Data Tools: Scripts, code, methods
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Technical Guidance and Tools
Resources and tools
What is the R value?
🌏🔗https://www.weforum.org/agenda/2020/05/covid-19-what-is-the-r-number/
What is the R number and why do countries need to reduce it to less than 1?
Recognising good COVID-19 data
🌏🔗https://hbr.org/2020/05/which-covid-19-data-can-you-trust
'Which COVID-19 data can you trust?' by Harvard Business Review
Top 50 R resources on COVID-19
🌏🔗https://towardsdatascience.com/top-5-r-resources-on-covid-19-coronavirus-1d4c8df6d85f
Best R resources (Shiny app, R packages, code and data) about COVID-19 Coronavirus.
tinyCOVID-19: Download, Tidy and Visualize COVID-19 Related Data
🌏🔗https://github.com/joachim-gassen/tidycovid19/
Easy to use R package created by Joachim Gassen caches new data from John Hopkins and other sources daily. It is very easy to use, even for beginners. (Also listed in Top 50 link above
Data for Good: New Tools to Help Health Researchers Track and Combat COVID-19
🔗 https://about.fb.com/news/2020/04/data-for-good/
Blog post from Facebook announcing new data tools.
R script for cleaning the Johns Hopkins data
🌏🔗https://github.com/jmcastagnetto/covid-19-data-cleanup
R scripts to cleanup data from Johns Hopkins University (JHU) dataset.
COVID-19 analytics
🌏🔗https://rdrr.io/github/kenarab/COVID19/f/README.md
This package curate (downloads, clean, consolidate, smooth) data from Johns Hopkins for analyzing international outbreak of COVID-19.
Python wrapper for getting Johns Hopkins Coronavirus data
🔗 https://pypi.org/project/COVID19Py/
A tiny Python package for easy access to up-to-date Coronavirus cases data. Uses the Johns Hopkins figures.
ReichLab Analyses related to COVID-19 outbreak
🇺🇸🔗 https://github.com/reichlab
GitHub repository from The Reich Lab at the University of Massachusetts at Amherst.
WHO List of Protocols for Laboratory Testing
Technical guidance for laboratories conducting COVID-19 testing.
openEHR
Open specifications, clinical models and software that can be used to create standards, and build information and interoperability solutions for healthcare.
[email protected] (FAH or [email protected])
🌏🔗https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/ also for citizen scientists and anyone with spare computing capacity to donate their down time.
Coronavirus Location
🇺🇸🔗https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/
COVID-19 Map by County and State
COVID-19 Material Distribution
Aid distribution analysis by region
Data / APIs
Anonymised Health Data for Research
🔗https://www.hmhospitales.com/prensa/notas-de-prensa/comunicado-covid-data-save-lives
HM Hospitales in Madrid, Spain is providing anonymized health data regarding patients being treated for the SARS-CoV-2 virus to worldwide health care institutions, universities, and scientific organizations who request it, and whose research project is approved.
COVID-19 API
🔗https://covid2019-api.herokuapp.com/
The daily updated API on the cases of a new Coronavirus disease. It contains a number of confirmed cases, deaths, and recovered cases based on the data provided by the Johns
Hopkins University Center for Systems Science and Engineering (JHU CCSE).
🔗 https://github.com/nat236919
Insights Quotient COVID-19 API
🔗https://www.insightsquotient.com/covid-api
Insights Quotient’s COVID-19 API allows users to query the underlying multidimensional models that UST Global's data practice team has developed. The API allows developers to submit a ANSI standard SQL statement. The API response includes the columns names for the data and the results in separate arrays in the response JSON.
Open source and citizen science
[email protected] (FAH or [email protected])
Crowdsourced computer memory power for the research and modeling of the SARS COV-2 virus behavior. The project is also open for citizen scientists and anyone with the spare computing capacity to donate it to make the supercomputer more powerful. Currently there are over a million volunteering machines - quite impressive.
openEHR
Open specifications, clinical models and software that can be used to create standards, and build information and interoperability solutions for healthcare.
Open dataset of scientific articles
🔗https://www.semanticscholar.org/cord19
In hope of inspiring the creation of new AI tools to fight Coronavirus, researchers and leaders from the Allen Institute for AI, Chan Zuckerberg Initiative (CZI), Georgetown University’s Center for Security and Emerging Technology (CSET), Microsoft, and the National Library of Medicine (NLM) at the National Institutes of Health released an open dataset of over 29,000 scientific articles published in journals and on preprint servers. Please note - the dataset has its flaws: only about 13,000 of the articles include full text, meaning that all of the figures and words within the article are available. The other roughly 16,000 articles include only metadata.
Research resources and articles
Describing Epidemiological Data
🇺🇸🔗https://www.cdc.gov/eis/field-epi-manual/chapters/Describing-Epi-Data.html
Understanding/exploring outbreak data - useful tips & case studies - the CDC field epidemiology manual.
Microsoft Academic resources for COVID-19 research
Guidance from Microsoft about how to use their academic resources for COVID-19 research.
Benchling
🌏🔗https://www.benchling.com/covid-19/
Benchling is undertaking several initiatives to support researchers and health care workers on the front lines of the COVID-19 crisis. We are collecting research resources such as sequences and protocols, centralizing donation requests from the scientific community, and offering the Benchling platform pro bono for COVID-19 testing.
Tracking COVID-19 using online searches
🌏🔗https://arxiv.org/abs/2003.08086
Research article on using Google search data for Coronavirus. Search data has been used by digital epidemiologists to understand public information needs during previous outbreaks of Zika and Ebola. A project led by @lampos is working on a model to track COVID-19 using search data.
Why It’s So Freaking Hard To Make A Good COVID-19 Model
🌏🔗https://fivethirtyeight.com/features/why-its-so-freaking-hard-to-make-a-good-covid-19-model/
Writers for the FiveThirtyEight statistics blog explain measurement and data definition issues in infectious disease modeling to a non-specialist audience.
Looking for Evidence of a High Burden of COVID-19 in the United States from Influenza-Like Illness Data
Article from ReichLab describing and testing a method to estimate undiagnosed COVID-19 cases based on influenza-like illness counts.
ReichLab Analyses related to COVID-19 outbreak
🇺🇸🔗 https://github.com/reichlab
GitHub repository from The Reich Lab at the University of Massachusetts at Amherst.
WHO List of Protocols for Laboratory Testing
Technical guidance for laboratories conducting COVID-19 testing.
