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Model updates with virology parameters

Luis Aleixo requested to merge feature/scientific_model_update into master

Modifications to be inline with the most recent paper:

  • Introducing a diameter as a vectorised parameter of Expiration. The BLO model is put back as part of the Monte-Carlo model, and new expiration_distributions are created in monte_carlo/data.py.

  • The exposure of ExposureModel is computed with a mean, when a diameter distribution is present - it correspond to the Monte-Carlo integration of the diameter-dependent model.

  • In the calculator, the model_generator now uses the Monte-Carlo BLO model and proper weighting of distributions when needed.

  • The BLO particle concentration emission values,cn, were updated on the B - 0.06 and L - 0.2 modes.

  • Number of samples increased to 250000 in model_generator and Monte-Carlo tests (because of the need to accurately sample the diameters).

  • The gravitational settling is now fully diameter dependent, as well as the f_dep (fraction of virus deposited on the respiratory tract). An evaporation factor (default value = 0.3) was also introduced in ConcentrationModel, reducing the size of the aerosols before applying the formulas.

  • Inhaled dose formula considers now the f_inf (fraction of infectious virus) with the host_immunity added to the InfectedPopulation, and the viable-to-RNA distribution (uniform [0.01 - 0.6]) added to the Virus class.

  • halflife value for low humidity changed to 6.43.

  • The infectious_dose_distribution is now a uniform distribution [10 - 100].

  • The formula for the probability of infection was updated according to the new values for the reported increase of transmissibility of a VoC - transmissibility_factor, as well as the respectivehost_immunity values. Added the Beta and Omicron VoCs.

  • Talking references replaced by Speaking.

  • Inclusion of the Toronto temperatures.

Pipeline was fixed according to these changes.

Edited by Luis Aleixo

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