blog/top-r-resources-on-covid-19-coronavirus/

[utterances-bot]

Top 100 R resources on Novel COVID-19 Coronavirus - Stats and R

Best R resources about Coronavirus (COVID-19). These resources are Shiny app, R packages or code that you can use freely to analyze the Coronavirus outbreak

https://statsandr.com/blog/top-r-resources-on-covid-19-coronavirus/

[AntoineSoetewey]

Comment written by Holger K. von Jouanne-Diedrich on March 13, 2020 08:41:26:

I wrote a blog post on how to model the outbreak of the coronavirus, which might be interesting in this context: https://blog.ephorie.de/epidemiology-how-contagious-is-novel-coronavirus-2019-ncov

[AntoineSoetewey]

Comment written by Holger K. von Jouanne-Diedrich on March 13, 2020 08:41:26:

I wrote a blog post on how to model the outbreak of the coronavirus, which might be interesting in this context: https://blog.ephorie.de/epidemiology-how-contagious-is-novel-coronavirus-2019-ncov

Comment written by Antoine Soetewey on March 13, 2020 11:36:19:

Dear Holger K. von Jouanne-Diedrich,

Thank you for your input. I have added your blog post as well!

Regards, Antoine

[AntoineSoetewey]

Comment written by Sachin Adnaik on March 14, 2020 06:35:33:

Thanks for sharing dear #AntoineSoetewey. Can anyone work on the data available (if they want to)? So that, we will get further insights about #coronavirus spread.

Thanks again.

[AntoineSoetewey]

Comment written by Sachin Adnaik on March 14, 2020 06:35:33:

Thanks for sharing dear #AntoineSoetewey. Can anyone work on the data available (if they want to)? So that, we will get further insights about #coronavirus spread.

Thanks again.

Comment written by Antoine Soetewey on March 14, 2020 06:52:50:

Dear Sachin,

Of course anyone can work on the data (see in the data section at the end of the article for more datasets) to get further insights about this coronavirus. This is even the point of the article: give ideas to researchers so they can do more analyses.

If you know anyone who produced some good insights with the data, do not hesitate to let me know so I can include it in the article as well.

Regards, Antoine

[AntoineSoetewey]

Comment written by Shubhram Pandey on March 22, 2020 15:48:51:

Thanks for sharing #AntoineSoetewey. It will an honour for me.

[AntoineSoetewey]

Comment written by Shubhram Pandey on March 22, 2020 15:48:51:

Thanks for sharing #AntoineSoetewey. It will an honour for me.

Comment written by Antoine Soetewey on March 22, 2020 15:51:40: You're welcome Shubhram!

[AntoineSoetewey]

Comment written by Anonymous on March 26, 2020 14:09:27:

Thanks

[AntoineSoetewey]

Comment written by cipperimerlo on March 31, 2020 19:41:46:

Beau travail

Je connais "https://statistichecoronavirus.it/". C'est vraiment bon. 

Salut

[AntoineSoetewey]

Comment written by cipperimerlo on March 31, 2020 19:41:46:

Beau travail

Je connais "https://statistichecoronavirus.it/". C'est vraiment bon. 

Salut

Comment written by Antoine Soetewey on March 31, 2020 22:20:21:

Bonjour,

En effet c'est très intéressant. Cependant cet article se concentre uniquement sur des ressources faites avec le programme R, ce qui (si je ne me trompe pas) n'est pas le cas de ce site.

Mais merci quand même pour votre suggestion.

Bien à vous, Antoine

[AntoineSoetewey]

Comment written by Aous Abdo on April 09, 2020 16:03:34:

Thank you for putting together this list of great resources, and it keeps growing!

[AntoineSoetewey]

Comment written by Aous Abdo on April 09, 2020 16:03:34:

Thank you for putting together this list of great resources, and it keeps growing!

Comment written by Antoine Soetewey on April 09, 2020 17:31:00:

Glad you like it. It's growing everyday thanks to all people who contribute to it!

