Run an epidemic model scenario using the function stored in
model_function with the arguments in parameters. Runs as many replicates
of the function as specified in replicates. The simulation output data are
stored under data.
Value
The original object with the data field populated with
simulation output. This object must be assigned.
Returns a scenario object when called on a scenario object as expected,
with the data field populated with epidemic simulation model outputs.
Returns a comparison object with the data fields of the scenario
objects contained in it populated.
Examples
# For a `scenario` object
# prepare a scenario
scenario_pandemic_flu <- scenario(
model_function = "finalsize::final_size",
parameters = make_parameters_finalsize_UK(), # using helper function
replicates = 1L
)
# print to check that data are not prepared
scenario_pandemic_flu
#> Epidemic scenario object
#> Scenario name: No name specified (NA)
#> Model function: finalsize::final_size
#> Extra information on:
#> Scenario replicates: 1
#> Scenario outcomes are not prepared
# generate scenario data
scenario_pandemic_flu <- run_scenario(scenario_pandemic_flu)
# print to check that data are prepared
scenario_pandemic_flu
#> Epidemic scenario object
#> Scenario name: No name specified (NA)
#> Model function: finalsize::final_size
#> Extra information on:
#> Scenario replicates: 1
#> Scenario outcomes are prepared
# For a `comparison` object
# prepare two scenarios of the final size of an epidemic
pandemic_flu <- scenario(
name = "pandemic_flu",
model_function = "finalsize::final_size",
parameters = make_parameters_finalsize_UK(r0 = 1.5),
replicates = 1L
)
covid19 <- scenario(
model_function = "finalsize::final_size",
parameters = make_parameters_finalsize_UK(r0 = 5.0),
replicates = 1L
)
# create a comparison object
x <- comparison(
pandemic_flu, covid19,
baseline = "pandemic_flu"
)
x <- run_scenario(x)
x
#> Scenario comparison object
#> Number of scenarios: 2
#> Baseline scenario: "pandemic_flu"
#> All scenario data are prepared, use `sce_get_outcomes()` to get data
#> Scenario matching variables:
#> No matching variables specified yet.
#> Scenario comparison variables:
#> No comparison variables specified yet.
#> Model functions found:
#> finalsize::final_size