lkorczowski/covid19-datasets

List of public datasets, visualization tools and machine-learning ressources on COVID-19 pandemic.

COVID19-datasets

List of all public datasets and interesting ressources on COVID19-desease (caused by virus strain SARS-CoV-2, a.k.a 2019-nCoV). This list is not exhaustive. If you find something new please, fork this repository, commit your update, and do a pull-request. You'll find interesting ressources for epidemiologic data analysis (ML algorithms, visualization, litterature, etc.) in the sections below.

Table of Content

1. Datasets
2. Raw Data Sources
3. Relevant ressources for COVID19 analysis
   • R
   • Python
   • Javascript
4. To be added/Others (unfiltered)

Datasets

Datasets are currently segmented by geography, but feel free to propose another organization if needed (open an issue). Please try to list first the aggregating datasets. You can use keywords for the spatial resolution (e.g. nationwide, regional, individual, etc.)

• Worldwide

  1. CSSEGISandData/COVID-19. Visual Dashboard operated by the Johns Hopkins University Center for Systems Science and Engineering. Aggregating several raw sources of the section below. nationwide daily reports and timeseries (.csv)
  2. datasets/covid-19. CSSEGISandData/COVID-19 normalized, unpivoted and transfered dates to be more machine readable (.csv).
  3. pomber/covid19. CSSEGISandData/COVID-19 in JSON. Used by several other projects.
  4. COVID-19 Open Research Dataset Challenge (CORD-19). The Kaggle initiative to find data-based answers on the desease. Also available on semanticscholar individual
  5. Novel Corona Virus 2019 Dataset individual (.csv)
  6. Corona Data Scraper. Pulls COVID-19 Coronavirus case data from verified sources (.json, .csv). Join the slack in #scraper-dev.
  7. Geographic distribution of COVID-19 cases worldwide. (.xlsx)
  8. Dimensions COVID-19. List several datasets used in accademics litteratures.

• Asia

  1. SOUTH KOREA jihoo-kim/Coronavirus-Dataset individual. also on kaggle

• North America

  1. TBC

• Europe

  1. FRANCE opencovid19-fr/data. Aggregation of the regional french data.
  2. FRANCE lperez31/coronavirus-france-dataset. aggregated individual french data. also on kaggle
  3. FRANCE Confirmed cased per region. individual official french gouvernement. (.csv, .svg)
  4. FRANCE Interventions on suspicous case of COVID-19. Three datasets: Medical acts, Hospitalisation rate and urgency rate (.csv, .ods, .xlsx)
  5. ITALY covid19-in-italy Kaggle with italian individualdata. So also the github pcm-dpc/COVID-19
  6. SPAIN Situación epidemiológica del coronavirus (COVID-19) en Castilla y León

Raw sources

Data not aggregated nor ready for analysis (e.g. press release)

• Worldwide

  1. World Health Organization (WHO): https://www.who.int/
  2. DXY.cn. Pneumonia. 2020. http://3g.dxy.cn/newh5/view/pneumonia.
  3. BNO News: https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/

• Asia

  1. National Health Commission of the People’s Republic of China (NHC): http://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml
  2. China CDC (CCDC): http://weekly.chinacdc.cn/news/TrackingtheEpidemic.htm
  3. Hong Kong Department of Health: https://www.chp.gov.hk/en/features/102465.html
  4. Macau Government: https://www.ssm.gov.mo/portal/
  5. Taiwan CDC: https://sites.google.com/cdc.gov.tw/2019ncov/taiwan?authuser=0
  6. Ministry of Health Singapore (MOH): https://www.moh.gov.sg/covid-19

• North America

  1. US CDC: https://www.cdc.gov/coronavirus/2019-ncov/index.html
  2. Government of Canada: https://www.canada.ca/en/public-health/services/diseases/coronavirus.html

• Oceania

  1. Australia Government Department of Health: https://www.health.gov.au/news/coronavirus-update-at-a-glance

• Europe

  1. European Centre for Disease Prevention and Control (ECDC): https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases
  2. Italy Ministry of Health: http://www.salute.gov.it/nuovocoronavirus

Relevant ressources for COVID19 analysis

Segmented by language for algorithms. Add the relevant keywords in description for the scope of the tools e.g. {COVID19, epidemiology, generic, ML, visualization}.