[AntoineSoetewey]

Comment written by Philippe de Brouwer on April 10, 2020 17:54:29:

Dear Antoine,

That is an amazing publication that you have there and a great source of information. There is some great work in your list and it is a pleasure to see that R is helping people to help others to provide comfort and insight from data. When I started my dashboard in February, it was partly out of frustration that I could find no such source.

May I draw your attention to a few features that still are unique? 

• the dashboard is created to provide insight and allow users to experiment
• rather than proposing a best model. (figure 1). One of the main issues is that a fit of a logistic curve for example won't fit too well on all data if actions have changed the reality. So, the user can choose the model, select a range of dates to use, etc. 
• In search for a way to provide to non-mathematicians a way to see if the situation is really getting better I added the plot (figure 2) that shows something like dN on the y-axis and N on the x-axis. It appears that we are all more or less on the same track, and that a dramatic improvement in the dynamics shows like an exit from the highway.

Further plans include to put the code on github and continue development with a team, etc. I would appreciate your opinion about this dashboard

[AntoineSoetewey]

Comment written by Philippe de Brouwer on April 10, 2020 17:54:29:

Dear Antoine,

That is an amazing publication that you have there and a great source of information. There is some great work in your list and it is a pleasure to see that R is helping people to help others to provide comfort and insight from data. When I started my dashboard in February, it was partly out of frustration that I could find no such source.

May I draw your attention to a few features that still are unique? 

• the dashboard is created to provide insight and allow users to experiment
• rather than proposing a best model. (figure 1). One of the main issues is that a fit of a logistic curve for example won't fit too well on all data if actions have changed the reality. So, the user can choose the model, select a range of dates to use, etc.
• In search for a way to provide to non-mathematicians a way to see if the situation is really getting better I added the plot (figure 2) that shows something like dN on the y-axis and N on the x-axis. It appears that we are all more or less on the same track, and that a dramatic improvement in the dynamics shows like an exit from the highway.

Further plans include to put the code on github and continue development with a team, etc. I would appreciate your opinion about this dashboard

Comment written by Antoine Soetewey on April 12, 2020 09:14:53:

Thanks for this dashboard Philippe. It is now included in the collection. Let me know if there is any inconsistency!

[AntoineSoetewey]

Comment written by Francesca Vitalini on April 20, 2020 09:19:05:

Very nice collection of R resources, thank you for gathering them all up. 

e-Rum2020 (https://2020.erum.io/)), the 2020 (virtutal and free) edition of the European R Users Meeting, has just launched  CovidR (https://2020.erum.io/covidr-contest/), a contest of R contributions around the topic of the COVID-19 pandemic, and an online pre-conference event. I do hope to see many of the listed contributions also submitted to the contest!

[AntoineSoetewey]

Comment written by Francesca Vitalini on April 20, 2020 09:19:05:

Very nice collection of R resources, thank you for gathering them all up. 

e-Rum2020 (https://2020.erum.io/)), the 2020 (virtutal and free) edition of the European R Users Meeting, has just launched  CovidR (https://2020.erum.io/covidr-contest/), a contest of R contributions around the topic of the COVID-19 pandemic, and an online pre-conference event. I do hope to see many of the listed contributions also submitted to the contest!

Comment written by Antoine Soetewey on April 20, 2020 16:44:21:

Thanks for your input Francesca. Let's grow this collection even further with the best resources you receive. 

Looking forward to hearing from you. 

Regards, Antoine

[AntoineSoetewey]

Comment written by Jean claude GBADA on April 27, 2020 17:16:37:

Bonjour cher Coach, merci pour les données que vous mettez à notre dispositions par rapport à la pandémie Covid-19. 

J'ai beaucoup apprécié chapitre "Top 50 R resources on Novel COVID-19 Coronavirus". Cependant, je ne retrouve pas les codes sur GitHub. Je ne trouve pas l'option appropriée pour y accéder. Si vous pouvez m'aider. 

