677-computation-of-the-effective-reproduction-number-in-the-secir-model

[johapau]

Changes

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[Describe here in 2-3 lines. For details, reference to issues to avoid redundant information.]

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[codecov-commenter]

Codecov Report

Attention: 8 lines in your changes are missing coverage. Please review.

Comparison is base (0904a39) 94.22% compared to head (b0b451c) 95.01%.
Report is 33 commits behind head on main.

❗ Current head b0b451c differs from pull request most recent head 200c9b7. Consider uploading reports for the commit 200c9b7 to get more accurate results

Files	Patch %	Lines
cpp/models/ode_secir/model.h	94.73%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #698      +/-   ##
==========================================
+ Coverage   94.22%   95.01%   +0.78%     
==========================================
  Files         108      112       +4     
  Lines        8540     8928     +388     
==========================================
+ Hits         8047     8483     +436     
+ Misses        493      445      -48     

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[mknaranja]

I know/assume that this contains the derivative of the ODE so a lot of code-doubling happens. Generally it is just not a very good a idea to introduce redudant code parts. We should maybe think of how only one responsible code part returns for instance the mechanism of X and then this is used for get_derivatives and get_reproduction_number.

[HenrZu]

Thank you for your work. Looks good. I made a few comments. We should also consider making the code more modular. In general we should avoid duplication of code. And increased modularity also creates a better opportunity for testing functionalities.

Im currently checking the equations separately and also try to verify the tested values.