Merge pull request #542 from cmu-delphi/ryan/about-covidcast

About COVIDcast update

Author: ryantibs

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/publications/index.md

@@ -43,12 +43,6 @@ papers:
     link: https://doi.org/10.1073/pnas.2111454118
     journal: Proceedings of the National Academy of Sciences
     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
-    year: 2021
   - title: "Causal Inference in the Time of COVID-19"
     image: causal.jpg
     authors: Bonvini, Kennedy, Ventura, Wasserman

content/covid19/_index.md

@@ -4,11 +4,75 @@ linkTitle: COVID-19
 layout: single
 ---
 
-In March 2020, Delphi pivoted from seasonal epidemic forecasting to COVID-19 tracking. Since then, we’ve created and maintained the nation’s largest public repository of diverse, geographically-detailed, real-time indicators of COVID-19 activity in the U.S. Our indicators cover every rung of the severity pyramid, and are freely available through [our public API]({{< apiref "api/covidcast.html" >}}) or our [data export tool]({{< relref "covidcast/export" >}}).
+COVIDcast is the name for Delphi's project in support of the COVID-19 response
+in the United States. It has several parts. 
 
-Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes:
+1. We procure unique data streams that reflect COVID activity from a wide
+  variety of sources, and extract COVID-related signals. These signals cover
+  every nearly every rung of the [severity pyramid](#severity-pyramid), and
+  constitute what we believe may be the nation's largest public repository of
+  real-time, geographically-detailed indicators of COVID activity in the U.S.
 
-* A [massive national daily survey]({{< relref "covid19/ctis" >}}) we’re running in partnership with Facebook. Over 20 million Americans have answered the survey since April 2020, providing real-time insights into, e.g., self-reported symptoms, mask wearing, testing, and contacts, all broken down by various demographics.
-* An enormous database of medical insurance claims that have been de-identified in accordance with HIPAA privacy regulations, covering more than half the US population, made possible through health system partners including Change Healthcare. We use this to produce a new syndromic COVID-19 indicator based on doctor visits, and other indicators based on hospitalizations and ICU admissions.
+2. We make all COVID-19 indicators freely available through a
+  [public API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html),
+  which is updated with new data daily. We also provide associated
+  [R](https://cmu-delphi.github.io/covidcast/covidcastR/) and
+  [Python](https://cmu-delphi.github.io/covidcast/covidcast-py/html/) packages, 
+  and a [dashboard]({{< relref "covidcast" >}}) to visualize a core set of
+  indicators. 
 
-An overview of our work and data was [published in the *Proceedings of the National Academy of Sciences*](https://doi.org/10.1073/pnas.2111452118). We have selected a small number of indicators to showcase in [COVIDcast]({{< relref "covidcast" >}}), a visualization system that helps place pandemic activity in geographic and temporal context. It includes a notion of correlation across time, for example, a spike in cases is often followed by a spike in hospital admissions some number of days later.
+3. Some of the underlying data sources (on which these indicators are built) 
+  would not exist or be publicly available without Delphi's efforts. These
+  include a massive national daily survey called the [COVID-19 Trends and
+  Impact Survey (CTIS)]({{< relref "covid19/ctis" >}}) that we're running in
+  partnership with Facebook, which has been taken by over 25 million Americans
+  since April 2020; and an enormous database of de-identified medical insurance
+  claims, covering more than 35% of the U.S. population, made possible through
+  health system partners including Change Healthcare. 
+
+4. We support and advise the U.S. CDC (in collaboration with the
+  [Reich Lab](https://reichlab.io/)) on short-term COVID forecasting, which 
+  includes creating and evaluating an ensemble forecast out of the models
+  submitted to the [COVID-19 Forecast Hub](https://covid19forecasthub.org/),
+  serving as the basis for the [CDC's official forecast
+  communications](https://www.cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html).
+
+## See Also
+
+- [COVIDcast dashboard]({{< relref "covidcast" >}})
+- [CTIS dashboard]({{< relref "covidcast/survey-results" >}})
+- [Export data tool]({{< relref "covidcast/export" >}})
+- [API documentation](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html)
+- [R package](https://cmu-delphi.github.io/covidcast/covidcastR/)
+- [Python package](https://cmu-delphi.github.io/covidcast/covidcast-py/html/)
+- [GitHub repo](https://www.github.com/cmu-delphi/covidcast/) (see also
+  [related repos](https://github.com/cmu-delphi/covidcast/#related-repos))
+  
+## Research Articles
+
+A summary of some key parts of COVIDcast can be found in the December 2021 *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/cc/beyond-cases-and-deaths):
+
+- [Epidemic tracking and forecasting: Lessons learned from a tumultuous
+  year](https://www.pnas.org/content/118/51/e2111456118?cct=2522)
+  by Rosenfeld and Tibshirani
+- [An open repository of real-time COVID-19
+  indicators](https://www.pnas.org/content/118/51/e2111452118?cct=2522)
+  by Reinhart et al.
+- [Can auxiliary indicators improve COVID-19
+  forecasting?](https://www.pnas.org/content/118/51/e2111453118?cct=2522)
+  by McDonald et al.
+- [Continuous real-time measurement of COVID-19 symptoms, risks, protective
+  behaviors, testing, and vaccination](https://www.pnas.org/content/118/51/e2111454118?cct=2522)
+  by Salomon et al.
+
+More recent work on nowcasting using COVID-19 indicators:
+
+- [Real-time estimation of COVID-19 infections via deconvolution and sensor
+  fusion](https://arxiv.org/abs/2112.06697)
+  by Jahja et al. 
+
+## Severity Pyramid
+
+![](images/severity-pyramid.svg)