Data Tools: Scripts, code, methods


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Technical Guidance and Tools

Resources and tools

What is the R value?

๐ŸŒ๐Ÿ”—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

๐ŸŒ๐Ÿ”—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

๐ŸŒ๐Ÿ”—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

๐ŸŒ๐Ÿ”—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

๐Ÿ”—ย 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

๐ŸŒ๐Ÿ”—https://github.com/jmcastagnetto/covid-19-data-cleanup

R scripts to cleanup data from Johns Hopkins University (JHU) dataset.

COVID-19 analytics

๐ŸŒ๐Ÿ”—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

๐Ÿ”—ย 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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—ย https://github.com/reichlab

GitHub repository from The Reich Lab at the University of Massachusetts at Amherst.

WHO List of Protocols for Laboratory Testing

๐Ÿ”—https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance

Technical guidance for laboratories conducting COVID-19 testing.

openEHR

๐ŸŒ๐Ÿ”—https://www.openehr.org

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])

๐ŸŒ๐Ÿ”—https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/ย also for citizen scientists and anyone with spare computing capacity to donate their down time.

Coronavirus Location

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/

COVID-19 Map by County and State

COVID-19 Material Distribution

๐Ÿ‡ฎ๐Ÿ‡น๐Ÿ”—https://app.powerbi.com/view?r=eyJrIjoiNTE2NWM3ZjktZGFlNi00MzYxLWJlMzEtYThmOWEzYjA1MGNhIiwidCI6ImFmZDBhNzVjLTg2NzEtNGNjZS05MDYxLTJjYTBkOTJlNDIyZiIsImMiOjh9

Aid distribution analysis by region

Data / APIs

Anonymised Health Data for Research

๐Ÿ”—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

๐Ÿ”—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).

๐Ÿ”—ย https://github.com/nat236919

Insights Quotient COVID-19 API

๐Ÿ”—https://www.insightsquotient.com/covid-api

Insights Quotientโ€™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])

๐ŸŒ๐Ÿ”—https://foldingathome.org/

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

๐ŸŒ๐Ÿ”—https://www.openehr.org

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

๐Ÿ”—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 Universityโ€™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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—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

๐ŸŒ๐Ÿ”—https://www.microsoft.com/en-us/research/project/academic/articles/microsoft-academic-resources-and-their-application-to-covid-19-research/

Guidance from Microsoft about how to use their academic resources for COVID-19 research.

Benchling

๐ŸŒ๐Ÿ”—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

๐ŸŒ๐Ÿ”—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 byย @lamposย is working on a model to track COVID-19 using search data.

Why Itโ€™s So Freaking Hard To Make A Good COVID-19 Model

๐ŸŒ๐Ÿ”—https://fivethirtyeight.com/features/why-its-so-freaking-hard-to-make-a-good-covid-19-model/ย 

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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://github.com/reichlab/ncov/blob/master/analyses/ili-labtest-report.pdf?fbclid=IwAR2Pyvathgqu5T4eBNUnezJqM5NWr5LKtII8u8NiLGZnz6f5Op19qEaKL_Y

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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—ย https://github.com/reichlab

GitHub repository from The Reich Lab at the University of Massachusetts at Amherst.

WHO List of Protocols for Laboratory Testing

๐Ÿ‡บ๐Ÿ‡ณ๐Ÿ”—https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance

Technical guidance for laboratories conducting COVID-19 testing.