Run daedalus for multiple infection parameter sets — daedalus_multi

Run daedalus() for multiple parameter sets, with the intended use case of running the model under uncertainty in infection parameters.

Usage

daedalus_multi_infection(
  country,
  infection,
  response_strategy = NULL,
  vaccine_investment = NULL,
  response_time = 30,
  auto_social_distancing = c("off", "independent", "npi_linked"),
  initial_state_manual = NULL,
  time_end = 600,
  ...
)

Arguments

country: A country or territory object of class <daedalus_country>, or a country or territory name from those included in the package; see daedalus.data::country_names, or a country ISO2 or ISO3 code; see daedalus.data::country_codes_iso2c and daedalus.data::country_codes_iso3c. Country-specific data such as the community and workplace contacts, the demography, and the distribution of the workforce into economic sectors is automatically accessed from package data for the relevant country name if it is passed as a string. To override package defaults for country characteristics, pass a <daedalus_country> object instead. See daedalus_country() for more.
infection: A list of <daedalus_infection> objects.
response_strategy: A string for the name of response strategy followed, a numeric of length 45 (number of economic sectors), or a <daedalus_npi> object. Defaults to "none". While the response strategy is active, economic contacts are scaled using the package data object daedalus.data::closure_strategy_data.
vaccine_investment: Either a single string or a <daedalus_vaccination> object specifying the vaccination parameters associated with an advance vaccine-investment scenario. Defaults to NULL for absolutely no vaccination in the model. A vaccination investment of "none" indicates no prior investment, but the model will include vaccination beginning after 1 year, at a low rate across all age groups. Other accepted values are "low", "medium" and "high". See daedalus_vaccination() for more information.
response_time: A single numeric value for the time in days at which the selected response is activated. This is ignored if the response has already been activated by the hospitalisation threshold being reached. Defaults to 30 days. Responses have a default maximum duration of 365 days. This can be changed by passing a <daedalus_npi> object to response_strategy.
auto_social_distancing: A string giving the option for the form of spontaneous social distancing in the model, which reduces infection transmission as a function of daily deaths. See Details for more.
initial_state_manual: An optional named list with the names p_infectious, p_asymptomatic, and p_immune. p_infectious and p_asymptomatic give the proportion of infectious and symptomatic individuals in each age group and economic sector. Defaults to 1e-6 and 0.0 respectively. p_immune may be a single number in the range 0.0 <= p_immune <= 1.0 or a 4-element vector in that range (the number of age groups in the model), for the proportion of individuals in the population or in each age group that have some pre-existing immunity to infection (reduced susceptibility). See Details for more.
time_end: An integer-like value for the number of timesteps at which to return data. This is treated as the number of days with data returned for each day. Defaults to 300 days.
...: Optional arguments that are passed to dust2::dust_ode_control().

Value

A list of <daedalus_output> objects.

Details

See details of how auto_social_distancing affects the model in documentation for daedalus().