Convert Matrices to Transmission Calendar — convert_mat_to_trans

This function converts dose and sero matrices into a transmission calendar based on the provided immune profile.

convert_mat_to_trans_cal(
  all_dose,
  all_sero,
  cal_vhr,
  daily_uptake_vhr,
  cal,
  daily_uptake,
  immune_profile
)

Arguments

all_dose: A matrix representing all doses.
all_sero: A matrix representing all sero values.
cal_vhr: A calendar matrix for very high risk (VHR) individuals.
daily_uptake_vhr: A matrix representing daily uptake for VHR individuals.
cal: A calendar matrix for the general population.
daily_uptake: A matrix representing daily uptake for the general population.
immune_profile: A list containing immune profiles for VHR and general population.

Value

A list containing updated dose and sero matrices.

Details

The function first creates a VHR calendar if the immune profile for VHR is not "none". It then calculates the sero and dose models using the get_sero_dose_cals helper function. The results are stored in the all_sero and all_dose matrices.

The get_sero_dose_cals function calculates the dose and sero models based on the provided calendar, daily uptake, and immune profile. It considers different sero delays and coverage values.