1386 implement influenza model #1387

HenrZu · 2025-09-29T15:04:16Z

Changes and Information

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

Implement influenza model from doi.org/10.1186/s12879-017-2344-6 into our framework
Add flowchart and rtd documentation

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codecov · 2025-10-06T20:26:42Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.29%. Comparing base (a1d8af8) to head (c3f4136).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff            @@
##             main    #1387    +/-   ##
========================================
  Coverage   97.28%   97.29%            
========================================
  Files         175      177     +2     
  Lines       15306    15422   +116     
========================================
+ Hits        14891    15005   +114     
- Misses        415      417     +2

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annawendler

Looks really good! :) Most of my comments are regarding naming of variables/parameters where I made some suggestions.

annawendler · 2025-10-24T13:26:38Z

cpp/examples/ode_seirv_example.cpp

+#include "memilio/utils/logging.h"
+
+/**
+ * @brief set_initial_population sets the initial population of the model 


The description of the parameters is missing

annawendler · 2025-10-24T13:27:06Z

cpp/examples/ode_seirv_example.cpp

+    auto& parameters = model.parameters;
+
+    FP cont_freq = 10.0;
+    FP fact      = FP(1) / FP(num_groups);


What is this factor for?

annawendler · 2025-10-24T13:27:13Z

cpp/models/ode_seirv/README.md

+Please cite the original study if you use this model:
+
+> Weidemann, F., Remschmidt, C., Buda, S. et al. *Is the impact of childhood influenza vaccination less than expected: a transmission modelling study.* **BMC Infect Dis** 17, 258 (2017).  
+> https://doi.org/10.1186/s12879-017-2344-6


Can you link the read the docs documentation and the example here?

annawendler · 2025-10-24T13:27:18Z

cpp/models/ode_seirv/model.h

+#include "ode_seirv/parameters.h"
+
+GCC_CLANG_DIAGNOSTIC(push)
+GCC_CLANG_DIAGNOSTIC(ignored "-Wshadow")


Where does this warning appear?

annawendler · 2025-10-24T13:27:33Z

cpp/models/ode_seirv/model.h

+        // Contact matrices
+        const auto cm_h_expr =
+            params.template get<ContactPatternsHealthy<FP>>().get_cont_freq_mat().get_matrix_at(SimulationTime<FP>(t));
+        const auto cm_s_expr =


Do you use cm_h_expr and cm_s_expr anywhere else or just below? If not, I would define H and S directly.

annawendler · 2025-10-24T13:31:54Z

cpp/tests/test_odeseirv.cpp

+    const double lambda  = (I + IV) / N; // expected force of infection
+    const double f_SE    = S * lambda;
+    const double f_SV_EV = SV * lambda;
+    const double f_E_I   = E; // gamma * E


Since gamma=1 this is correct but I would find it easier to understand if you wrote f_E_I = gamma*E here and below

annawendler · 2025-10-24T13:31:57Z

cpp/tests/test_odeseirv.cpp

+    auto idx_EI =
+        model.template get_flat_flow_index<mio::oseirv::InfectionState::Exposed, mio::oseirv::InfectionState::Infected>(
+            mio::AgeGroup(0));
+    auto idx_EVI =


Suggested change

auto idx_EVI =

auto idx_EIV =

More intuitive? Or EVIV? Same below.

annawendler · 2025-10-24T13:32:02Z

cpp/tests/test_odeseirv.cpp

+{
+    mio::oseirv::Model<double> model(2);
+    mio::ContactMatrixGroup<ScalarType>& cm_h = model.parameters.get<mio::oseirv::ContactPatternsHealthy<double>>();
+    // Each group only contacts itself so that λ_i = I_i / N_i


Suggested change

// Each group only contacts itself so that λ_i = I_i / N_i

// Let each group have only contacts with itself and set other parameters so that λ_i = I_i / N_i

annawendler · 2025-10-24T13:32:15Z

cpp/tests/test_odeseirv.cpp

+    model.parameters.set<mio::oseirv::SeasonalityAmplitude<double>>(0.0);
+    model.parameters.set<mio::oseirv::OutsideFoI<double>>(0.0);
+
+    // Group 0


I would find a comment helpful that you in particular have no vaccinated individuals and thus only one layer

annawendler · 2025-10-24T13:32:21Z

cpp/tests/test_odeseirv.cpp

+    }
+}
+
+TEST(TestOdeSeirv, flowSimulation)


Suggested change

TEST(TestOdeSeirv, flowSimulation)

TEST(TestOdeSeirv, flowSimulationEuler)

first draft influenza model

c111ba3

HenrZu linked an issue Sep 29, 2025 that may be closed by this pull request

Implement influenza model #1386

Open

2 tasks

HenrZu added 4 commits October 6, 2025 12:25

add example and readme

1e8a70f

adjust params and cast in example

35262a6

[ci skip] rtd doc

7019e1d

add tests and rework model.h

c3f4136

HenrZu requested a review from annawendler October 6, 2025 21:10

annawendler requested changes Oct 24, 2025

View reviewed changes

	// Each group only contacts itself so that λ_i = I_i / N_i
	// Let each group have only contacts with itself and set other parameters so that λ_i = I_i / N_i

	TEST(TestOdeSeirv, flowSimulation)
	TEST(TestOdeSeirv, flowSimulationEuler)

1386 implement influenza model #1387

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1386 implement influenza model #1387

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codecov bot commented Oct 6, 2025

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HenrZu commented Sep 29, 2025 •

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