L'autre chose qui m'intéresse est la démarche de détection du pic de l'épidémie dans un pays avec Rstudio. J'entends parler très souvent mais comment arriver à le faire et à bien l'interpréter. De quelles données a t-on besoin pour le représenter, le prédire et comment utiliser ces données pour y parvenir? 

Merci encore et bonne journée

[AntoineSoetewey]

Comment written by Jean claude GBADA on April 27, 2020 17:16:37:

Bonjour cher Coach, merci pour les données que vous mettez à notre dispositions par rapport à la pandémie Covid-19. 

J'ai beaucoup apprécié chapitre "Top 50 R resources on Novel COVID-19 Coronavirus". Cependant, je ne retrouve pas les codes sur GitHub. Je ne trouve pas l'option appropriée pour y accéder. Si vous pouvez m'aider. 

L'autre chose qui m'intéresse est la démarche de détection du pic de l'épidémie dans un pays avec Rstudio. J'entends parler très souvent mais comment arriver à le faire et à bien l'interpréter. De quelles données a t-on besoin pour le représenter, le prédire et comment utiliser ces données pour y parvenir? 

Merci encore et bonne journée

Comment written by Antoine Soetewey on April 28, 2020 06:40:12:

Bonjour Jean-Claude,

Si vous cherchez le code de cet article, il se trouve sur GitHub. Si vous cherchez le code d'un article mentionné dans cette liste, il se trouve soit directement dans l'article, soit aussi sur GitHub. La plupart des auteurs partagent le code, mais pas tous. Vous pouvez toujours contacter les auteurs des articles qui vous intéressent si vous ne trouvez pas le code facilement.

Concernant la détection du pic de l'épidémie, je vous invite à lire cet article que j'ai fait pour la Belgique et à l'adapter pour le pays que vous souhaitez.

Bien à vous, 
Antoine

[AntoineSoetewey]

Comment written by Jean claude GBADA on April 27, 2020 17:16:37: Bonjour cher Coach, merci pour les données que vous mettez à notre dispositions par rapport à la pandémie Covid-19.  J'ai beaucoup apprécié chapitre "Top 50 R resources on Novel COVID-19 Coronavirus". Cependant, je ne retrouve pas les codes sur GitHub. Je ne trouve pas l'option appropriée pour y accéder. Si vous pouvez m'aider.  L'autre chose qui m'intéresse est la démarche de détection du pic de l'épidémie dans un pays avec Rstudio. J'entends parler très souvent mais comment arriver à le faire et à bien l'interpréter. De quelles données a t-on besoin pour le représenter, le prédire et comment utiliser ces données pour y parvenir?  Merci encore et bonne journée

Comment written by Antoine Soetewey on April 28, 2020 06:40:12:

Bonjour Jean-Claude,

Si vous cherchez le code de cet article, il se trouve sur GitHub. Si vous cherchez le code d'un article mentionné dans cette liste, il se trouve soit directement dans l'article, soit aussi sur GitHub. La plupart des auteurs partagent le code, mais pas tous. Vous pouvez toujours contacter les auteurs des articles qui vous intéressent si vous ne trouvez pas le code facilement.

Concernant la détection du pic de l'épidémie, je vous invite à lire cet article que j'ai fait pour la Belgique et à l'adapter pour le pays que vous souhaitez.

Bien à vous,  Antoine

Comment written by Jean claude GBADA on April 28, 2020 08:10:56:

Vraiment merci pour votre réaction.

[AntoineSoetewey]

Comment written by ANA on May 15, 2020 20:35:26:

Could I make this map, but about Spain? I have tried but it say me that covid19spain no exist.    

https://ramikrispin.github.io/italy_dash/#regional-level 

Thanks

[AntoineSoetewey]

Comment written by ANA on May 15, 2020 20:35:26:

Could I make this map, but about Spain? I have tried but it say me that covid19spain no exist.    

https://ramikrispin.github.io/italy_dash/#regional-level 

Thanks

Comment written by Antoine Soetewey on May 15, 2020 20:45:15:

Dear Ana,

This map uses the covid19italy package (see it here: https://statsandr.com/blog/top-r-resources-on-covid-19-coronavirus/#covid19italy). I don't think there exists a package like this one for Spain.

