Update references and documentation of dampings by charlie0614 · Pull Request #1597 · SciCompMod/memilio

charlie0614 · 2026-10-23T08:20:36Z

Changes and Information

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

Add a short documentation of damping levels and types
Update references

If need be, add additional information and what the reviewer should look out for in particular:

Merge Request - Guideline Checklist

Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.

Checks by code author

Every addressed issue is linked (use the "Closes #ISSUE" keyword below).
New code adheres to coding guidelines.
No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
Tests are added for new functionality and a local test run was successful (with and without OpenMP).
Appropriate documentation within the code (Doxygen) for new functionality has been added in the code.
Appropriate external documentation (ReadTheDocs) for new functionality has been added to the online documentation and checked in the preview.
Proper attention to licenses, especially no new third-party software with conflicting license has been added.
(For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

Corresponding issue(s) is/are linked and addressed.
Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.).
Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease).
No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

codecov · 2026-10-23T08:51:56Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.47%. Comparing base (4c83297) to head (d46913a).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1597      +/-   ##
==========================================
- Coverage   97.48%   97.47%   -0.02%     
==========================================
  Files         190      190              
  Lines       16033    16033              
==========================================
- Hits        15630    15628       -2     
- Misses        403      405       +2

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

jubicker · 2026-10-29T13:08:29Z

 group-specific reductions are possible through setting particular rows or columns differently. With a constant 
 reduction factor :math:`r`, the reduced contact rate is :math:`(1-r) * c_{i,j}`.

+Each ``Damping`` also has a *level* and a *type*, given as ``DampingLevel`` and ``DampingType``. You set them with ``mio::DampingLevel(level)`` and


Suggested change

Each ``Damping`` also has a *level* and a *type*, given as ``DampingLevel`` and ``DampingType``. You set them with ``mio::DampingLevel(level)`` and

Each ``Damping`` also has a ``DampingLevel`` and ``DampingType``. They can be set via ``mio::DampingLevel(level)`` and

jubicker · 2026-10-29T13:09:43Z

+``mio::DampingType(type)``, where ``level`` and ``type`` are integers. They control how dampings that are
+active at the same time are combined:
+
+- **Same level, different type:** the dampings are *added*. Use this for measures that act on separate parts of


Suggested change

- **Same level, different type:** the dampings are *added*. Use this for measures that act on separate parts of

- **Same level, different type:** the dampings are *added*. Use this for measures that act on separate contact locations

jubicker · 2026-10-29T13:09:55Z

+active at the same time are combined:
+
+- **Same level, different type:** the dampings are *added*. Use this for measures that act on separate parts of
+  the contacts, e.g., a school closure and an office closure. 


Suggested change

the contacts, e.g., a school closure and an office closure.

, e.g., a school closure and an office closure.

jubicker · 2026-10-29T13:10:33Z

+- **Same level, different type:** the dampings are *added*. Use this for measures that act on separate parts of
+  the contacts, e.g., a school closure and an office closure. 
+- **Different levels:** the dampings are combined *multiplicatively*. Use this for measures that act on the same
+  contacts, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and


Suggested change

contacts, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and

contact locations, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and

Why "with sum"? Do you mean "with factors"?

jubicker · 2026-10-29T13:11:45Z

+- **Different levels:** the dampings are combined *multiplicatively*. Use this for measures that act on the same
+  contacts, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and
+  :math:`b` is :math:`1 - (1-a)(1-b)`.
+- **Same level and same type:** the newer damping *replaces* the older one from its start time on. Use this to


Suggested change

- **Same level and same type:** the newer damping *replaces* the older one from its start time on. Use this to

- **Same level and same type:** the newer damping *replaces* the older one from its start time point onward. Use this to

jubicker · 2026-10-29T13:12:20Z

 Then, dampings can be added as a relative factor to (partially) reduce the contacts defined by the ``ContactPatterns`` beginning at a time step ``t=30``. 
+Besides the coefficients and the start time, every damping has a ``level`` and a ``type``. They decide how dampings that are active at the same time are combined:
+
+- **Same level, different type:** the reductions are added (e.g., measures that act on separate parts of the contacts).


Suggested change

- **Same level, different type:** the reductions are added (e.g., measures that act on separate parts of the contacts).

- **Same level, different type:** the reductions are added (e.g., measures that act on separate contact locations).

jubicker · 2026-10-29T13:12:50Z

+- **Same level, different type:** the reductions are added (e.g., measures that act on separate parts of the contacts).
+- **Different levels:** the reductions are combined multiplicatively, :math:`1 - (1-a)(1-b)` (e.g., measures that act 
+   on top of an already existing measure).
+- **Same level and type:** the newer damping replaces the older one from its start time on (e.g., to tighten or relax a measure).


Suggested change

- **Same level and type:** the newer damping replaces the older one from its start time on (e.g., to tighten or relax a measure).

- **Same level and type:** the newer damping replaces the older one from its start time point onward (e.g., to tighten or relax a measure).

charlie0614 and others added 2 commits October 23, 2026 09:48

add short documentation for damping levels and types

78315a6

Update references and citation

d46913a

jubicker self-requested a review October 29, 2026 12:02

jubicker reviewed Oct 29, 2026

View reviewed changes

Navigation Menu

Repository navigation

Update references and documentation of dampings - #1597

Update references and documentation of dampings #1597
charlie0614 wants to merge 2 commits into
mainfrom
docs_10_26

charlie0614 commented Oct 23, 2026 •

edited by jubicker

Loading

Uh oh!

codecov Bot commented Oct 23, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

jubicker Oct 29, 2026

Uh oh!

This branch has not been deployed

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

	Each ``Damping`` also has a level and a type, given as ``DampingLevel`` and ``DampingType``. You set them with ``mio::DampingLevel(level)`` and
	Each ``Damping`` also has a ``DampingLevel`` and ``DampingType``. They can be set via ``mio::DampingLevel(level)`` and

	- Same level, different type: the dampings are added. Use this for measures that act on separate parts of
	- Same level, different type: the dampings are added. Use this for measures that act on separate contact locations

	the contacts, e.g., a school closure and an office closure.
	, e.g., a school closure and an office closure.

	contacts, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and
	contact locations, e.g., a mask mandate on top of closures. The total reduction of two levels with sums :math:`a` and

	- Same level and same type: the newer damping replaces the older one from its start time on. Use this to
	- Same level and same type: the newer damping replaces the older one from its start time point onward. Use this to

	- Same level, different type: the reductions are added (e.g., measures that act on separate parts of the contacts).
	- Same level, different type: the reductions are added (e.g., measures that act on separate contact locations).

	- Same level and type: the newer damping replaces the older one from its start time on (e.g., to tighten or relax a measure).
	- Same level and type: the newer damping replaces the older one from its start time point onward (e.g., to tighten or relax a measure).

Conversation

charlie0614 commented Oct 23, 2026 • edited by jubicker Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Changes and Information

Merge Request - Guideline Checklist

Checks by code author

Checks by code reviewer(s)

Uh oh!

codecov Bot commented Oct 23, 2026

Codecov Report

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

This branch has not been deployed

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

charlie0614 commented Oct 23, 2026 •

edited by jubicker

Loading