Disease Simulation Codebook

Author

Chris Soria, Dennis Feehan, Ayesha Mahmud, and Audrey Dorelien

Core Epidemiological Parameters

N0: Initial total population size (N0 = 10000000 in default setup)
trans_p: Probability of transmission per contact (q matrix parameter)
kappa: Scaling factor for transmission reduction from protective behavior (0=perfect protection, 1=no protection)
ell: Time window (in days) for considering cumulative deaths that influence behavior
rho: Rate of leaving infectious state (1/infectious period)
gamma: Rate of waning natural immunity
vstart: Vaccination start time
time: Number of time steps (days) in the simulation. Each day represents a “snapshot” of the pandemic on that specific day.

N0_[a/b/c]: Initial population sizes calculated as:
- N0a = N0 * fraca # Republican initial population
- N0b = N0 * fracb # Democrat initial population
- N0c = N0 * (1 - fraca - fracb) # Independent initial population
pi_[a/b/c]: Base rate of adopting protective behavior
phi_[a/b/c]: Waning rate of protective behavior
zeta_[a/b/c]: Responsiveness of contact rates to deaths
mu_[a/b/c]: Infection fatality rate
vacc_[a/b/c]: Vaccination rate
I0_[a/b/c]: Initial infected individuals
cmin_[a/b/c]: Minimum daily contacts per group
cmax_[a/b/c]: Maximum daily contacts per group
beta [a/b]: Within group homophily parameter. Independent homophily is implied by beta_a and beta_b
h [a/b]:

ca_a/ca_b/ca_c: Republican group’s contact rates with Republicans/Democrats/Independents (R_R, R_D, R_I)
cb_a/cb_b/cb_c: Democrat group’s contact rates (D_R, D_D, D_I)
cc_a/cc_b/cc_c: Independent group’s contact rates (I_R, I_D, I_I)

lambda_aa: Republican-to-Republican transmission potential = trans_p*(ca_a*(IUa/pop_a + kappa*IPa/pop_a))
lambda_ab: Democrat-to-Republican transmission potential = trans_p*(ca_b*(IUb/pop_b + kappa*IPb/pop_b))
lambda_ac: Independent-to-Republican transmission potential
lambda_ba/lambda_bb/lambda_bc: Republican/Democrat/Independent-to-Democrat potentials
lambda_ca/lambda_cb/lambda_cc: Republican/Democrat/Independent-to-Independent potentials

prop_infections_from: Proportion of new infections in group X from group Y
- Calculated as lambda_xy/total_lambda_x
- Example: prop_rep_infections_from_dems = lambda_ab/lambda_a

**rep_from_*_new_cases**: New Republican cases from each source group = SUa*lambda_x + SPa*lambda_x*kappa
**dem_from_*_new_cases**: New Democrat cases from each source group
**ind_from_*_new_cases**: New Independent cases from each source group
Initialized with 1/3 weighting in first row for model stability