Feel free to contact the author of the package to see whether he expects to release a package for Spain, otherwise you'll have to try to adapt the code for your country.

Best, 
Antoine

[AntoineSoetewey]

Comment written by José Moniz Fernandes on May 29, 2020 04:00:07:

Dear,

I did update today the dashboard from Cabo Verde and I had this error.
Error: object 'Country.Region' not found  

Why?
Thanks,

[AntoineSoetewey]

Comment written by José Moniz Fernandes on May 29, 2020 04:00:07:

Dear,

I did update today the dashboard from Cabo Verde and I had this error. Error: object 'Country.Region' not found  

Why? Thanks,

Comment written by Antoine Soetewey on May 29, 2020 05:38:16:

Dear José,

I suppose you are talking about this dashboard?

If yes, it's normal you have an issue: the maintainer of the package changed the variable Country.Region by country. So replace this variable name and you should be good. See an example in line 33 of this code.

Hope this helps.

Best,
Antoine

[AntoineSoetewey]

Comment written by José Moniz Fernandes on May 29, 2020 04:00:07: Dear, I did update today the dashboard from Cabo Verde and I had this error. Error: object 'Country.Region' not found   Why? Thanks,

Comment written by Antoine Soetewey on May 29, 2020 05:38:16:

Dear José,

I suppose you are talking about this dashboard?

If yes, it's normal you have an issue: the maintainer of the package changed the variable Country.Region by country. So replace this variable name and you should be good. See an example in line 33 of this code.

Hope this helps.

Best, Antoine

Comment written by José Moniz Fernandes on June 15, 2020 01:24:19:

Thanks! Other problem Error: Column Province.State is unknown

[AntoineSoetewey]

Comment written by José Moniz Fernandes on May 29, 2020 04:00:07: Dear, I did update today the dashboard from Cabo Verde and I had this error. Error: object 'Country.Region' not found   Why? Thanks,

Comment written by Antoine Soetewey on May 29, 2020 05:38:16: Dear José, I suppose you are talking about this dashboard? If yes, it's normal you have an issue: the maintainer of the package changed the variable Country.Region by country. So replace this variable name and you should be good. See an example in line 33 of this code. Hope this helps. Best, Antoine

Comment written by José Moniz Fernandes on June 15, 2020 01:24:19:

Thanks! Other problem Error: Column Province.State is unknown

Comment written by Antoine Soetewey on June 15, 2020 07:29:02:

Dear José,

As already said, the author of the package changed the names of the variables, leading to the error you mention.

Here is the code for Cabo Verde on GitHub.

Hope this helps.

Best,
Antoine

[AntoineSoetewey]

Comment written by EAL MORG on June 15, 2020 17:14:52:

Dear Antoine,

first of all, thank you very much. when I run the code devtools::install_github("RamiKrispin/coronavirus") it gave me the following error: Error in utils::download.file(url, path, method = method, quiet = quiet,  :   cannot open URL 'https://api.github.com/repos/RamiKrispin/coronavirus/tarball/master'

how I can fix it?

[AntoineSoetewey]

Comment written by EAL MORG on June 15, 2020 17:14:52:

Dear Antoine,

first of all, thank you very much. when I run the code devtools::install_github("RamiKrispin/coronavirus") it gave me the following error: Error in utils::download.file(url, path, method = method, quiet = quiet,  :   cannot open URL 'https://api.github.com/repos/RamiKrispin/coronavirus/tarball/master'

how I can fix it?

Comment written by Antoine Soetewey on June 15, 2020 19:51:56:

Hello,

Try again with this:
devtools::install_github("RamiKrispin/coronavirus", force = TRUE)

and make sure that you have access to internet.

Hope this helps.

