIDcast
 category: update
+image: placeholder-thumb.jpg
 ---
 
 We launched our [COVIDcast system]({{< relref "covidcast">}}), which makes available indicators related to COVID-19 activity level across the U.S. These indicators are derived from a variety of anonymized, aggregated data sources made available by multiple partners, and are publicly available at the [COVIDcast endpoint]({{< apiref "api/covidcast.html">}}) of our [Epidata API]({{< apiref "api/README.html">}}).

content/about/news/headless/2020_10_fellows.md

@@ -2,6 +2,7 @@
 date: 2020-10-01
 title: Google Fellows Join Delphi for 6 Months
 category: update
+image: placeholder-thumb.jpg
 ---
 
 We've welcomed [14 Google Fellows](https://www.cmu.edu/news/stories/archives/2020/september/covidcast-google.html) to Delphi and are excited to have them on board!

content/about/news/headless/2020_12_chng_partnership.md

@@ -2,6 +2,7 @@
 date: 2020-12-01
 title: COVIDcast Enhanced with Change Healthcare Claims Data
 category: update
+image: placeholder-thumb.jpg
 ---
 
 Change Healthcare and Delphi announce the [launch of new COVIDcast indicators](https://newsroom.changehealthcare.com/press-releases/carnegie-mellon-university-s-delphi-research-group-enhances-covi) using de-identified claims data from Change Healthcare.

content/about/news/headless/2021_05_12_spaig_award.md

@@ -2,6 +2,7 @@
 date: 2021-05-12
 title: Delphi and Collaborators Honored for COVIDcast
 category: update
+image: 2021-05-12-spaig-award-thumb.jpg
 ---
 
 The American Statistical Association (ASA) presented the 2021 [Statistical Partnerships Among Academe, Industry, and Government (SPAIG) award](https://www.cmu.edu/dietrich/news/news-stories/2021/may/spaig-covid.html) to Delphi and their COVIDcast collaborators.

content/about/news/headless/2021_11_22_nyt.md

@@ -1,7 +1,8 @@
 ---
 date: 2021-11-22
-title: Delphi PI Featured in New York Times
+title: New York Times Magazine Features Delphi PI
 category: update
+image: 2021-11-22-nyt-thumb.jpg
 ---
 
-The New York Times featured Delphi PI, Roni Rosenfeld, in the article [Inside the C.D.C.’s Pandemic ‘Weather Service’](https://www.nytimes.com/2021/11/22/magazine/cdc-pandemic-prediction.html).
+The New York Times Magazine features Roni Rosenfeld in an article exploring efforts to forecast infectious-disease outbreaks, [Inside the C.D.C.’s Pandemic ‘Weather Service’](https://www.nytimes.com/2021/11/22/magazine/cdc-pandemic-prediction.html).

content/about/news/headless/2021_12_14_pnas.md

@@ -0,0 +1,13 @@
+---
+date: 2021-12-14
+title: Delphi Papers Highlighted in Proceedings of the National Academy of Sciences Special Feature
+category: update
+image: 2021-12-14-pnas-thumb.jpg
+---
+
+The Proceedings of the National Academy of Sciences Special Feature, ["Beyond Cases and Deaths: The Benefits of Auxiliary Data Streams In Tracking the COVID-19 Pandemic"](https://www.pnas.org/content/118/51#BeyondCasesandDeathsTheBenefitsofAuxiliaryDataStreamsInTrackingtheCOVID-19Pandemic), highlights Delphi papers, including:
+
+ - [Epidemic Tracking and Forecasting: Lessons Learned from a Tumultuous Year](https://www.pnas.org/content/118/51/e2111456118)
+ - [An Open Repository of Real-Time COVID-19 Indicators](https://doi.org/10.1073/pnas.2111452118)
+ - [Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?](https://www.pnas.org/content/118/51/e2111453118)
+ - [The US COVID-19 Trends and Impact Survey: Continuous Real-Time Measurement of COVID-19 Symptoms, Risks, Protective Behaviors, Testing, and Vaccination](https://www.pnas.org/content/118/51/e2111454118)

content/about/news/images/index.md

@@ -0,0 +1,4 @@
+---
+# flag to disable rendering individual pages
+headless: true
+---

