Fritz Obermeyer

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

See `plot_emergence()` in that file. We do not store plots with code; rather plots are stored in [paper/](https://github.com/broadinstitute/pyro-cov/tree/master/paper) and code is stored in notebooks.

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()`?

> how we currently support different parametrisations of the same distribution We're now leaning towards creating different distribution classes for each parametrization. Early in the development of torch.distributions we thought...

Is there anything intrinsically complex in this distribution, or is it simply a multivariate distribution over the `(n * 2)`-long real vector? If the latter, then this would probably be...

Hi @joicy, the easiest way to start work on this feature would be to update [scripts/preprocess_gisaid.py](https://github.com/broadinstitute/pyro-cov/blob/master/scripts/preprocess_gisaid.py) and [scripts/preprocess_nextclade.py](https://github.com/broadinstitute/pyro-cov/blob/master/scripts/preprocess_nextclade.py) to read from files other than `results/gisaid.json`. The least amount of code...

Hi @joicy, realistically I won't have time to help out with this task until say January at earliest. We are focusing on just being able to run the model ourselves,...

@dpark01 can you provide any other links to the Nextstrain GenBank data feed you recommended? The docs [are broken](https://github.com/nextstrain/ncov/issues/802), so maybe I can follow one of your existing pipelines. EDIT...

Hi @joicy, we've revised our preprocessing pipeline to input an UShER tree using open GENBANK data, rather than a GISAID tree, so hopefully you should be able to run the...

@GStechschulte contributions are welcome! I don't believe @HenryWard is working on this. If you do make a PR could you cc @eb8680 as he as thought a lot about how...