1003 implement ODE SEIR metapopulation model by charlie0614 · Pull Request #1273 · SciCompMod/memilio

charlie0614 · 2025-05-12T12:24:47Z

Changes and Information

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

implement a different mobility model without the graph approach and only using ODEs
contactmatrices are set globally (region-specific contactmatrices are handled in Enable region-specific dampings for the implicit mobility model #1513)

Replacement for #1128

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…s-integrated-into-the-odes

…function

HenrZu

Great work :) Only some comments, and then we can merge :)

pycode/memilio-epidata/memilio/epidata/getNRWCounties.py

cpp/models/ode_seir_metapop/regions.h

cpp/models/ode_seir_metapop/parameters.h

cpp/models/ode_seir_metapop/model.h

cpp/models/ode_seir_metapop/CMakeLists.txt

HenrZu

Sorry for the delay. Let's get this done soon. Overall, it looks very good and is an interesting addition. However, we still need to work on the presentation and documentation :)

docs/source/cpp/ode_metapop.rst

HenrZu · 2026-03-06T12:41:17Z

cpp/examples/ode_seir_metapop.cpp

+
+    auto result = simulate(t0, tmax, dt, model);
+
+    result.print_table();


What is the insight of this output? Maaybe you can output smth more interesting, or at least label the cols.

Labelled the cols. Not sure what is more interesting than the simulation result

The labels don't change the fact that the output is way too wide. Right now, it's just pointless because you can't see anything anyway due to the formatting, just a lot of numbers. So you might as well just remove the example entirely :D

The examples should be used to demonstrate the advantage or the function of the approaach

You can also create your own time series from the results.
Maybe plot the percentage of infeted in each region? (interpolate the time points before?)

cpp/models/ode_seir_metapop/model.h

HenrZu · 2026-03-06T12:49:34Z

cpp/models/ode_seir_metapop/model.h

+{
+
+/********************
+* define the model *


there is no readme file in this dir.
I think it is important to note there, that is just an implementation of a implicit mobility scheme and that we also have a generic mobility scheme with explicit mobility (the graph-ode) for each of the available ODE models.

I added the readme file, but only with the two short references to the example and documentation. I also added the reference to the Graph-ODE model to the documentation as I think it should rather belong there.

"This directory contains a metapopulation model implementation based on an ODE formulation. "

Please add there, what the difference to the graph ODE metapopulation formulation is.
(indirect mobility, impact from others in the force of incfection)

I'm still wondering. We actually wanted to get rid of the README's for every model completely. Then decided to use them only to reference to the actual documentation. Why don't we just collect all information in one place?

Added two sentences

docs/source/cpp/deterministic_metapop.rst

HenrZu · 2026-03-06T13:05:42Z

docs/source/cpp/deterministic_metapop.rst

+    model.parameters.set<mio::oseirmetapop::TimeInfected<>>(8.097612257);
+    model.parameters.set<mio::oseirmetapop::TransmissionProbabilityOnContact<>>(0.07333);
+
+Construct an ``Eigen::MatrixXd`` of size :math:`n_{regions} \times n_{regions}` which describes the fraction of individuals commuting from one region to another. The matrix should satify the sum of each row equal to 1.0, e.g.:


Theres not real "commuting from one region to another" in this model

That's true, but it still is what we try to model.

No, we model the impact from commuters in the transmission process in other patches. We do not model the commuting from one region to another :)

We model the impact of that fraction commuting from one region to another

docs/source/cpp/ode_metapop.rst

Co-authored-by: Henrik Zunker <69154294+HenrZu@users.noreply.github.com>

….com:SciCompMod/memilio into 1003-implement-ode-seir-metapopulation-model

docs/source/cpp/ode_metapop.rst

HenrZu · 2026-03-27T09:19:35Z

docs/source/cpp/deterministic_metapop.rst

+    model.parameters.set<mio::oseirmetapop::TimeInfected<>>(8.097612257);
+    model.parameters.set<mio::oseirmetapop::TransmissionProbabilityOnContact<>>(0.07333);
+
+Construct an ``Eigen::MatrixXd`` of size :math:`n_{regions} \times n_{regions}` which describes the fraction of individuals commuting from one region to another. The matrix should satify the sum of each row equal to 1.0, e.g.:


