Documentation

[tdrvlad]

I worked on a project on Covid using your repository. I am sharing the project documentation, in case it's of use to you - it contains some images I've made in order to represent the different models.

Very good work, btw!

https://github.com/tdrvlad/covid_sir_modelling

[lisphilar]

Dear @tdrvlad,
Thank you very much for your work and using CovsirPhy!
I read your "ModellingCovid19.pdf" and I'd like to invite you to our project as a member.
https://github.com/tdrvlad/covid_sir_modelling/blob/main/ModellingCovid19.pdf

Could your edit "example/*.ipynb" files (not the files in docs directory) to improve our documentation with the images and expalanations?
They will be automatically deployed to https://lisphilar.github.io/covid19-sir/usage_quickest.html

One comment regarding SIR-F model for more improvement:
S* (confirmed and un-categorized) is an auxiliary variable/status, not an actual. This was created for ODE modelling because we do not know the ratio of the cases who died before confirmation.
In the images for understanding, "S -> I" with (1-alpha1) beta I and "S-> F" with (alpha1) beta I could be more descriptive than "S -> S* -> I" and "S -> S* -> F" if this does not make the figure complexed.

may travel, meet with their peers, thus easily spreading the virus.

This appears the description of "Waiting".

Thank you!

[tdrvlad]

Hello, Thanks for your quick reply. I am glad for your proposal to contribute to your repository. I can modify any of the models diagrams - I agree on the discussion on S*, in the formulas it's not an explicit state but at the time I considered it useful in the diagram. But I can change it as you said. So you would like me to add the images in the /example/*.ipynb files wherever the models are mentioned? I am a little caught up with work right now, but I can do that next week. If you want to add them, it's fine by me also. I just want them to be of use :) Cheers, Vlad

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On Mon, 8 Feb 2021 at 14:55, Lisphilar ***@***.***> wrote: Dear @tdrvlad <https://github.com/tdrvlad>, Thank you very much for your work and using CovsirPhy! I read your "ModellingCovid19.pdf" and I'd like to invite you to our project as a member. https://github.com/tdrvlad/covid_sir_modelling/blob/main/ModellingCovid19.pdf Could your edit "example/*.ipynb" files (not the files in docs directory) to improve our documentation with the images and expalanations? They will be automatically deployed to https://lisphilar.github.io/covid19-sir/usage_quickest.html One comment regarding SIR-F model for more improvement: S* (confirmed and un-categorized) is an auxiliary variable/status, not an actual. This was created for ODE modelling because we do not know the ratio of the cases who died before confirmation. In the images for understanding, "S -> I" with (1-alpha1) beta I and "S-> F" with (alpha1) beta I could be more descriptive than "S -> S* -> I" and "S -> S* -> F" if this does not make the figure complexed. may travel, meet with their peers, thus easily spreading the virus. This appears the description of "Waiting". Thank you! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3BQEGGIXSGWCOL5BJIGATS57NK5ANCNFSM4XH3WWGA> .

[lisphilar]

Hello,
I used S* for explanation of SIR-F model for about one year, but I sometimes receive questions regarding S* meaning. It will be better for users to remove it.

Your contribution will be welcomed any time.
The images (and explanation of reproduction number Rt) will be added to "example/usage_theoretical.ipynb" file. Because SIR-F model is the main model at this time, the image for SIR-F model may be added to some other files. We will discuss this later.

Additionally, if you have a time later, please edit the other files of "example/*.ipynb" to document the analysis methods, including "Since we expect the system non-linear,...which would enable us to deploy the proposed models." and the explanation regarding RMSLE score.

Best Regards!

[tdrvlad]

Ok, I'll do this. I used to teach at a laboratory at my university so explanations are something I enjoy doing :) So how do we proceed, you add me as contributor and I make the changes and push them? Thanks! Vlad

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On Mon, 8 Feb 2021 at 15:45, Lisphilar ***@***.***> wrote: Hello, I used S* for explanation of SIR-F model for about one year, but I sometimes receive questions regarding S* meaning. It will be better for users to remove it. Your contribution will be welcomed any time. The images (and explanation of reproduction number Rt) will be added to "example/usage_theoretical.ipynb" file. Because SIR-F model is the main model at this time, the image for SIR-F model may be added to some other files. We will discuss this later. Additionally, if you have a time later, please edit the other files of "example/*.ipynb" to document the analysis methods, including "Since we expect the system non-linear,...which would enable us to deploy the proposed models." and the explanation regarding RMSLE score. Best Regards! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#591 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3BQEGA4EUH2BGP3MWNVJTS57TGFANCNFSM4XH3WWGA> .

[lisphilar]

Thank you, I'm looking forward to collaborate with you ;)

I will add you as a collaborator and you can select the way from

• forking this repository and creating issue/pull request, and
• creating a branch with a issue and a merge request to the default branch.

The first one is explained in https://lisphilar.github.io/covid19-sir/CONTRIBUTING.html so that any users can join our project using issues/pull requests without my confirmation as the author.

[tdrvlad]

Thank you for your patience! All the best,

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On Mon, 8 Feb 2021 at 16:36, Lisphilar ***@***.***> wrote: Thank you, I'm looking forward to collaborate with you ;) I will add you as a collaborator and you can select the way from - forking this repository and create issue/pull request, and - creating a branch with a issue and a merge request to the default branch. The first one is explained in https://lisphilar.github.io/covid19-sir/CONTRIBUTING.html so that any users can join our project using issues/pull requests without my confirmation as the author. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3BQED3SYO6ERZ4KNJRO7LS57ZF3ANCNFSM4XH3WWGA> .

[lisphilar]

FYI.
We continue to use SEWIR-F model for simulaion with set parameter values, but parameter estimation with SEWIR-F model may be deprecated because we do not have datasets regarding "Exposed" and "Waiting" as discussed in #573 and #379.

Dear @tdrvlad , how did you use this model in your analysis?

[lisphilar]

Dear @tdrvlad,
Could we use the figures in CovsirPhy documentation?

[tdrvlad]

Yes, that was the idea all along!

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On Fri, Mar 26, 2021 at 12:14 PM Hirokazu Takaya ***@***.***> wrote: Dear @tdrvlad <https://github.com/tdrvlad>, Could we use the figures in CovsirPhy documentation? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3BQEFPV5HJBNVSUNMIVETTFRNABANCNFSM4XH3WWGA> .

[lisphilar]

Dear @tdrvlad,
We discussed using the images in the documentation in the previous comments, but could you try to add a new method of covsirphy.SIRF which shows the image? i.e. Images will be saved in the "data" directory of this repository under Apache-2.0 license and the new method will retrieve it with requests pacage etc.

[tdrvlad]

Good day, sir, Unfortunately, I am caught up with work this period. I can specifically modify the images if that helps you but I cannot promise to modify much in the documentation / repo. I am sorry. Besides that, you can use any of my resources, including the text from pdf. All the best, Vlad

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On Thu, 1 Apr 2021 at 14:10, Hirokazu Takaya ***@***.***> wrote: Dear @tdrvlad <https://github.com/tdrvlad>, We discussed using the images in the documentation in the previous comments, but could you try to add a new method of covsirphy.SIRF which shows the image? i.e. Images will be saved in the "data" directory of this repository under Apache-2.0 license and the new method will retrieve it with requests pacage etc. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#591 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3BQECR3UCOSMMKIJLXL33TGRIC5ANCNFSM4XH3WWGA> .