where to find the code to plot the following figure?

[liamxg]

[fritzo]

https://github.com/broadinstitute/pyro-cov/blob/master/notebooks/mutrans.ipynb

[liamxg]

@fritzo thanks.

[liamxg]

@fritzo not find this plot in https://github.com/broadinstitute/pyro-cov/blob/master/notebooks/mutrans.ipynb.

[fritzo]

See plot_emergence() in that file. We do not store plots with code; rather plots are stored in paper/ and code is stored in notebooks.

[liamxg]

[liamxg]

this figure?

[fritzo]

yes, I believe plot_emergence() creates that figure. Can you be more specific about what you're looking for and what you haven't found in plot_emergence()?

[Jialu-Zuo]

Hi @barkasn , @martinjankowiak , @JacobLemieux , @bkotzen , @corneliusroemer. @fritzo ,
I'm trying to plot strain emergence figure, it seems that there is something wrong with the 95% confidence intervals. Looking forward to your explaination!

[liamxg]

Dear @Jialu-Zuo,
what kind of problems?

[Jialu-Zuo]

Dear @Jialu-Zuo, what kind of problems?

As the figure shows，the confidence intervals are really wide，I guess it is because of the small amount of sample. Besides，the "cases/day" of top ten lineages are all zeros.

[Jialu-Zuo]

Hi @barkasn , @martinjankowiak , @JacobLemieux , @bkotzen , @corneliusroemer. @fritzo ,
as the figure shows，the confidence intervals are really wide. Besides，the "cases/day" of top ten lineages are all zeros，I think it is because of the lack of the data. JHU has stopped collecting data as of 2023/3/10, I'm also wondering if there is other appropriate data to take place of the origin. Looking forward to your reply!