Parameters

This file describes each of the input parameters in Covasim. Note: the overall infection rate can be explored using sim.results['doubling_time'] and sim.results['r_eff'] (a higher infection rate means lower doubling times and higher R_eff), as well as by simply looking at the epidemic curves.

Population parameters

• pop_size = Number ultimately susceptible to CoV

• pop_infected = Number of initial infections

• pop_type = What type of population data to use – random (fastest), synthpops (best), hybrid (compromise), or clustered (not recommended)

• location = What location to load data from – default Seattle

Simulation parameters

• start_day = Start day of the simulation

• end_day = End day of the simulation

• n_days = Number of days to run, if end_day isn’t specified

• rand_seed = Random seed, if None, don’t reset

• verbose = Whether or not to display information during the run – options are 0 (silent), 1 (default), 2 (everything)

Rescaling parameters

• pop_scale = Factor by which to scale the population – e.g. 1000 with pop_size = 10e3 means a population of 10m

• rescale = Enable dynamic rescaling of the population

• rescale_threshold = Fraction susceptible population that will trigger rescaling if rescaling

• rescale_factor = Factor by which we rescale the population

Basic disease transmission

• beta = Beta per symptomatic contact; absolute

• contacts = The number of contacts per layer; set below

• dynam_layer = Which layers are dynamic; set below

• beta_layer = Transmissibility per layer; set below

• n_imports = Average daily number of imported cases (actual number is drawn from Poisson distribution)

• beta_dist = Distribution to draw individual level transmissibility; see https://wellcomeopenresearch.org/articles/5-67

• viral_dist = The time varying viral load (transmissibility); estimated from Lescure 2020, Lancet, https://doi.org/10.1016/S1473-3099(20)30200-0

Efficacy of protection measures

• asymp_factor = Multiply beta by this factor for asymptomatic cases; no statistically significant difference in transmissibility: https://www.sciencedirect.com/science/article/pii/S1201971220302502

• iso_factor = Multiply beta by this factor for diganosed cases to represent isolation; set below

• quar_factor = Quarantine multiplier on transmissibility and susceptibility; set below

• quar_period = Number of days to quarantine for; assumption based on standard policies

Time for disease progression

• exp2inf = Duration from exposed to infectious; see Lauer et al., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081172/, subtracting inf2sim duration

• inf2sym = Duration from infectious to symptomatic; see Linton et al., https://doi.org/10.3390/jcm9020538

• sym2sev = Duration from symptomatic to severe symptoms; see Linton et al., https://doi.org/10.3390/jcm9020538Duration from severe symptoms to requiring ICU; see Wang et al., https://jamanetwork.com/journals/jama/fullarticle/2761044Duration from severe symptoms to requiring ICU

Time for disease recovery

• asym2rec = Duration for asymptomatic people to recover; see Wölfel et al., https://www.nature.com/articles/s41586-020-2196-x

• mild2rec = Duration for people with mild symptoms to recover; see Wölfel et al., https://www.nature.com/articles/s41586-020-2196-x

• sev2rec = Duration for people with severe symptoms to recover, 22.6 days total; see Verity et al., https://www.medrxiv.org/content/10.1101/2020.03.09.20033357v1.full.pdf

• crit2rec = Duration for people with critical symptoms to recover, 22.6 days total; see Verity et al., https://www.medrxiv.org/content/10.1101/2020.03.09.20033357v1.full.pdf

• crit2die = Duration from critical symptoms to death, 17.8 days total; see Verity et al., https://www.medrxiv.org/content/10.1101/2020.03.09.20033357v1.full.pdf

Severity parameters

• rel_symp_prob = Scale factor for proportion of symptomatic cases

• rel_severe_prob = Scale factor for proportion of symptomatic cases that become severe

• rel_crit_prob = Scale factor for proportion of severe cases that become critical

• rel_death_prob = Scale factor for proportion of critical cases that result in death

• prog_by_age = Whether to set disease progression based on the person’s age

• prognoses = The actual arrays of prognoses by age; this is populated later

Events and interventions

• interventions = The interventions present in this simulation; populated by the user

• analyzers = Custom analysis functions; populated by the user

• timelimit = Time limit for the simulation (seconds)

• stopping_func = A function to call to stop the sim partway through

Health system parameters

• n_beds_hosp The number of hospital (adult acute care) beds available for severely ill patients (default is no constraint)

• n_beds_icu The number of ICU beds available for critically ill patients (default is no constraint)

• no_hosp_factor Multiplier for how much more likely severely ill people are to become critical if no hospital beds are available

• no_icu_factor Multiplier for how much more likely critically ill people are to die if no ICU beds are available