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Define and use parameters that handle the state transitions in the Infection #664

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DavidKerkmann opened this issue Jun 12, 2023 · 2 comments · May be fixed by #710
Open
2 tasks done

Define and use parameters that handle the state transitions in the Infection #664

DavidKerkmann opened this issue Jun 12, 2023 · 2 comments · May be fixed by #710
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@DavidKerkmann
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class::improvement Cleanup that doesn't affect functionality loc::backend This issue concerns the C++ backend implementation. model::abm This issue concerns any kind of agent-based model. prio::high The priority of this task is high.
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ABM v1.0

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@DavidKerkmann
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DavidKerkmann commented Jun 12, 2023 •
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Motivation / Current Behaviour

The infection state drawing inside the infection needs to be updated by including parameters that define state transition probabilities. Currently, we use fixed default numbers that don't represent any realistic scenario, e.g.

case InfectionState::InfectedNoSymptoms:
            // roll out next infection step
            v = uniform_dist();
            if (v < 0.5) { // TODO: subject to change
                time_period = days(params.get<InfectedNoSymptomsToSymptoms>()[{
                    m_virus_variant, age, VaccinationState::Unvaccinated}]); // TODO: subject to change
                next_state  = InfectionState::InfectedSymptoms;
            }
            else {
                time_period = days(params.get<InfectedNoSymptomsToRecovered>()[{
                    m_virus_variant, age, VaccinationState::Unvaccinated}]); // TODO: subject to change
                next_state  = InfectionState::Recovered;
            }

Enhancement description

Our parameters that we have already describe the state transition times. We now need additional parameters that determine individual transition probabilities and add up to 1.

Additional context

No response

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  • Attached labels, especially loc:: or model:: labels.
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@DavidKerkmann DavidKerkmann added loc::backend This issue concerns the C++ backend implementation. model::abm This issue concerns any kind of agent-based model. class::improvement Cleanup that doesn't affect functionality labels Jun 12, 2023
@DavidKerkmann DavidKerkmann mentioned this issue Jun 12, 2023
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@mknaranja
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@DavidKerkmann We also recently discussed that we should change the infection parameters to that used in the ODE models to have it
a) more consistent
b) more precise, as e.g., InfectedNoSymptomsToSymptoms does not provide information if the parameter means to be a duration/time or probability.

Did this not go into a new issue? Couldnt find anything...

@DavidKerkmann DavidKerkmann moved this from Product Backlog to Sprint Backlog in MEmilio: Agent-Based-Model Jul 17, 2023
@DavidKerkmann DavidKerkmann added the prio::high The priority of this task is high. label Jul 17, 2023
@xsaschako xsaschako self-assigned this Jul 25, 2023
@xsaschako xsaschako moved this from Sprint Backlog to Development in MEmilio: Agent-Based-Model Jul 31, 2023
@xsaschako xsaschako linked a pull request Jul 31, 2023 that will close this issue
664 Define and use parameters that handle the state transitions in the Infection #710
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@DavidKerkmann DavidKerkmann moved this from Development to Sprint Backlog in MEmilio: Agent-Based-Model Oct 9, 2023
@DavidKerkmann DavidKerkmann added this to the ABM v0.1 milestone Oct 17, 2023
@DavidKerkmann DavidKerkmann self-assigned this Oct 18, 2023
@DavidKerkmann DavidKerkmann moved this from Sprint Backlog to Development in MEmilio: Agent-Based-Model Oct 20, 2023
@DavidKerkmann DavidKerkmann mentioned this issue Oct 26, 2023
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@xsaschako xsaschako moved this from Product Backlog to Development in MEmilio: Agent-Based-Model Development Nov 21, 2023
@xsaschako xsaschako removed their assignment Nov 30, 2023
@DavidKerkmann DavidKerkmann mentioned this issue Dec 6, 2024
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@DavidKerkmann
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One point here is to also include a description of all parameters related to state transitions.

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@DavidKerkmann DavidKerkmann

Labels
class::improvement Cleanup that doesn't affect functionality loc::backend This issue concerns the C++ backend implementation. model::abm This issue concerns any kind of agent-based model. prio::high The priority of this task is high.
Projects
MEmilio: Agent-Based-Model Development
Status: Development 🧑‍💻👩‍💻
Milestone
ABM v1.0
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664 Define and use parameters that handle the state transitions in the Infection SciCompMod/memilio
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@DavidKerkmann @xsaschako @mknaranja