No, we model the impact from commuters in the transmission process in other patches. We do not model the commuting from one region to another :)

charlie0614 added 30 commits April 11, 2024 16:29

add model with Populations with Regions

2d4aec1

working SIR model without infections during commuting

9416256

add infections during commuting and age groups

12c9c09

read in mobility data for new model

2b883b6

only add edges if weight is big enough

d49a048

correct age resolution

56c4dd4

add tests

0efa8db

add seir version of mobility model

05e3717

small adjustments sir version

f475e3c

Merge branch 'main' into 1003-implement-model-in-which-the-mobility-i…

68632c5

…s-integrated-into-the-odes

fixes after merge

f19bcf6

Renaming

6ace8cf

Renaming

232f705

Set up examples for comparison

6045e1f

changes for plots and corrections

dfdac2d

add improved model

16a07da

changes for comparing simulations

23196bc

Merge branch 'main' into 1003-implement-model-in-which-the-mobility-i…

4193cd6

…s-integrated-into-the-odes

adjust plot file

bfc2562

reformat py file

c6b56e9

py file

5e51d69

py file

0eff4d1

change commuting strengths to contact matrix and implement indicator …

3d3b007

…function

return to factor 0.5

9f0fba7

read in data and time measurement 400 counties

8908d01

small corrections model

06950d9

corrections again

aad78a9

change integrator in graph model

2bdb791

fix bug with age groups and discard transmissions during commuting

3c6f630

adapt structure of old model

aa6b393

charlie0614 added 6 commits December 1, 2025 16:44

forgot FP

0b812e8

still forgot SimulationTime

3e57b61

fix bugs in tests

7861885

Still forgot ScalarType

e8d8e30

readd the tests for parameter checks

fd60e1b

add license header

fdbf3a7

charlie0614 requested a review from HenrZu December 1, 2025 18:40

Merge branch 'main' into 1003-implement-ode-seir-metapopulation-model

7edc608

HenrZu requested changes Jan 5, 2026

View reviewed changes

charlie0614 added 2 commits January 7, 2026 15:43

apply suggestions from review

8e122aa

add serialize and deserialize

d1296e3

charlie0614 requested a review from HenrZu January 8, 2026 08:22

HenrZu requested changes Mar 6, 2026

View reviewed changes

charlie0614 and others added 4 commits March 23, 2026 08:06

Update docs/source/cpp/ode_metapop.rst

acdbcd3

Co-authored-by: Henrik Zunker <69154294+HenrZu@users.noreply.github.com>

Merge branch 'main' into 1003-implement-ode-seir-metapopulation-model

f16bfce

Merge branch '1003-implement-ode-seir-metapopulation-model' of github…

bbc1169

….com:SciCompMod/memilio into 1003-implement-ode-seir-metapopulation-model

apply suggestions from review

93ecb2f

charlie0614 requested a review from HenrZu March 23, 2026 17:29

charlie0614 added 4 commits March 24, 2026 07:39

remove test

110f172

remove wrong tests

3c23867

add README

2891b37

correct license header

607f868

HenrZu requested changes Mar 27, 2026

View reviewed changes

docs/source/cpp/ode_metapop.rst Outdated Show resolved Hide resolved

HenrZu requested changes Mar 27, 2026

View reviewed changes

charlie0614 added 6 commits March 27, 2026 13:39

apply suggestions from review

2aa9a01

apply suggestions

f3c8098

fix bug

27bd1fe

apply suggestion

66de083

fix bug

592bc54

fix bug

f9099da


		auto result = simulate(t0, tmax, dt, model);

		result.print_table();

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charlie0614 commented May 12, 2025 •

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