apply VE_infection and VE_disease - Githubissues

yangclaraliu / covid_vac_africa

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apply VE_infection and VE_disease #2

Closed yangclaraliu closed 2 years ago

yangclaraliu commented 2 years ago

apply VE_infection to S/V => E, Ev, Ev2 aspect
apply VE_disease to E, Ev, Ev2 => Ip vs Ia aspect

This process is captured by the modification of u, uv and uv2; y, yv and yv2.

https://github.com/yangclaraliu/covid_vac_africa/blob/394b3623e50b1a1d50351402aa12d1ae3a82963e/code/2_0_Build_Scenarios.R#L23-L28 https://github.com/yangclaraliu/covid_vac_africa/blob/394b3623e50b1a1d50351402aa12d1ae3a82963e/code/util_functions.R#L83-L86

The specific transitions using these variables are here: https://github.com/yangclaraliu/covid_vac_africa/blob/394b3623e50b1a1d50351402aa12d1ae3a82963e/code/covidm_for_fitting/model_v2/sim_compartment.cpp#L239-L273

We update these values when VOC is introduced to account for both changes in transmissibility and vac escape https://github.com/yangclaraliu/covid_vac_africa/blob/394b3623e50b1a1d50351402aa12d1ae3a82963e/code/util_functions.R#L248-L269