COVID-19 Modelling Resources, Data and Challenges (updated: 16 Dec 2020)

Rensselaer data analytics students, researchers and colleagues are analyzing the data emerging from the 2019-2020 COVID-19 outbreak/pandemic. In early March 2020 The Rensselaer IDEA started gathering a set of resources on exploring and modelling current global data. This list will be updated periodically as new resources become available. Many thanks to our friends and colleagues near and for for contributing to this list!

SEE ALSO: The White House Office of Science and Technology Policy has formed The COVID-19 High Performance Computing (HPC) Consortium, a unique private-public effort involving IBM, RPI and others from federal government, industry, and academia to volunteer free compute time and resources on their world class machines. See https://bit.ly/2y51Hac (info) and https://bit.ly/2UBa5G9 (CfP form)

VISUALIZATIONS	BACKGROUND	TUTORIALS	SIMULATIONS	DATASETS	LINKED DATA	PROXIMITY TRACING	CHALLENGES & COLLABORATIONS

NEW: COVID-19 Projects from The Rensselaer IDEA:
- COVIDMINDER (From the creators of the award-winning MORTALITYMINDER)
  - Live deployment: http://covidminder.idea.rpi.edu (production) http://bit.ly/COVIDMinder (alternate)
  - Webinar overview (16 Apr): https://bit.ly/3bfCngr
  - Press release: https://bit.ly/covidminder_pr
  - App github: https://github.com/TheRensselaerIDEA/COVIDMINDER
  - R Notebook version (esp. for students!): https://github.com/TheRensselaerIDEA/COVID-Notebooks
- SOCIAL MEDIA ANALYSIS: "Clustering COVID-19 Discourse on Twitter with Natural Language Processing" (The Rensselaer IDEA)
  - COVID-19-related Tweet ID repository: https://github.com/TheRensselaerIDEA/COVID-TweetIDs
    (41M+ original tweets; 82M+ retweets 17 Mar-15 Apr 2020) (more coming!)
  - COVID-19 Twitter harvesting code: https://github.com/TheRensselaerIDEA/COVID-Twitter
- MACHINE LEARNING: Malik Magdon-Ismail, "Machine Learning the Phenomenology of COVID-19 From Early Infection Dynamics" (pre-print) https://arxiv.org/pdf/2003.07602.pdf
  - NEW: COVID WarRoom, based on Magdon-Ismail's modelling: http://covidwarroom.idea.rpi.edu (updated daily!)
  - NEW: COVID Back-to-School, based on Magdon-Ismail's modelling: http://covidspread.idea.rpi.edu (updated daily!)
FEATURED DATASETS AND RESOURCES:
- COVID-19 Data Hub https://covid19datahub.io/ (The R Consortium, et.al.)
  - Includes data and policy sets from around the world
  - Download page: https://covid19datahub.io/articles/data.html
  - R Interface (package): https://cloud.r-project.org/web/packages/COVID19/index.html
- COVID-19 Mobility Data Network: https://www.covid19mobility.org/
  - Social Distancing Reporter (Camber Systems): https://covid19.cambersystems.com/
  - Facebook Data for Good Mobility Dashboard (CMDN & Facebook): https://visualization.covid19mobility.org/
- The COVID Information Commons, an open resource for exploring NSF-funded research addressing the COVID-19 pandemic.
- By the Health Data Research UK COVID-19 Team
  - HDR UK COVID-19 Team https://bit.ly/37HB4pE
  - All HDR UK COIVD-19 related https://bit.ly/3deorDo
  - COVID-19 CovidSim Microsimulation Model https://bit.ly/2BiSv3o
- By the International Long Term Care Policy Network
  - LTC Network resources: https://ltccovid.org/
  - LTC Network Country reports: https://ltccovid.org/country-reports-on-covid-19-and-long-term-care/
  - LTC Network COVID impacts on long term care reports: https://ltccovid.org/international-reports-on-covid-19-and-long-term-care/
- Via WordData.AI
  - COVID-19 Datasets (Free membership for academic use)
INSPIRATION: see these real-time VISUALIZATIONS and other data viewers:
- JHU CSSE dashboard: http://bit.ly/39M4WRW
- Interactive Exploration of COVID-19 Exit Strategies (11 Jun2020):
  - R-based Web App: https://scienceversuscorona.shinyapps.io/covid-exit/
  - Descriptive post: https://fabiandablander.com/r/Covid-Exit.html
  - Paper: https://www.medrxiv.org/content/10.1101/2020.03.29.20046011v2
- Novel Coronavirus Infection Map (Univ. of Washington) https://hgis.uw.edu/virus/
- COVID-19 Projections (IHME) https://bit.ly/2yZU0mC
- PolicyMap COVID-19 Quick Maps (including comorbidity layers) https://covid19.policymap.com/app
- "Coronavirus tracked: the latest figures as the pandemic spreads" (FT.cm / John Burn-Murdoch) https://www.ft.com/coronavirus-latest
- "COVID-LAB: MAPPING COVID-19 IN YOUR COMMUNITY" (PolicyLab) https://bit.ly/2VKSdu5
- "The COVID-19 Graph - Knowledge Dashboard" (AMiner team, China) https://bit.ly/35ekJr4
- "91-DIVOC: An interactive visualization of the exponential spread of COVID-19" (nice epi curves!) https://bit.ly/2Vr7xvG
- "Index of (ArcGIS) Applications related to COVID-19 in the USA" (Apps like JHU's...) https://bit.ly/3bRkAvZ
- Novel Coronavirus (COVID-19) Situation (WHO): http://bit.ly/2vkJ80C
- Genomic epidemiology of novel coronavirus (hCoV-19): https://nextstrain.org/ncov
- nCoV2019.live (by 17-yr-old Avi Schiffmann!): https://ncov2019.live/data
- Novel Coronavirus (COVID-19) Animated Map (Harvard, et.al.) https://www.healthmap.org/covid-19/
- worldometer Coronavirus Data Tracker https://www.worldometers.info/coronavirus/ (handy tables and charts from freshly-updated sources)
- "Why you must act now" interactive US model https://covidactnow.org/
  CovidActNow.org was created by a team of data scientists, engineers, and designers in partnership with epidemiologists, public health officials, and political leaders to help understand how the COVID-19 pandemic will affect their region. See details of their model: https://bit.ly/2QDHvm0
- "The COVID-19 Tracking Project" (up-to-date tables and data access) https://covidtracking.com/data/
- "COVID-19 Epidemic Curve Explorer" (Databrew) https://bit.ly/3dEoAkY (See the tutorial!)
- "Coronavirus Map: Tracking the Global Outbreak"(NYTimes ) https://nyti.ms/3byKaph
- "COVID-19 Projections: Projected hospital resource use based on COVID-19 deaths" https://bit.ly/39Eo5V7
- "Social Distancing Scoreboard" (Unacast, based on cell data) https://bit.ly/2X21S0k
BACKGROUND: see JHU's COVID-19 Resource Center: https://coronavirus.jhu.edu/
- For deeper background, see the "COVID-19 Open Research Dataset (CORD-19)" https://pages.semanticscholar.org/coronavirus-research
- This article offers critical PERSPECTIVE on official vs actual reporting of cases: Coronavirus: Why You Must Act Now http://bit.ly/2II7YKZ
- "COVID-19: Science, Stories, and Resources," a comprehensive, curated list from The Biophysical Society: https://bit.ly/2UIO5t1
- "Coronavirus Disease (COVID-19) – Statistics and Research" by Our World in Data https://ourworldindata.org/coronavirus# (see also Datasets, below)
- "State Data and Policy Actions to Address Coronavirus" https://bit.ly/2JeEHYx (See also Datasets, below)
- "Forecasting COVID-19 impact on hospital bed-days, ICU-days, ventilator days and deaths by US state in the next 4 months" https://bit.ly/2UwITJw
- "Social Distancing Scoreboard Methodology" (Unacast) https://bit.ly/3dOaPAw
- "Figshare COVID-19 Research Publishing Portal" https://covid19.figshare.com/ (a mix of papers, tutorials and links to data)
- "Coronavirus Disease 2019" (Congressional Research Service) https://crsreports.congress.gov/Content/html/covid19.html
- "The COVID Impact Survey" https://www.covid-impact.org/

