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@annawendler annawendler commented Jan 9, 2026

Changes and Information

In the IDE-SECIR model, two indices were not adapted for multiple age groups. This was corrected here and appropriate test was added to check the correctness of the ageresolved simulation.

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Closes #1469

@annawendler annawendler self-assigned this Jan 9, 2026
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codecov bot commented Jan 9, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.30%. Comparing base (79088be) to head (8fd7324).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1472      +/-   ##
==========================================
- Coverage   97.31%   97.30%   -0.02%     
==========================================
  Files         187      187              
  Lines       16017    16017              
==========================================
- Hits        15587    15585       -2     
- Misses        430      432       +2     

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Very nice documentation for the new test. The only important comment is on line 278 regarding testing interactions between age groups.

int Ri = get_state_flat_index(Eigen::Index(InfectionState::Recovered), group);
int Di = get_state_flat_index(Eigen::Index(InfectionState::Dead), group);
// The scheme of the ODE model for initialization is applied here.
populations[Eigen::Index(0)][Ri] = total_confirmed_cases[group] - populations[Eigen::Index(0)][ISyi] -
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Off topic, but if a value is used as much as this Eigen::Index(0), it helps readability to give it a name. E.g. const Eigen::Index init_time_point = 0, if I read the context correctly.

Comment on lines +278 to +281
// Model with whole population in second age group with index 1. Use baseline values scaled by baseline_scaling.
considered_group = 1;
std::vector<ScalarType> N_vec_group1 = {0., baseline_scaling * population_baseline};
std::vector<ScalarType> deaths_vec_group1 = {0., baseline_scaling * deaths_baseline};
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I would have expected that the second test uses both populations to check that there are no unexpected interactions between age groups. With the current setup, any interactions between age groups vanishes (as the "other" age group is always 0), so in theory that could hide indexing errors.
Do you want to cover that case?

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Fix indices in IDE-SECIR model that have not been adapted to multiple age groups

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