content/about/publications/index.md

@@ -1,35 +1,47 @@
 ---
 title: Research
 papers:
-  - title: "Epidemic Tracking and Forecasting: Lessons Learned from a Tumultuous Year"
-    image: perspective.jpg
-    authors: Rosenfeld, Tibshirani
-    link: https://github.com/cmu-delphi/covidcast-pnas/blob/main/perspective/paper.pdf
-    journal: Preprint
+  - title: "Real-Time Estimation of COVID-19 Infections via Deconvolution and Sensor Fusion"
+    image: nowcasting-thumb.jpg
+    authors: Jahja, Chin, Tibshirani
+    link: https://arxiv.org/abs/2112.06697
+    journal: arXiv
     year: 2021
+  - title: "Recalibrating Probabilistic Forecasts of Epidemics"
+    image: recalibrating-thumb.jpg
+    authors: Rumack, Tibshirani, Rosenfeld
+    link: https://arxiv.org/abs/2112.06305
+    journal: Preprint
+    year: 2021 
   - title: "Big Data, Big Problems: Responding to \"Are We There Yet?\""
     image: response.jpg
     authors: Reinhart, Tibshirani
     link: https://arxiv.org/abs/2109.00680
     journal: arXiv
     year: 2021
-  - title: "Continuous Real-Time Measurement of COVID-19 Symptoms, Risks, Protective Behaviors, Testing and Vaccination"
-    image: survey.jpg
-    authors: Salomon, Reinhart, Bilinski, Chua, La Motte-Kerr, Rönn, Reitsma, Morris, LaRocca, Farag, Kreuter, Rosenfeld, Tibshirani
-    link: https://doi.org/10.1101/2021.07.24.21261076
-    journal: medRxiv
+  - title: "Epidemic Tracking and Forecasting: Lessons Learned from a Tumultuous Year"
+    image: perspective.jpg
+    authors: Rosenfeld, Tibshirani
+    link: https://doi.org/10.1073/pnas.2111456118
+    journal: Proceedings of the National Academy of Sciences
     year: 2021
   - title: "An Open Repository of Real-Time COVID-19 Indicators"
     image: indicators.jpg
     authors: Reinhart, Brooks, Jahja, Rumack, Tang, Agrawal, Al Saeed, Arnold, Basu, Bien, Cabrera, Chin, Chua, Clark, Colquhoun, DeFries, Farrow, Forlizzi, Grabman, Gratzl, Green, Haff, Han, Harwood, Hu, Hyde, Hyun, Joshi, Kim, Kuznetsov, La Motte-Kerr, YJ Lee, K Lee, Lipton, Liu, Mackey, Mazaitis, McDonald, McGuinness, Narasimhan, O’Brien, Oliveira, Patil, Perer, Politsch, Rajanala, Rucker, Scott,  Shah, Shankar, Sharpnack, Shemetov, Simon, Smith,  Srivastava,  Tan, R Tibshirani, Tuzhilina, Van Nortwick, Ventura, Wasserman, Weaver, Weiss, Whitman, Williams, Rosenfeld, RJ Tibshirani
-    link: https://www.medrxiv.org/content/10.1101/2021.07.12.21259660
-    journal: medRxiv
+    link: https://doi.org/10.1073/pnas.2111452118
+    journal: Proceedings of the National Academy of Sciences
     year: 2021
   - title: "Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?"
     image: forecasting.jpg
     authors: McDonald, Bien, Green, Hu, DeFries, Hyun, Oliveira, Sharpnack, Tang, Tibshirani, Ventura, Wasserman, Tibshirani
-    link: https://www.medrxiv.org/content/10.1101/2021.06.22.21259346
-    journal: medRxiv
+    link: https://doi.org/10.1073/pnas.2111453118
+    journal: Proceedings of the National Academy of Sciences
+    year: 2021 
+  - title: "The US COVID-19 Trends and Impact Survey: Continuous Real-Time Measurement of COVID-19 Symptoms, Risks, Protective Behaviors, Testing, and Vaccination"
+    image: ctis-thumb.jpg
+    authors: Salomon, Reinhart, Bilinski, Chua, La Motte-Kerr, Rönn, Reitsma, Morris, LaRocca, Farag, Kreuter, Rosenfeld, Tibshirani
+    link: https://doi.org/10.1073/pnas.2111454118
+    journal: Proceedings of the National Academy of Sciences
     year: 2021
   - title: "Causal Inference in the Time of COVID-19"
     image: causal.jpg