decided on parameter rather than argument
@@ -63,11 +63,12 @@ def make_pars(set_prognoses=False, prog_by_age=True, version=None, **kwargs):
pars['total_strains'] = None # Set during sim initialization, once strains have been specified and processed
# Parameters used to calculate immunity
+ pars['use_immunity'] = False # Whether to use dynamically calculated immunity
pars['NAb_init'] = dict(dist='normal', par1= 0, par2= 2) # Parameters for the distribution of the initial level of log2(NAb) following natural infection, taken from fig1b of https://doi.org/10.1101/2021.03.09.21252641
pars['NAb_decay'] = dict(form='nab_decay', pars={'init_decay_rate': np.log(2)/90, 'init_decay_time': 250, 'decay_decay_rate': 0.001}) # Parameters describing the kinetics of decay of NAbs over time, taken from fig3b of https://doi.org/10.1101/2021.03.09.21252641
pars['NAb_kin'] = None # Constructed during sim initialization using the NAb_decay parameters
pars['NAb_boost'] = 2 # Multiplicative factor applied to a person's NAb levels if they get reinfected. TODO, add source
- pars['NAb_eff'] = {'slope': 3.43297265, 'n_50': {'sus': 0.5, 'symp': 0.19869944, 'sev': 0.031}} # Parameters to map NAbs to efficacy
+ pars['NAb_eff'] = {'slope': 3.433, 'n_50': {'sus': 0.5, 'symp': 0.1987, 'sev': 0.031}} # Parameters to map NAbs to efficacy
pars['cross_immunity'] = 0.5 # Default cross-immunity protection factor that applies across different strains
pars['rel_imm'] = {} # Relative immunity from natural infection varies by symptoms
pars['rel_imm']['asymptomatic'] = 0.7
