check_immunity

class check_immunity(people)

Calculate people’s immunity on this timestep from prior infections. As an example, suppose HPV16 and 18 are in the sim, and the cross-immunity matrix is:

pars[‘immunity’] = np.array([[1., 0.5],

[0.3, 1.]])

This indicates that people who’ve had HPV18 have 50% protection against getting 16, and people who’ve had 16 have 30% protection against getting 18. Now suppose we have 3 people, whose immunity levels are

people.nab_imm = np.array([[0.9, 0.0, 0.0],

[0.0, 0.7, 0.0]])

This indicates that person 1 has a prior HPV16 infection, person 2 has a prior HPV18 infection, and person 3 has no history of infection.

In this function, we take the dot product of pars[‘immunity’] and people.nab_imm to get:

people.sus_imm = np.array([[0.9 , 0.35, 0. ],

[0.27, 0.7 , 0. ]])

This indicates that the person 1 has high protection against reinfection with HPV16, and some (30% of 90%) protection against infection with HPV18, and so on.