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pg2455 / covid_p2p_simulation

Simulator for COVID-19 spread
GNU Affero General Public License v3.0
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Incubation period past the plateau start #110

Open tristandeleu opened 4 years ago

tristandeleu commented 4 years ago

The number of days for incubation incubation_days is defined as something which can be past the start of the plateau for the viral load: https://github.com/pg2455/covid_p2p_simulation/blob/62c7e416c803ed9f00e8f561b6bdb69a2d9ff800/simulator.py#L445

Does that mean that the progression looks like

infection (day 0) -> viral load plateau start -> incubation ends -> viral load plateau ends -> recovery

In the creation of the symptoms, the progression is defined in phases, where phase 1 corresponds to a duration of pre_plateau_duration (the name suggests that this phase happens before the plateau starts), which I guess is the phase between "end of incubation" and "plateau starts" https://github.com/pg2455/covid_p2p_simulation/blob/62c7e416c803ed9f00e8f561b6bdb69a2d9ff800/utils.py#L920-L924

Currently symptom_onset_delay is likely to be negative more often, so there might be no symptoms during phase 0.

@teganmaharaj

pg2455 commented 4 years ago

It is pre-symptomatic phase, which means there shouldn't be any symptoms.

The progression you mentioned looks right!