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Run daedalus for multiple infection parameter sets

Source: R/daedalus_multi.R
daedalus_multi_infection.Rd

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,
  response_duration = 365,
  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; defaults to "none". The response strategy determines the country-specific response threshold following which the response is activated. See response_threshold.

While the response strategy is active, economic contacts are scaled using the package data object daedalus.data::closure_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.

response_duration

A single integer-ish number that gives the number of days after response_time that an NPI should end.

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 and p_asymptomatic for the proportion of infectious and symptomatic individuals in each age group and economic sector. Defaults to 1e-6 and 0.0 respectively.

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().