Best,
Antoine

[AntoineSoetewey]

Comment written by EAL MORG on June 15, 2020 17:14:52: Dear Antoine, first of all, thank you very much. when I run the code devtools::install_github("RamiKrispin/coronavirus") it gave me the following error: Error in utils::download.file(url, path, method = method, quiet = quiet,  :   cannot open URL 'https://api.github.com/repos/RamiKrispin/coronavirus/tarball/master' how I can fix it?

Comment written by Antoine Soetewey on June 15, 2020 19:51:56:

Hello,

Try again with this: devtools::install_github("RamiKrispin/coronavirus", force = TRUE)

and make sure that you have access to internet.

Hope this helps.

Best, Antoine

Comment written by EAL MORG on June 17, 2020 14:31:54:

still the same problem

[AntoineSoetewey]

Comment written by EAL MORG on June 15, 2020 17:14:52: Dear Antoine, first of all, thank you very much. when I run the code devtools::install_github("RamiKrispin/coronavirus") it gave me the following error: Error in utils::download.file(url, path, method = method, quiet = quiet,  :   cannot open URL 'https://api.github.com/repos/RamiKrispin/coronavirus/tarball/master' how I can fix it?

Comment written by Antoine Soetewey on June 15, 2020 19:51:56: Hello, Try again with this: devtools::install_github("RamiKrispin/coronavirus", force = TRUE) and make sure that you have access to internet. Hope this helps. Best, Antoine

Comment written by EAL MORG on June 17, 2020 14:31:54:

still the same problem

Comment written by Antoine Soetewey on June 17, 2020 15:19:31:

Is the devtools package also installed?

[AntoineSoetewey]

Comment written by Sarah on September 27, 2020 09:49:08:

If you're in the UK, this is a very useful Sheet which helps with tracking of the local lockdowns: https://sourceful.co.uk/doc/533/public-covid-19-data-table-lower-tier-regional-bre

[AntoineSoetewey]

Comment written by Sarah on September 27, 2020 09:49:08:

If you're in the UK, this is a very useful Sheet which helps with tracking of the local lockdowns: https://sourceful.co.uk/doc/533/public-covid-19-data-table-lower-tier-regional-bre

Comment written by Antoine Soetewey on September 28, 2020 12:52:39:

Dear Sarah,

Thanks for your input. It has been added in the section about datasets.

Regards,
Antoine

[EmilyHaag]

Fantastic list of resources! Here's another: Outbreak.info is an open source tool built by Scripps Research that standardizes and aggregates COVID-19 data. The interface aggregates journal articles, preprints, datasets, clinical trials, protocols, and other resources in one place, standardizing metadata and applying NLP to make these sources searchable and more accessible. The interactive data dashboards allow for quick comparison of countries, states, counties, and metro areas, and includes an API and R Package for researchers who want to access all of the raw data: https://outbreak.info/

[AntoineSoetewey]

Fantastic list of resources! Here's another: Outbreak.info is an open source tool built by Scripps Research that standardizes and aggregates COVID-19 data. The interface aggregates journal articles, preprints, datasets, clinical trials, protocols, and other resources in one place, standardizing metadata and applying NLP to make these sources searchable and more accessible. The interactive data dashboards allow for quick comparison of countries, states, counties, and metro areas, and includes an API and R Package for researchers who want to access all of the raw data: https://outbreak.info/

Dear Emily,

Thanks for your input! It has been added to the list: https://statsandr.com/blog/top-r-resources-on-covid-19-coronavirus/#other-lists-or-collections-of-resources.

Regards, Antoine

[prem2panigrahi]

Dear Antoine I new to R. I am modelling COVID epidemic break out in India. Actually how to do Outbreak size distribution using R. Like degree distribution i want to perform outbreak size distribution

[AntoineSoetewey]

Dear Antoine I new to R. I am modelling COVID epidemic break out in India. Actually how to do Outbreak size distribution using R. Like degree distribution i want to perform outbreak size distribution

Feel free to share your results here!