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1279 minor additions to how infections work #1320

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@DavidKerkmann DavidKerkmann commented Jul 21, 2025 •
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Changes and Information

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

  • Add InfectionRateFromViralShed parameter
  • Rename infectivity functionality to viral shed functionality
  • Removed distributions from viral shed parameters; this is not required to have
  • Rework infection setup, initial stay duration is now drawn randomly when initialized somewhere in the middle of the infection

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Closes #1279
Closes #1247

@DavidKerkmann DavidKerkmann linked an issue Jul 21, 2025 that may be closed by this pull request
Minor additions to how infections work #1279
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@DavidKerkmann DavidKerkmann marked this pull request as draft July 21, 2025 13:25
@DavidKerkmann DavidKerkmann requested a review from jubicker July 21, 2025 13:26
jubicker
jubicker reviewed Sep 10, 2025
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cpp/models/abm/infection.cpp
get_forward_transition(rng, age, params, current_state, current_time, latest_protection);
if (init && current_state != InfectionState::Susceptible) { // random init within first time period
ScalarType p = uniform_dist(rng);
start_of_init_state -= transition.duration.multiply(1 - p);
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Should we fix the uniform distribution here or provide the possibility to insert any distribution (also a constant distribution for the case you exactly know how long somebody has been infected)?

jubicker
jubicker reviewed Sep 10, 2025
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cpp/models/abm/parameters.h
}
};

struct InfectivityDistributions {
using Type = CustomIndexArray<InfectivityDistributionsParameters, VirusVariant, AgeGroup>;
struct ViralShedDistribution {
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As this is no distribution any more, the name should problably be changed

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Minor additions to how infections work Implement infectionratefromviralshed
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@DavidKerkmann @jubicker @xsaschako