1469 Correct nonageresolved indices in IDE-SECIR model

[annawendler]

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

[codecov]

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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[reneSchm]

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

[reneSchm]

Did you mean to use a new test suite, or do you want to reuse the one from above?

Suggested change

	TEST(IdeSecirAgeres, checkSimulationFunctions)
	TEST(TestIdeAgeres, checkSimulationFunctions)

[reneSchm]

It is a best practice to avoid C style comments, i.e. use // instead of /* */.

If you want to separate sections, IMO it is best to use text as titles, e.g.

// <section title>

But I won't stop you from getting fancy with added stars or hash signs.

[reneSchm]

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.

[reneSchm]

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?

[reneSchm]

This loop seems to be exactly the same as above, except for using model_group1. You could move some of the fairly lengthy setup into one or more functions (or lambda functions), so it is easier to spot that the setup is the same, and to make the test shorter.

[reneSchm]

I found these additional vectors and the following copy-transform-copy very confusing. You can replace the copy and the checks (i.e. lines 353-402) by the following:

    // Compare simulated compartments at time points t0 and t1.
    for (Eigen::Index i = 0; i < (Eigen::Index)secihurd_simulated_group0.get_num_elements(); i++) {
        EXPECT_NEAR(secihurd_simulated_group0[0][i], secihurd_t0_baseline[i], 1e-8);
        EXPECT_NEAR(secihurd_simulated_group0[1][i], 0.0, 1e-8);
        EXPECT_NEAR(secihurd_simulated_group1[0][i], 0.0, 1e-8);
        EXPECT_NEAR(secihurd_simulated_group1[1][i], baseline_scaling * secihurd_t1_baseline[i], 1e-8);
    }

    ASSERT_EQ(transitions_t1_baseline.size() * 2, transitions_simulated_group0.get_num_elements());
    // Compare simulated transitions with expected results at time point t1.
    for (size_t i = 0; i < transitions_t1_baseline.size(); i++) {
        const size_t age1 = i;
        const size_t age2 = i + transitions_t1_baseline.size();
        EXPECT_NEAR(transitions_simulated_group0.get_last_value()[age1], transitions_t1_baseline[i], 1e-8);
        EXPECT_NEAR(transitions_simulated_group1.get_last_value()[age1], 0.0, 1e-8);
        EXPECT_NEAR(transitions_simulated_group0.get_last_value()[age2], 0.0, 1e-8);
        EXPECT_NEAR(transitions_simulated_group1.get_last_value()[age2], baseline_scaling * transitions_t1_baseline[i],
                    1e-8);
    }