135 contact reduction npi local

[DavidKerkmann]

Changes

Implements tool to compute NPI reduction for any given county. What can be improved:

• Age resolved data for each county. For now, 'cases_all_county_age.json' is used because it contains the required age resolution.
• Read-in of NPI is not implemented. For now, the NPI can be hard-coded in the file. Once we have some fixed NPI object structure and a way to export them in some way, this can be implemented.

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closes #135

[mknaranja]

I changed the title to 135 as this is related to issue #135 (and not issue #257)

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.98%. Comparing base (aaacb23) to head (2aba838). Report is 134 commits behind head on main.

Additional details and impacted files

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  Coverage   94.98%   94.98%           
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  Files         112      112           
  Lines        8776     8776           
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  Hits         8336     8336           
  Misses        440      440           

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[mknaranja]

My comments dated from long ago, I forgot to submit them. I think the script is still useful and important to compute estimated total contact reduction. I am not sure though if it is correct. We would need to look at it again. In the future, one could think of integrating a similar output directly to C++.

[mknaranja]

@HenrZu We should discuss how to continue and output contact reduction for ODE model summary statistics

[mknaranja]

@HenrZu I think an output on this information is important. Maybe even better to directly do this in cpp. I close this here. Could you address this in https://github.com/SciCompMod/memilio/issues/135?