R

• EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves. {epidemiology, ML}
• COVID-19 epidemiology with R. Visualization of CSSEGISandData datasets + scraping wikipedia data. {COVID19, visualization}
• HospiCov. estimate hospital resources required to treat patients infected by SARS-CoV-2. Related paper: Forecasting short term hospital needs in France. 2020.
• epiforecasts/EpiNow Estimate Realtime Case Counts and Time-varying Epidemiological Parameters https://www.epiforecasts.io/EpiNow {COVID19, prediction}
• epiforecasts/EpiSoon Forecasting the effective reproduction number over short timescales https://epiforecasts.io/EpiSoon {COVID19, prediction}
• thibautjombart/covid19_bed_occupancy Shiny app providing estimates of future bed occupancy given recent admissions https://cmmid-lshtm.shinyapps.io/hospital_bed_occupancy_projections/ {COVID19, prediction}
• sangeetabhatia03/covid19-short-term-forecasts forecast for the daily number of COVID-19 Death in countries with sustained local transmission {COVID19, prediction}

Python

• ImperialCollegeLondon/covid19model Code for modelling estimated deaths and cases for COVID19.
• DmitrySerg/COVID-19. "combining two general strategies to infection modelling: using Susceptible-Infectious-Recovered/Removed (SIR) model". {COVID19, ML}
• j-i-l/EndemicPy. "Python package to simulate a vast range of transmission processes on various structures". {epidemiology, ML}
• scispaCy spaCy models for processing biomedical, scientific or clinical text.
• allenai/scibert A Pretrained Language Model for Scientific Text
• scrouzet/covid19-incrementality quantify global death increase due to COVID-19 in France at the department level
• Yu-Group/covid19-severity-prediction COVID19 data + modeling at the county-level + hospital-level. https://covidseverity.com/ {COVID19, ML, prediction}
• Rank23/COVID19 Using Kalman Filter to Predict Corona Virus Spread https://medium.com/@rank23/using-kalman-filter-to-predict-corona-virus-spread-72d91b74cc8
• tarunk04/COVID-19-CaseStudy-and-Predictions This repository is a case study, analysis and visualization of COVID-19 Pandemic spread along with prediction models.
• therealcyberlord/coronavirus_visualization_and_prediction tracks the spread of the novel coronavirus, also known as SARS-CoV-2
• kieshaprem/covid19-agestructureSEIR-wuhan-social-distancing Age-structured SEIR model for COVID-19 outbreak in Wuhan, China

javascript

• aitahtman/coronavirus-api. "api dedicated to serve Coronavirus data"
• xithiox/disease. "A simple disease spread simulation in p5.js. It can be played here." {epidemiology, visualization}
• gabgoh/Epidemic Calculator. a visual calculator for modeling possible paths of COVID19. index
• stevenliuyi/covid19 an interactive, animated COVID-19 coronavirus map to track the outbreak over time by country and by region for selected countries https://covid19.health

To be added/Others (unfiltered)

There is so much accademic/non-accedemic publications that it is difficult to link the different initiatives the ressources. Please add links to publications that relies on datasets or methods not yet public. Before adding elements here, please double check it is not included in another section.

1. A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing. Leon Danon, Ellen Brooks-Pollock, Mick Bailey, Matt J Keeling. medRxiv 2020.02.12.20022566; doi: https://doi.org/10.1101/2020.02.12.20022566
2. COVID-19: Forecasting short term hospital needs in France. Massonnaud, C., Roux, J., Crépey P.. https://www.ea-reperes.com/wp-content/uploads/2020/03/PredictedFrenchHospitNeeds-EHESP-20200316.pdf
3. Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf