https://github.com/bgonzalezbustamante/covid19-r

Collection of analyses, packages, visualisations of COVID19 data in R

https://github.com/bgonzalezbustamante/covid19-r

Repository

Collection of analyses, packages, visualisations of COVID19 data in R

https://github.com/bgonzalezbustamante/covid19-r/blob/master/

[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](https://www.contributor-covenant.org/version/2/0/code_of_conduct/)

# covid19-r

This repo links to a collection of analyses on and representations of COVID19 data in R. Inclusion on the list does not mean the analysis was verified by me or that I endorse the findings. It should also be noted that some of the analysis / data might be out of date, so these should not be viewed, by default, as current findings.

I'm collecting them as they get posted online so that I can come back to them later to develop educational examples based on theses data. I should also note that one should think about using these as class examples thoroughly -- the situation is affecting all of us (and our students) greatly and it's possible some students are personally affected by the pandemic.

Subheadings are in flux as of now, as more analyses get added I might recategorize them. 

If you have examples to add, please open an issue or make a pull request.

## Blog posts

- [Simulating COVID-19 interventions with R](https://rviews.rstudio.com/2020/03/19/simulating-covid-19-interventions-with-r/)
- [Analysing COVID-19 (2019-nCoV) outbreak data with R - part 1](https://timchurches.github.io/blog/posts/2020-02-18-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-1/)
- [Analysing COVID-19 (2019-nCoV) outbreak data with R - part 2](https://timchurches.github.io/blog/posts/2020-03-01-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-2/)
- [Modelling the effects of public health interventions on COVID-19 transmission using R - part 1](https://timchurches.github.io/blog/posts/2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1/)
- [Modelling the effects of public health interventions on COVID-19 transmission using R - part 2](https://timchurches.github.io/blog/posts/2020-03-18-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2/)
- [COVID-19: The Case of Germany](https://blog.ephorie.de/covid-19-the-case-of-germany)
- [Map Visualization of COVID-19 Across the World with R](https://datascienceplus.com/map-visualization-of-covid19-across-world)
- [COVID-19 cumulative observed case fatality rate over time](http://freerangestats.info/blog/2020/03/17/covid19-cfr)
- [Impact of a country's age breakdown on COVID-19 case fatality rate](http://freerangestats.info/blog/2020/03/21/covid19-cfr-demographics)
- [COVID-19 Tracker: Days since N](https://mentalbreaks.rbind.io/posts/covid-19-tracker/)
- [COVID-19 Has Become a Partisan Issue (How to Make Dumbbell Plots in R](https://connorrothschild.github.io/covid/)
- [Get Your Epidemiology from Epidemiologists](https://kieranhealy.org/blog/archives/2020/03/21/covid-19-tracking/)
- [Flatten the COVID-19 curve](https://staff.math.su.se/hoehle/blog/2020/03/16/flatteningthecurve.html)
- [A Beginners Guide to Creating a Corona Dashboard](https://medium.com/@jonas.schroeder1991/a-beginners-guide-to-creating-a-corona-dashboard-3553b01d8d44)
- [Infectious diseases and nonlinear differential equations](https://fabiandablander.com/r/Nonlinear-Infection.html)
- [COVID-19: The Case of Spain](https://diarium.usal.es/jose/2020/03/20/covid-19-the-case-of-spain/)
- [Epidemic modelling of COVID-19 in the UK using an SIR model](https://tjwilding.wordpress.com/2020/03/20/epidemic-modelling-of-covid-19-in-the-uk-using-an-sir-model/)
- [Modeling Pandemics (2)](https://freakonometrics.hypotheses.org/60543)
- [Dont speculate, simulate!](https://timchurches.github.io/blog/posts/2020-03-20-dont-speculate-simulate/)
- [Coronavirus model using R  Colombia](https://medium.com/@daniel.pena.chaves/simple-coronavirus-model-using-r-cf6b1bc93949)
- [Epidemiology: How contagious is Novel Coronavirus (2019-nCoV)?](https://blog.ephorie.de/epidemiology-how-contagious-is-novel-coronavirus-2019-ncov)
- [A COVID Small Multiple](https://kieranhealy.org/blog/archives/2020/03/27/a-covid-small-multiple/)
- [Merge Covid-19 Data with Governmental Interventions Data](https://joachim-gassen.github.io/2020/03/merge-covid-19-data-with-governmental-interventions-data/)
- [COVID-19 Data and Prediction for Michigan](https://iamnagdev.com/2020/03/26/covid-19-data-and-prediction-for-michigan/)
- [Tidying the new Johns Hopkins Covid-19 time-series datasets](https://joachim-gassen.github.io/2020/03/tidying-the-new-johns-hopkins-covid-19-datasests/)
- [Covid deaths graphs -- a walk-through (part 1)](https://calumdavey.github.io/Covid-Deaths/)
- [Covid deaths graphs -- school closure (part 2)
](https://calumdavey.github.io/Covid-Deaths-schools/)
- [Covid deaths graphs -- lockdown (part 3)](https://calumdavey.github.io/Covid-Deaths-lockdown/)
- [Coverage of COVID research by the A&I databases](https://rpubs.com/alexeilutay/covid_coverage)
- [Top 25 R resources on Novel COVID-19 Coronavirus](https://www.statsandr.com/blog/top-r-resources-on-covid-19-coronavirus)
- [How to create a simple Coronavirus dashboard specific to your country in R](https://www.statsandr.com/blog/how-to-create-a-simple-coronavirus-dashboard-specific-to-your-country-in-r/)
- [COVID-19 in Belgium](https://www.statsandr.com/blog/covid-19-in-belgium/)
- [Why log ratios are useful for tracking COVID-19](https://robjhyndman.com/hyndsight/logratios-covid19/)
- [Another "flatten the COVID-19 curve" simulation... in R](https://allthiswasfield.blogspot.com/2020/04/another-flatten-covid-19-curve.html)
- [The COVID-19 Initial Unemployment Claims Spike in Context](http://svmiller.com/blog/2020/03/the-covid19-initial-claims-spike-in-context-r/)
- [Facts About Coronavirus Disease 2019 (COVID-19) in 5 Charts created with R and ggplot2](https://novyden.blogspot.com/2020/03/facts-about-coronavirus-disease-2019.html)
- [Making Of: A Free API For COVID-19 Data](https://www.statworx.com/de/blog/making-of-a-free-api-for-covid-19-data/)
- [COVID-19 decease animation map](http://r.iresmi.net/2020/04/01/covid-19-decease-animation-map/)
- [Merge Covid-19 Data with Governmental Interventions Data](https://joachim-gassen.github.io/2020/03/merge-covid-19-data-with-governmental-interventions-data/)

## Shiny apps / dashboards

- [COVID-19 tracker](https://vac-lshtm.shinyapps.io/ncov_tracker/) [[Code]](https://github.com/eparker12/nCoV_tracker)
- [Coronavirus (COVID-19) Across The World](https://dash.datascienceplus.com/covid19/)
- [Coronavirus COVID-19 Global Cases](http://www.paulamoraga.com/coronavirus/)
- [Utah.gov Coronavirus Dashboard](https://coronavirus.utah.gov/latest/) (Access seems restricted outside of the US)
- [Visualisation of Covid-19 case data for the Island of Ireland
](https://github.com/mathsnuig/coronaviz) [[Code]](https://github.com/mathsnuig/coronaviz)
- [COVID-19 Cases in Ontario](https://gregrousell.shinyapps.io/COVID-19/)
- [Observatrio COVID-19 BR ](https://covid19br.github.io/)
- [Coronavirus dashboard](https://ramikrispin.github.io/coronavirus_dashboard/)
- [Covid-19](https://thereseanders.shinyapps.io/covid19/) [Code linked in app]
- [CoronaDash](https://petolau.shinyapps.io/coronadash/)
- [Coronavirus COVID-19 : Rpartition des cas infects en Tunisie](https://mounabelaid.shinyapps.io/coronavirus/)
- [COVID-19 Tracker](https://mentalbreaks.shinyapps.io/covid19/)
- [Thailand: COVID-19 Growth Dashboard](https://paulapivat.shinyapps.io/covidgrowth/)
- [Covid-19: country comparison](https://scitilab.shinyapps.io/Covid19/)
- [Covid-19 Italy](https://alessiopassalacqua.github.io/covid19_italy/)
- [Government of Alberta COVID-19 dashboard](https://covid19stats.alberta.ca/)
- [Covid-19 Turkey](https://rpydaneogrendim.shinyapps.io/covid19turkey/)
- [Tableau de bord de suivi de lpidmie de coronavirus en France](https://veille-coronavirus.fr/)
- [Modeling COVID-19 Spread vs Healthcare Capacity](https://alhill.shinyapps.io/COVID19seir/) - [[Twitter thread]](https://twitter.com/alison_l_hill/status/1239072817678823425?s=20) [[Code]](https://github.com/alsnhll/SEIR_COVID19)
- [Covid-19 in United States](https://tarko.shinyapps.io/covid/)
- [COVID-19 in India](https://rstudio-pubs-static.s3.amazonaws.com/583827_1958ebf6748d4835864082bd95a631e0.html)
- [The math behind flatten the curve](https://ahurford.shinyapps.io/flatten-the-curve/) [[Code]](https://github.com/ahurford/flatten-the-curve)
- [Flatten the Curve](https://tinu.shinyapps.io/Flatten_the_Curve/)
- [Tracking COVID-19](https://dartthrowingchimp.shinyapps.io/covid19-app/)
- [#explainCovid19 challenge](https://medium.com/@ModelOriented/explaincovid19-challenge-2453b255a908)
- [COVID-19: Modeling the Flattening of the Curve](http://smaldino.com/wp/covid-19-modeling-the-flattening-of-the-curve/)
- [An R Package to Explore the Novel Coronavirus](https://towardsdatascience.com/an-r-package-to-explore-the-novel-coronavirus-590055738ad6)
- [COVID-19 call-to-arms](https://timchurches.github.io/blog/posts/2020-03-06-covid-19-call-to-arms/)
- [COVID-19 State Tracker Dashboard](https://ausmeyer.shinyapps.io/covid_states/)
- [COVID-19 Explorer](https://ethan-tenison.shinyapps.io/covid-19/)
- [Analisis descriptivo de contagio por Coronavirus](https://analyticsrlun.shinyapps.io/Shiny-AnalyticsRLUN/)
- [Datos COVID-19 (SARS-CoV-2)](https://baguadoramirez.shinyapps.io/covid/)
- [Covid19-Cases](https://monty.shinyapps.io/rcoronavirus/)
- [US Coronavirus Tracker](https://rdwinkelman.shinyapps.io/US_COVID_Explorer/)
- [Covid-19 cases](https://mpalanco.shinyapps.io/coronavirus_shiny/)
- [COVID-19 Schweiz - Open Source Version](https://chschoenenberger.shinyapps.io/covid19_dashboard_ch/) [[Code]](https://github.com/chschoenenberger/covid19_dashboard_ch)
- [COVID-19 Dashboard](https://billpetti.shinyapps.io/covid_19_country_state_dashboard/)
- [Examining COVID-19 data](https://ebsmonash.shinyapps.io/covid19/)
- [Plotting when covid-19 growth trend slows](https://jeanimal.shinyapps.io/covid_log_log_diff/)
- [Coronavirus Tracker](https://shiny.john-coene.com/coronavirus/) [[Code]](https://github.com/JohnCoene/coronavirus)
- [Monitoring COVID-19 evolution in Italy](http://achab94.shinyapps.io/covid-19/)
- [COVID-19 Global Meter](https://shivam-panchal.shinyapps.io/coronavirus/)
- [CoVid-19 in Italia](https://www.pangeadds.eu/demos/CoVid19/)
- [Number of confirmed Covid-19 cases](https://abbaskesh.shinyapps.io/covidgithub/)
- [Modeling COVID-19 Spread vs Healthcare Capacity](https://shinyapps-recent.appspot.com/detail.html?id=220830001)
- [Canadian COVID Dashboard](https://art-bd.shinyapps.io/covid19canada/)
- [COVID-19 Outbreak](https://thibautfabacher.shinyapps.io/covid-19/)
- [Coronavirus 10-day forecast](http://covid19.science.unimelb.edu.au/)
- [Reporting, epidemic growth, and reproduction numbers for the 2019-nCoV epidemic: understanding control](https://art-bd.shinyapps.io/nCov_control/)
- [COVID-19 in LAC](https://robertmitchellv.com/projects-covid-19-lac.html)
- [Material Design Corona/COVID-19 Dashboard](https://sebastianwolf.shinyapps.io/Corona-Shiny/)
- [Coronavirus in Belgium](https://www.antoinesoetewey.com/files/coronavirus-dashboard.html) [[Code]](https://github.com/AntoineSoetewey/coronavirus_dashboard)
- [Visualization of Covid-19 Cases](https://nicohahn.shinyapps.io/covid19/) [[Code]](https://github.com/nicoFhahn/covid_shiny) [[Narrative]](https://community.rstudio.com/t/visualization-of-covid-19-cases-2020-shiny-contest-submission/57211)
- [COVID-19 Live Report](https://behroozh.shinyapps.io/COVID19/) [[Code]](https://rstudio.cloud/project/1029711) [[Narrative]](https://community.rstudio.com/t/covid-19-live-report-2020-shiny-contest-submission/57061)
- [COVID-19 in derivatives](https://pernaletec.shinyapps.io/covid_derivative_db/) [[Code]](https://github.com/pernaletec/covid19_derivatives) [[Narrative]](https://community.rstudio.com/t/covid-19-in-derivatives-2020-shiny-contest-submission/56796)
- [COVID-19 Data Visualization Platform](https://shubhrampandey.shinyapps.io/coronaVirusViz/) [[Code]](https://github.com/shubhrampandey/coronaVirus-dataViz) [[Narrative]](https://community.rstudio.com/t/covid-19-data-visualization-platform-2020-shiny-contest-submission/56992)
- [COVID-19 Acute and Intensive Care Resource Tool](https://caic-rt.shinyapps.io/CAIC-RT/) [[Code]](https://github.com/mattwarkentin/CAIC-RT) [[Narrative]](https://community.rstudio.com/t/covid-19-acute-and-intensive-care-resource-tool-2020-shiny-contest-submission/58448)
- [COVID-19 Global Meter](https://shivam-panchal.shinyapps.io/coronavirus/) [[Narrative]](https://community.rstudio.com/t/covid-19-global-meter-2020-shiny-contest-submission/58312)
- [covid-19 monitor](https://trafforddatalab.shinyapps.io/covid-19/) [[Code]](https://github.com/traffordDataLab/covid-19) [[Narrative]](https://community.rstudio.com/t/covid-19-monitor-2020-shiny-contest-submission/58047)
- [Painel Covid-19](https://caique.shinyapps.io/COVID-Panel/) [[Code]](https://github.com/caiqueth/Covid19-Panel) [[Narrative]](https://community.rstudio.com/t/painel-covid-19-2020-shiny-contest-submission/59803)
- [Covid-19 Dashboard by HBAP Team Shiny](https://jeff-renz.shinyapps.io/HBAPShiny2020/) [[Narrative]](https://community.rstudio.com/t/covid-19-dashboard-by-hbap-team-shiny-2020-shiny-contest-submission/59768)
- [Covid-O-Meter](https://alhenry.shinyapps.io/covid-o-meter/) [[Code]](https://github.com/alhenry/covid-o-meter) [[Narrative]](https://community.rstudio.com/t/covid-o-meter-2020-shiny-contest-submission/59612)
- [NZ COVID-19 Dashboard](https://nzcoviddashboard.esr.cri.nz/)

## Videos

- [Playlist of COVID-19 related R tutorials](https://www.youtube.com/playlist?list=PLuak_bGvcWZPsLGEBv5LM1MxpdZuaBB0Q) by CradleToGraveR
- [Cleaning and exploring the COVID-19 Open Research Dataset](https://www.youtube.com/watch?v=-5HYdBq_PTM) by David Robinson

## Packages

Most of these are data only packages, but sone omly feature functions for creating visualisations and dashboard from the data in the package.

-  [coronavirus](https://github.com/RamiKrispin/coronavirus)
-  [nCoV2019.data](https://github.com/qingyuanzhao/2019-nCov-Data)
-  [covidR](https://github.com/CaRdiffR/covidR-api)
-  [coronabr](https://liibre.github.io/coronabr/index.html)
-  [covid19br](https://paternogbc.github.io/covid19br/index.html)
-  [coronabr](https://liibre.github.io/coronabr/index.html)
-  [covid19italy](https://github.com/RamiKrispin/covid19Italy)
-  [covid19nytimes](https://github.com/Covid19R/covid19nytimes)
-  [covid19at](https://github.com/joph/Covid19-Austria)
-  [ncovmap](https://github.com/yiluheihei/ncovmap) - data of China and global world, China map, Province map of china
World map, maps of Italy, Japan, Korea and Iran
-  [nCov2019](https://guangchuangyu.github.io/nCov2019/)
-  [covid19us](https://github.com/aedobbyn/covid19us)
-  [covid19germany](https://github.com/nevrome/covid19germany)
-  [tidycovid19](https://github.com/joachim-gassen/tidycovid19)

## Data

These are not necessarily R specific resources, but they're mostly what the analyses in R rely on and/or are stored in a format that is easily digestable by R.

- [COVID-19 data API updated daily](https://analythium.github.io/covid-19/) with a simple [plotting interface](https://analythium.github.io/covid-19/) (based on JHU repo)
- NY data: https://github.com/car325/nytc19
- NY Times data: https://github.com/nytimes/covid-19-data
- Australia data: https://github.com/covid-19-au
- NZ data: https://github.com/nzherald/nz-covid19-data
- French data: 
  - https://github.com/opencovid19-fr/data
  - https://github.com/lperez31/coronavirus-france-dataset
- Italy data: https://github.com/pcm-dpc/COVID-19
- US data from NYTimes: https://github.com/nytimes/covid-19-data
- Infotorch COVID-19 Australia Data API: https://github.com/infotorch/covid19-australia-api
- TO DO: SFBart said they'll be posting ridership numbers each day (https://twitter.com/SFBART/status/1239904439542005760?s=20), need to track down how to compile. Also see [here](https://www.bart.gov/news/articles/2020/news20200225).
  
## Journal articles

- [Adjusted age-specific case fatality ratio during the COVID-19 epidemic in Hubei, China, January and February 2020](https://www.medrxiv.org/content/10.1101/2020.03.04.20031104v2) [[Data & Code]](https://github.com/jriou/covid_adjusted_cfr) [[Tweet]](https://twitter.com/konstantinoudis/status/1244888431232253952?s=20)
- [Overview from MIDAS network](https://github.com/midas-network/COVID-19/wiki/Documents)

## Educational activities

- [Visualizing COVID-19](https://rpruim.github.io/ds303/S20/hw/covid-19/covid-19.html) by Randy Prium

## Misc.

- [Maps made from the Johns Hopkins Coronavirus Data](https://github.com/jonhersh/Hopkins_Maps)
- [Discussion of resources on rOpenSci forum](https://discuss.ropensci.org/t/openvirus-tools-and-resources-for-covid-19-knowledge/1998)
- [U.S. COVID-19 Data Explorer](https://rdwinkelman.shinyapps.io/US_COVID_Explorer/)
- [Peru calculations](https://github.com/jmcastagnetto/covid-19-data-cleanup/blob/peru/peru-calculations.R)
- [#COVID19 testing by US state](https://github.com/aaronolsen/aaronolsen.github.io/tree/master/corona)
- [COVID-19 Resource Gallery](https://mirai-solutions.ch/covid-19-gallery/)
- [US COVID-19 Trends](https://www.uscovidtrends.com/)
- [Coronavirus Global Cases leaflet map](http://mesquitadata.com/corona.html)
- How Iceland is predicting COVID-19 cases: [Hierarchical Logistic Growth Curves](https://rpubs.com/bgautijonsson/HierarchicalLogisticGrowthCurves)
- [Mapping COVID-19 in Missouri](https://slu-opengis.github.io/covid_daily_viz/) [[Repo]](https://github.com/slu-openGIS/covid_daily_viz)
- [Florida COVID19 Data parsed from Florida DOH Dashboard and PDF reports](https://github.com/gadenbuie/covid19-florida)
- [Seattle Children's Hospital - Novel Coronavirus COVID-19 Daily Update of Confirmed Cases and Deaths](http://www.schdatascience.org/) (I believe the plots are made with R and plotly)
- [PHE's COVID-19 case data by IMD](https://github.com/VictimOfMaths/Experiments/blob/master/COVID19IMD.R)
- [Positive COVID-19 cases in NYC by zip code](https://github.com/natalieoshea/covid-nyc)
- [Exploring the Temporal Evolution of COVID-19 Cases in the Ohio Counties](https://rpubs.com/rdwinkelman/covid19_ohio_gifs)

## Analysing COVID data responsibly

These are not #rstats specific, but important to digest before diving into the data.

- [Ten Considerations Before You Create Another Chart About COVID-19](https://medium.com/nightingale/ten-considerations-before-you-create-another-chart-about-covid-19-27d3bd691be8)

-----

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