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Inconsistency and minor naming corrections across the library #704

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mknaranja opened this issue Jul 19, 2023 · 1 comment
Open
2 of 7 tasks

Inconsistency and minor naming corrections across the library #704

mknaranja opened this issue Jul 19, 2023 · 1 comment
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@DavidKerkmann @xsaschako @mknaranja @HenrZu @annawendler @jubicker
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class::documentation Improvements or additions to documentation class::improvement Cleanup that doesn't affect functionality Epic loc::backend This issue concerns the C++ backend implementation. loc::data analysis This issue concerns any kind of data analysis. loc::python interface This issue concerns the python interface to the backend implementation. model::abm This issue concerns any kind of agent-based model. model::ide This issue concerns any kind of integro differential equations-based model. model::ml machine learning surrogate model model::ode This issue concerns any kind of ODE-based model.

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@mknaranja
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mknaranja commented Jul 19, 2023 •
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Motivation / Current Behaviour

Across the library, we still have a lot of inconsistencies and minor corrections that we would like to do.

They are

  • across models: some but not all of them can be harmonized as different models obviously differ...
  • inside models: the same objects appear with slightly different descriptions or documentations, parameter names are inconsistent, ...

However, many of these small naming changes touch many different files and thus produce merge conflicts with open pull requests.

Enhancement description

Here, I'd like you to collect all these small changes that we want to do. Then, we can check regularly if this change can be done without conflicting too much with open pull requests. As admins of the repository, @DavidKerkmann @HenrZu @jubicker @annawendler @xsaschako you are able to edit this message so that we can maybe collect all this here in one post.

For model harmonizations, please do identically at #400

For now, we have

  • Make probability parameters in ODEs consistent: We have probabilities from all states to the next "worse" state in the course of the disease except for InfectedNoSymptoms where we have the probability to recover, i.e., RecoveredPerInfectedNoSymptoms. We should rather work with InfectedSymptomsPerInfectedNoSymptoms
  • Rename migration to mobility (for ABM change wording: replace abm migration by mobility and epi by mio #842)
  • Using TestAndTraceCapacity to calc riskFromInfectedNoSymptoms ... is missing in the ode_secir but implemented in the ode_secirvvs model.
  • Using ScalarType instead of double
  • Python ode examples are inconsistent (different ways using AgeGroups, Calling the infection states ....)

Additional context

No response

Checklist

  • Attached labels, especially loc:: or model:: labels.
  • Linked to project
@mknaranja mknaranja added class::documentation Improvements or additions to documentation loc::backend This issue concerns the C++ backend implementation. loc::python interface This issue concerns the python interface to the backend implementation. loc::data analysis This issue concerns any kind of data analysis. model::abm This issue concerns any kind of agent-based model. model::ode This issue concerns any kind of ODE-based model. model::ide This issue concerns any kind of integro differential equations-based model. class::improvement Cleanup that doesn't affect functionality model::ml machine learning surrogate model labels Jul 19, 2023
@mknaranja mknaranja self-assigned this Jul 19, 2023
@mknaranja mknaranja added the Epic label Jul 19, 2023
@xsaschako xsaschako moved this from Product Backlog to EPIC in MEmilio: Agent-Based-Model Jul 24, 2023
@xsaschako xsaschako pinned this issue Jul 24, 2023
@MaxBetzDLR MaxBetzDLR unpinned this issue Jul 31, 2023
@jubicker
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jubicker commented Aug 1, 2023 •
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I'll do the renaming of migration to mobility in #687

@HenrZu HenrZu pinned this issue Aug 1, 2023
@khoanguyen-dev khoanguyen-dev unpinned this issue Sep 12, 2023
@xsaschako xsaschako moved this from Product Backlog to EPIC in MEmilio: Agent-Based-Model Development Nov 21, 2023
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@DavidKerkmann DavidKerkmann

@xsaschako xsaschako

@mknaranja mknaranja

@HenrZu HenrZu

@annawendler annawendler

@jubicker jubicker

Labels
class::documentation Improvements or additions to documentation class::improvement Cleanup that doesn't affect functionality Epic loc::backend This issue concerns the C++ backend implementation. loc::data analysis This issue concerns any kind of data analysis. loc::python interface This issue concerns the python interface to the backend implementation. model::abm This issue concerns any kind of agent-based model. model::ide This issue concerns any kind of integro differential equations-based model. model::ml machine learning surrogate model model::ode This issue concerns any kind of ODE-based model.
Projects
MEmilio: Agent-Based-Model Development
Status: EPIC 🌋
MEmilio: Data science, tools and more
Status: Product Backlog
MEmilio: Equation-Based-Models Development
Status: Product Backlog
MEmilio: Surrogate-Modeling with Machine Learning
Status: 📋 Product backlog
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@DavidKerkmann @xsaschako @mknaranja @HenrZu @annawendler @jubicker