201 add visualizations using arviz to tutorials

[sbidari]

Added arviz plots to two tutorials

• basic Rt model (Getting started)
• hospital admissions model

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[dylanhmorris]

Thanks, @sbidari!

One quick fix to start. The website build in CI is failing:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[8], line 1
----> 1 import arviz as az
      2 idata = az.from_numpyro(model1.mcmc)
      3 az.plot_trace(idata.posterior["Rt"],compact=True);

ModuleNotFoundError: No module named 'arviz'

Adding arviz as a dependency to docs/pyproject.toml should resolve this. Can do that at the command line from the top level project directory with:

poetry add -C docs arviz

https://github.com/CDCgov/multisignal-epi-inference/blob/99cdf4272358d80966ce92007d896245d53d59e2/docs/pyproject.toml#L9-L19

[dylanhmorris]

My mistake; I should've looked more closely at the source yaml for website / render-docs. The rendering of the tutorials uses the dependencies in model/pyproject.toml not those in docs/pyproject.toml. I think we should add arviz as a dev dependency for model in the first instance:

poetry add -C model --group dev arviz

Can remove it from the docs dependencies for now

poetry remove -C docs arviz

[sbidari]

poetry add -C model --group dev arviz

This command is not changing any dependencies in the model

[dylanhmorris]

what's the output of git diff model/pyproject.toml?

[sbidari]

My bad, the command did work as expected.

[sbidari]

Can we try to make something with plot_hdi? Or at a minimum swap the x and y axes in these plots so they are more readable as a time series?

Yep! Working on it

[sbidari]

I created hdi plots that are more readable to replace the forest plots. Let me know what you think and if there are any other type of plots you'd like to be added @damonbayer

[gvegayon]

This is looking great, @sbidari! Quarto and rst format are picky. I noticed sometimes figures wouldn't render or be added to the website if some conditions were unmet:

You have to:

1. Explicitly plot the figure using plot.show().
2. Have the code-chunk label with no empty spaces and starting with the fig prefix.
3. Have a caption.

In your case, the code chunk labelled fig2-trace-Rt should be renamed to something like fig-trace-Rt2 (point 2). I believe that should fix it. For more details, see this PR.

cc @damonbayer @dylanhmorris @AFg6K7h4fhy2

[sbidari]

Thanks for catching this @gvegayon

[sbidari]

ready for review @damonbayer