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323 SECIRTS model with waning immunity #963

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merged 68 commits into from
Dec 10, 2024
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@HenrZu HenrZu commented Mar 6, 2024

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

  • Added a new model including waning immunity and temporary immunity states build upon the secirvvs model
  • New initialization method

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closes #323

@HenrZu HenrZu changed the title 323 novel SECIRTS with waning immunity 323 novel SECIRTS model with waning immunity Mar 6, 2024
@HenrZu HenrZu changed the title 323 novel SECIRTS model with waning immunity 323 SECIRTS model with waning immunity Mar 7, 2024
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codecov bot commented Mar 8, 2024

Codecov Report

Attention: Patch coverage is 96.98551% with 52 lines in your changes missing coverage. Please review.

Project coverage is 96.92%. Comparing base (4343b92) to head (6b7433f).
Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
cpp/models/ode_secirts/parameters_io.h 92.38% 38 Missing ⚠️
cpp/models/ode_secirts/parameters.h 98.52% 6 Missing ⚠️
cpp/models/ode_secirvvs/parameters_io.h 80.00% 3 Missing ⚠️
cpp/models/ode_secirts/parameter_space.h 98.33% 2 Missing ⚠️
cpp/models/ode_secirvvs/model.h 71.42% 2 Missing ⚠️
cpp/models/ode_secirts/parameters_io.cpp 95.65% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #963      +/-   ##
==========================================
- Coverage   96.98%   96.92%   -0.07%     
==========================================
  Files         142      148       +6     
  Lines       11873    13558    +1685     
==========================================
+ Hits        11515    13141    +1626     
- Misses        358      417      +59     

☔ View full report in Codecov by Sentry.
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@reneSchm reneSchm left a comment

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I had a quick look at a few files.

cpp/models/ode_secirts/parameters_io.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters_io.cpp Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters_io.h Outdated Show resolved Hide resolved
cpp/memilio/io/epi_data.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters_io.h Outdated Show resolved Hide resolved
cpp/tests/test_odesecirts.cpp Outdated Show resolved Hide resolved
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Great rework, there are still some fairly large functions, but they are a lot more focused. Most requested changes are about small cleanups.

There are a lot of uncovered lines for error handling, especially in ode_secirts/parameters_io.h. While it would be better to test these functions extensively, I think this is okay, for now. But make a note that this can be improved upon.

cpp/models/ode_secirts/README.md Show resolved Hide resolved
cpp/models/ode_secirts/parameter_space.h Outdated Show resolved Hide resolved
cpp/simulations/CMakeLists.txt Outdated Show resolved Hide resolved
cpp/models/ode_secirts/infection_state.h Outdated Show resolved Hide resolved
cpp/memilio/io/epi_data.h Show resolved Hide resolved
cpp/models/ode_secirts/model.h Show resolved Hide resolved
cpp/models/ode_secirts/parameters_io.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/parameters_io.h Outdated Show resolved Hide resolved
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I think this PR is in a pretty good state now. Unless @mknaranja wants to have a final look, we can merge it soon.

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I really only did an incomplete review but as @reneSchm did I full one I am OK with merging if we briefly address the open items.

cpp/models/ode_secirts/README.md Outdated Show resolved Hide resolved
cpp/models/ode_secirts/infection_state.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/model.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/model.h Outdated Show resolved Hide resolved
cpp/models/ode_secirts/model.h Show resolved Hide resolved
cpp/models/ode_secirts/model.h Outdated Show resolved Hide resolved
@HenrZu HenrZu merged commit f9b7610 into main Dec 10, 2024
49 of 56 checks passed
@HenrZu HenrZu deleted the 323-waning-immunity-model branch December 10, 2024 09:07
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Implement new SECIRTS Model including waning immunity
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