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counterfactual excess covid deaths notebook #391

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merged 9 commits into from
Jul 13, 2022

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drbenvincent
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@drbenvincent drbenvincent commented Jul 4, 2022

So this PR replaces #387 but without the extra unintended changes.

Basically, a new notebook (with accompanying data) on counterfactual inference using excess deaths as the topic.

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@drbenvincent drbenvincent changed the title add excess deaths files counterfactual excess covid deaths notebook Jul 4, 2022
@drbenvincent drbenvincent requested review from cluhmann and twiecki July 4, 2022 15:38
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FYI: Need to commit the myst file, but it won't pass the tests until we sort the codespell stuff in the pre commit checks

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twiecki commented on 2022-07-06T11:15:08Z
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where we can ask


twiecki commented on 2022-07-06T11:27:36Z
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Technically I think it's called COVID-19, but I also saw Covid-19 used in many newspapers so it's probably fine.

drbenvincent commented on 2022-07-06T15:56:17Z
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Thanks. Will update to correct convention

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twiecki commented Jul 6, 2022

Technically I think it's called COVID-19, but I also saw Covid-19 used in many newspapers so it's probably fine.


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Thanks. Will update to correct convention


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michaelosthege commented on 2022-07-07T13:54:38Z
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Not sure if I understand the trick correctly, but could you use the ZeroSumNormal here?


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michaelosthege commented on 2022-07-07T13:54:38Z
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Isn't the target_accept=0.85 already the default?


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michaelosthege commented on 2022-07-07T13:54:39Z
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Line #6.    ax.set(title="Posterior predictive distribution since COVID-19 onset in the UK")

Maybe rephrase to clarify that this is a counterfactual?

"Posterior predictive forecast of deaths if COVID-19 had not appeared"


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Very nice notebook!
Please understand my comments as non-blocking nitpicks.

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Thanks @michaelosthege! I'll address these shortly.

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I'm going to temporarily close this PR because we want to time this for after some other promotional activity.

@drbenvincent drbenvincent reopened this Jul 13, 2022
@drbenvincent drbenvincent merged commit 8901181 into pymc-devs:main Jul 13, 2022
@drbenvincent drbenvincent deleted the excess-deaths3 branch July 13, 2022 14:17
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3 participants