1547 (LCT) implement possibility of death from hospitalization without intensive care

[annawendler]

Changes and Information

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

• Add transition from Hospitalized to Dead compartment for LCT-SECIR, LCT-SECIR with two diseases and GLCT-SECIR models

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Closes #1547

[annawendler]

When thinking about the initialization again with regard to the LCT model, I noticed that the new transition doesn't actually affect the initialization based on RKI data which is why I removed this comment here for the IDE-SECIR model again.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.46%. Comparing base (8851d5b) to head (94b636a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1556      +/-   ##
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- Coverage   97.47%   97.46%   -0.02%     
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  Files         190      190              
  Lines       15966    16030      +64     
==========================================
+ Hits        15563    15623      +60     
- Misses        403      407       +4     

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[Copilot]

Pull request overview

This PR adds the ability for individuals to die directly from the hospitalized/severe compartment (i.e., without passing through intensive care/critical) in the LCT-SECIR, LCT-SECIR (two diseases), and GLCT-SECIR model variants, including corresponding parameterization and tests.

Changes:

• Introduce DeathsPerSevere (and _a/_b variants) and update LCT-SECIR / LCT-SECIR-2D models to split Severe outflow into Critical/Recovered/Dead.
• Extend GLCT-SECIR with an additional InfectedSevere “strain” and a new TransitionMatrixInfectedSevereToDead, updating model equations and constraints.
• Update tests, examples, and model documentation to reflect the new Severe→Dead transition (with some documentation inconsistencies remaining).

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
docs/source/cpp/models/lsecir.rst	Documents new DeathsPerSevere parameter for LCT-SECIR.
docs/source/cpp/models/lsecir2d.rst	Documents new severe-death parameters for two-disease LCT-SECIR.
docs/source/cpp/models/glsecir.rst	Updates GLCT-SECIR docs for additional Severe→Dead transition (currently inconsistent in example/notation).
cpp/models/lct_secir/parameters.h	Adds DeathsPerSevere parameter and constraints.
cpp/models/lct_secir/model.h	Implements Severe→Dead flow split and fixes Dead accumulation from multiple sources.
cpp/models/lct_secir/infection_state.h	Adds InfectedSevereToDead transition enum entry.
cpp/models/lct_secir_2_diseases/parameters.h	Adds DeathsPerSevere_a/b parameters and constraints.
cpp/models/lct_secir_2_diseases/model.h	Implements Severe→Dead flow split for both diseases/paths.
cpp/models/glct_secir/parameters.h	Adds TransitionMatrixInfectedSevereToDead and updates dimension/validity checks.
cpp/models/glct_secir/model.h	Adds Severe→Dead strain dynamics and contributes Severe deaths into Dead compartment.
cpp/examples/glct_secir.cpp	Updates example configuration to include the new Severe→Dead strain and matrix.
cpp/tests/test_lct_secir.cpp	Extends parameter constraint tests and adds Severe→Dead flow test.
cpp/tests/test_lct_secir_2_diseases.cpp	Extends parameter constraint tests and adds Severe→Dead flow test (two diseases).
cpp/tests/test_lct_parameters_io.cpp	Ensures I/O-related tests set DeathsPerSevere explicitly.
cpp/tests/test_glct_secir.cpp	Updates GLCT tests to the new Severe-strain layout and adds Severe→Dead flow test.
cpp/models/ide_secir/parameters_io.h	Removes outdated documentation comment about Severe→Dead being impossible.

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[kilianvolmer]

Thanks for adding this feature! I found one broken link in the documentation and I think improving one code comment would be good.
Apart from that I am fine with the code, but I think the LCT examples should be updated and I am wondering if it would be nicer to set a value different from 0 in the GLCT example so that actually something happens on this transition.

[kilianvolmer]

Why do we have DeathPerSevere a and b? Could you please specify in the comments what the difference is?

[kilianvolmer]

Suggested change

	.. image:: http://martinkuehn.eu/research/images/glct_equations.png
	.. image:: http://martinkuehn.eu/research/images/glct.png