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675 alternative computation of compartments in IDE model#702

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mknaranja merged 16 commits intomainfrom
675-alternative-for-compartments-of-ide
Apr 26, 2024
Merged

675 alternative computation of compartments in IDE model#702
mknaranja merged 16 commits intomainfrom
675-alternative-for-compartments-of-ide

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@annawendler annawendler commented Jul 17, 2023 •
edited by mknaranja
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Changes

  • In the simulation, we update the compartment sizes now using the flows calculated for the current time step.
  • In the initialization, we compute the compartment sizes using the sum formula from the flows as before.
  • The order of the member functions is changed to clarify which functions are used to compute the initial size of the compartments and which functions are used for later time steps.

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Closes #675

@annawendler annawendler self-assigned this Jul 17, 2023
@annawendler annawendler linked an issue Jul 17, 2023 that may be closed by this pull request
Implement alternative computation of compartments in IDE model #675
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@annawendler annawendler marked this pull request as ready for review July 17, 2023 07:46
@lenaploetzke lenaploetzke self-assigned this Mar 20, 2024
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codecov bot commented Mar 20, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.35%. Comparing base (79158d1) to head (9d5af9f).
Report is 3 commits behind head on main.

❗ Current head 9d5af9f differs from pull request most recent head 6151dd0. Consider uploading reports for the commit 6151dd0 to get more accurate results

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #702   +/-   ##
=======================================
  Coverage   96.34%   96.35%           
=======================================
  Files         129      129           
  Lines       10072    10087   +15     
=======================================
+ Hits         9704     9719   +15     
  Misses        368      368

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lenaploetzke commented Mar 22, 2024

The pipeline currently failed only because of the lower patch coverage due to added lines. When PR #923 is merged, the code coverage will be at 100% also with the changes of this PR.

@lenaploetzke lenaploetzke requested a review from mknaranja March 22, 2024 10:41
@lenaploetzke lenaploetzke added status::in review This issues is in review. model::ide This issue concerns any kind of integro differential equations-based model. labels Mar 22, 2024
@mknaranja mknaranja changed the title 675 alternative for compartments of ide 675 alternative computation of compartments in IDE model Apr 25, 2024
mknaranja
mknaranja requested changes Apr 26, 2024
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Thank you @lenaploetzke for these changes. I mostly have small suggestions (which however might change code lines in many occasions). Could you check them?

Comment thread cpp/models/ide_secir/simulation.cpp Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.h Outdated
Comment thread cpp/models/ide_secir/model.cpp Outdated
Comment thread cpp/models/ide_secir/model.cpp Outdated
@lenaploetzke lenaploetzke requested a review from mknaranja April 26, 2024 11:20
mknaranja
mknaranja reviewed Apr 26, 2024
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Comment thread cpp/models/ide_secir/infection_state.h Outdated
@mknaranja mknaranja merged commit 8d0d615 into main Apr 26, 2024
@mknaranja mknaranja deleted the 675-alternative-for-compartments-of-ide branch April 26, 2024 13:13
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@lenaploetzke lenaploetzke lenaploetzke left review comments

@mknaranja mknaranja mknaranja approved these changes

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@annawendler annawendler

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Implement alternative computation of compartments in IDE model

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