config.yml

# Config file for airline_testing_strategies ----

default:
  ## Simulation settings 
  ## We want 3000 simulations per parameter set, so we do 60 rounds with 50 
  ## simulations per round (each round is stored as an intermediate 
  ## file with 50 realizations). This is more than enough simulations to get
  ## stable estimates -- reduce n_rounds_of_sims to 20 if you're in a hurry. 
  n_reps_per_round: 50  # Number of replications per round of simulations
  n_rounds_of_sims: 60  # Number of rounds of simulations per parameter setting
  
  ## Local settings
  n_cores: null         # null will result in n/2 cores being used
  
  ## Transmission settings 
  days_quarantine: 14         # Number of days people quarantine (days.quarantine) 
  n_burnin_days: 62           # Fast forward simulation this many days
  day_of_flight: 70           # Time 0 in the simulation
  n_outcome_day: 14           # Time + x to count up infectious days
  n_passengers: 100000        # Number of passengers per simulation 
  subclin_infectious: .5      # Sub-clinical infectiousness is discounted (alpha.a)
  prop_subclin: .3            # Proportion of infections that are subclinical (p.a)
  prob_inf: [50, 100, 200, 500, 1000, 1500, 2500, 5000] # Static daily risk of infection per 1M
  primary_prob_inf: 1500       # Which prob_inf to use for generating plots/tables
  risk_multiplier: 2        # Day-of-flight risk multiplier
  sens_type:  "upper"         # Time-varying test sensitivity from He et al paper 
  rt_sens_multiplier: [.9]    # Rapid test sensitivity reduction factor

dev:
  n_cores: 15

## Sensitivity analysis around changing the risk multiplier
sensitivity_risk_multiplier:
  n_rounds_of_sims: 20
  risk_multiplier: [1, 2, 4, 10] 

## Sensitivity analysis around the rapid testing discount factor
sensitivity_rt_multiplier:
  n_rounds_of_sims: 20
  rt_sens_multiplier: [.6, .75, .9, 1.0]

## Sensitivity analysis with higher fraction of asymptomatic (subclinical)
sensitivity_sub_clin:
  n_rounds_of_sims: 20
  prop_subclin: .4

## Sensitivity analysis with lower PCR sensitivity
sensitivity_test_sens:
  n_rounds_of_sims: 20
  sens_type: "median"

## Sensitivity baseline for other testing scenarios
sensitivity_scenarios:
  n_rounds_of_sims: 20