rsvsim.immunity module

Defines classes and methods for calculating immunity

class rsvsim.immunity.genotype(genotype, days, label=None, n_imports=1, rescale=True)

Bases: sciris.sc_utils.prettyobj

Add a new genotype to the sim

Parameters

• genotype (str/dict) – name of genotype, or dictionary of parameters specifying information about the genotype

• days (int/list) – day(s) on which new genotype is introduced

• label (str) – if genotype is supplied as a dict, the name of the genotype

• n_imports (int) – the number of imports of the genotype to be added

• rescale (bool) – whether the number of imports should be rescaled with the population

Example:

groupA    = cv.genotype('groupA', days=10) # Make genotype groupA active from day 10
groupB    = cv.genotype('groupB', days=15) # Make genotype groupB active from day 15
my_geno   = cv.genotype(genotype={'rel_beta': 2.5}, label='My genotype', days=20)
sim       = cv.Sim(genotype=[groupA, groupB, my_geno]).run() # Add them all to the sim

parse(genotype=None, label=None)

Unpack genotype information, which may be given as either a string or a dict

initialize(sim)

Update genotype info in sim

apply(sim)

Introduce new infections with this genotype