TUTORIALS on DATA ANALYTICS CODING (esp. in R) by Tim Churches and others:
- "COIVD-19 epidemiology with R": http://bit.ly/2IH5OuX
- "Analysing COVID-19 (2019-nCoV) outbreak data with R - part 1": http://bit.ly/2xvevpT
- "Analysing COVID-19 (2019-nCoV) outbreak data with R - part 2": http://bit.ly/2Qdii1B
- "Modelling the effects of public health interventions on COVID-19 transmission using R - part 1": http://bit.ly/2TXlBv2
- "Modelling the effects of public health interventions on COVID-19 transmission using R - part 2": https://bit.ly/2UeeW0U
- "Simulating COVID-19 interventions with R" https://bit.ly/39mw3C9
- "Flatten the COVID-19 curve" (R Tutorial) https://bit.ly/2xo0TN4
R RESOURCES for COVID-19 Research
- Epidemiological R PACKAGES (The R Epidemics Consortium): https://www.repidemicsconsortium.org/projects/
- EpModel: Mathematical Modeling of Infectious Disease Dynamics: http://www.epimodel.org/
- "Top 50 R resources on Novel COVID-19 Coronavirus" (Antoine Soetewey): https://www.statsandr.com/blog/top-r-resources-on-covid-19-coronavirus/
TUTORIALS on COVID-19 and Knowlege Graphs
- "Building a COVID-19 Knowledge Graph" (KG Hub) https://bit.ly/34jqbIT
- "Working with Apple's COVID Mobility Data using" (Kieran Healy) https://bit.ly/2VR7SZ3
  - Related github repo: https://github.com/kjhealy/apple_covid_post
Interactive SIMULATIONS with code:
- (R, Shiny) "Modeling COVID-19 Spread vs Healthcare Capacity" https://alhill.shinyapps.io/COVID19seir/
  Code available via github: https://github.com/alsnhll/SEIR_COVID19
- (R, Shiny) "Predicting the effects of COVID intervention strategies" https://covid-measures.github.io (Click "Interactive Model" tab for simulator)
  Code available via github at: https://github.com/morgankain/COVID_interventions
COVID-19 DATASETS:
- The mother lode is JHU CSSE's curated repository, updated with global data multiple times daily; forms the basis for the JHU CSSE dashboard: http://bit.ly/39PMWpD
- Global Health Data Exchange (GHDx) http://ghdx.healthdata.org/
- "Census Bureau Demographic and Economic Resources" https://bit.ly/2Y3mBRN
- "Epidemiological data from the COVID-19 outbreak, real-time case information" (Nature) https://go.nature.com/2QMtlPP
  Live version of their data, via github: https://github.com/beoutbreakprepared/nCoV2019
- Eric Brown's global outbreak dataset (from WHO situation reports) on github, formatted as an R package for easy installation; data is available as an Rda file: http://bit.ly/2QeQKsN
- Kaggle Novel Corona Virus 2019 Dataset: Day level information on COVID-19 in Data) https://ourworldindata.org/coronavirus# (see also Background, above)
- "COVID-19 in US and Canada" (county-level case data) https://coronavirus.1point3acres.com/en
- "The COVID-19 Tracking Project" (up-to-date tables and data access) https://covidtracking.com/data/ (see also above)
  - Data as spreadsheet: https://bit.ly/2vKxa0D
  - Data API: https://covidtracking.com/api/
- "State Data and Policy Actions to Address Coronavirus" https://bit.ly/2JeEHYx
- (Tableau) "COVID-19 Case Counts" https://data.world/covid-19-data-resource-hub/covid-19-case-counts (accessible via SQL and SPARQL!)
- (NYTimes) "Coronavirus (COVID-19) Data in the United States" https://github.com/nytimes/covid-19-data
- "COVID-19 Testing Data" (time series) https://ourworldindata.org/covid-testing
- "The COVID Impact Survey: Data" https://www.covid-impact.org/results
- SafeGraph COVID-19 Data Consortium https://www.safegraph.com/covid-19-data-consortium
  - NOTE: Use of SafeGraph's COVID-19 related data requires signing a license agreement; consider carefully before signing. The Rensselaer IDEA is not currently a member of this consortium.
- New York State Data API:
  - Info: https://health.data.ny.gov/Health/New-York-State-Statewide-COVID-19-Testing/xdss-u53e
  - CSV daily testing: https://health.data.ny.gov/resource/xdss-u53e.csv
  - JSON daily testing: https://health.data.ny.gov/resource/xdss-u53e.json
- Tweets:
  - COVID-19-TweetIDs (USC ISI): https://github.com/echen102/COVID-19-TweetIDs
  - RPI: COVID-19-related Tweet ID repository: https://github.com/TheRensselaerIDEA/COVID-TweetIDs
    (Tweet IDs for 41M+ original tweets; 82M+ retweets as of 17 Apr 2020)
  - RPI: COVID-19 Twitter harvesting code: https://github.com/TheRensselaerIDEA/COVID-Twitter
- Other Social Media:
  - The How We Feel app (http://www.howwefeel.org/) lets users self-report age, sex, ZIP code, and any health symptoms they experience. Aggregate data is securely shared with select scientists, doctors and public health professionals who are actively working to stop the spread of COVID-19. The data are not publicly available but researchers can apply to use the resource.
SEMANTIC WEB, LINKED DATA and KNOWLEDGE GRAPH resources:
- COVID-19 Linked Data https://github.com/Research-Squirrel-Engineers/COVID-19
  - Includes a COVID-198 ontology https://bit.ly/3h2Q8SG
- JHU-sourced structured data (CSV) converted to KG (OpenLink, using URLBurner): https://bit.ly/2JapLdW
  Faceted browser-based view of the above https://bit.ly/39f49aQ
- Bio2RDF datasets, via SPARQL endpoints: https://bio2rdf.org/sparql
- Other life science data providers include:
  - linkedlifedata http://linkedlifedata.com/
  - dbcls https://sparql-support.dbcls.jp/
  - uniprot https://sparql.uniprot.org/
- From Tableau: "COVID-19 Case Counts" https://data.world/covid-19-data-resource-hub/covid-19-case-counts (accessible via SQL and SPARQL!)
- "WikiProject COVID-19: A Wiki Project to collect Wikidata resources related to COVID-19 and SARS-CoV-2" https://bit.ly/33XQ5Si
- "The KG-COVID-19 Knowledge Graph Hub" (github) https://github.com/Knowledge-Graph-Hub/kg-covid-19
- "COVID-19 Open Datasets" (AMiner team, China): https://aminer.cn/data-covid19/?from=yx
Data on STATE GOVERNMENT ACTIONS:
- COVID-19 RESOURCES FOR STATE LEADERS (The Council of State Governments) https://bit.ly/3boQsqY
  - State Executive Orders: https://web.csg.org/covid19/executive-orders/
  - State Reopen Plans: https://web.csg.org/covid19/state-reopen-plans/
  - COVID-219 Related Legislation: https://web.csg.org/covid19/schedule-of-legislative-sessions-by-state/
PROXIMITY and CONTACT TRACING::
- Safe Paths: Private Kit (MIT) http://safepaths.mit.edu/
  - COVID Safe Paths (non-profit MIT partner) https://covidsafepaths.org/
- Covid Watch https://www.covid-watch.org/
- CoEpi https://www.coepi.org/
- "Privacy-Preserving Contact Tracing" (Google/Apple spec) https://www.apple.com/covid19/contacttracing
CHALLENGES and Invitations:
- The COVID-19 High Performance Computing (HPC) Consortium https://bit.ly/2UBa5G9 (form)
- March 2020 R Consortium ISC CfP: http://bit.ly/2TLo1ht
- NSF 20-052: Dear Colleague Letter on the Coronavirus Disease 2019 (COVID-19): http://bit.ly/39OPjsW
- Kaggle COVID-19 Open Research Dataset Challenge (CORD-19): http://bit.ly/2WqcYvL
  - Other COVID-19-related Kaggle challenges https://bit.ly/2xXhTdp
- IBM 2020 Call for Code Global Challenge: Take on COVID-19: https://developer.ibm.com/callforcode/
  Take on COVID-19 challenge details: https://developer.ibm.com/callforcode/getstarted/covid-19/
- (GovLab) COLLECTIVE CRISIS INTELLIGENCE Site: http://covidcourse.thegovlab.org/
  - (GovLab) #DATAFORCOVID19 Call for Action: COVID-19 Data Collaboratives https://bit.ly/2XvMl9f

This list is brought to you by The Rensselaer IDEA and RPIrates: The RPI R Users' Group

Please email John Erickson erickj4@rpi.edu with suggestions or additions!

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