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Represent non-pharmaceutical intervention strategies for DAEDALUS

Source: R/class_npi.R, R/class_timed_npi.R
class_npi.Rd

Helper functions to create and work with S3 class <daedalus_npi> objects for use with daedalus(). These objects store NPI parameters for reuse and have methods for easy parameter access and editing, as well as processing raw NPI characteristics for the DAEDALUS model.

Most NPIs must be initialised with an associated country and infection; these are used to determine flag positions as well as the state-values (hospital capacity) and incidence-prevalence ratio (IPR) at which the NPI starts and ends reactively.

daedalus_timed_npi() is a helper function to create a <daedalus_npi> that is only trigged by time, and is not responsive to state variables. Primarily intended for use in real time modelling.

Usage

daedalus_npi(
  name,
  country,
  infection,
  openness = NULL,
  start_time = 30,
  end_time = NULL,
  max_duration = 365
)

is_daedalus_npi(x)

# S3 method for class 'daedalus_npi'
print(x, ...)

daedalus_timed_npi(start_time, end_time, openness, country)

Arguments

name

An NPI strategy name from among daedalus.data::closure_strategy_names, or NA. Passing a pre-defined strategy name automatically pulls in openness parameters for the associated response strategy; these are stored as packaged data in daedalus.data::closure_strategy_data.

Pass NA to define a custom response strategy by passing a vector to openness.

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

An infection parameter object of the class <daedalus_infection>, or an epidemic name for which data are provided in the package; see daedalus.data::epidemic_names for historical epidemics or epidemic waves for which parameters are available. Passing the name as a string automatically accesses the default parameters of an infection. Create and pass a <daedalus_infection> to tweak infection parameters using daedalus_infection().

openness

For daedalus_npi(), an optional numeric vector giving the openness of each economic sector in the model when the NPI is in effect.

For daedalus_timed_npi(), a list of numeric vectors giving the openness coefficients for each interval specified by corresponding elements of start_time and end_time.

Expected to have a length of N_ECON_SECTORS (currently 45), with all values are in the range \([0, 1]\),

start_time

For daedalus_npi(), a single number giving the number of days after the start of the model that the NPI response begins. Defaults to 30.

For daedalus_timed_npi(): may be a vector of NPI start times, with no default values.

end_time

For daedalus_npi(), a single number giving the number of days after the start of the model that the NPI response ends. Defaults to NULL, indicating that the response ends (if no other condition is met), at the maximum duration.

For daedalus_timed_npi(): may be a vector of NPI end times, with no default values. Timed NPIs have no default duration.

max_duration

The maximum number of days that an NPI response is active whether started by passing the start_time or when a state threshold is crossed. Defaults to 365 days. NPIs created using daedalus_timed_npi() have no default maximum duration and are encoded by pairs of start and end times.

x

An object to be tested or printed as a <daedalus_npi>.

...

For daedalus_npi(), other parameters passed to new_daedalus_response(). For the print method, other parameters passed to print().

Value

daedalus_npi(): A <daedalus_npi> class object that specifies an NPI that may be responsive to both model state and time.

daedalus_timed_npi(): A <daedalus_npi> class object which specifies time-limited interventions only.

Details

Note that NPIs created using daedalus_npi() are reactive to the model state (i.e., the epidemic state), and can trigger multiple times when state conditions are met.

Examples

# for a school closure strategy
daedalus_npi("school_closures", "GBR", "sars_cov_1")
#> <daedalus_npi/daedalus_response>
#> NPI strategy: school_closures
#> • Start time (days): 30
#> • End time (days): NA
#> • Openness (mean prop.): 0.93
#> • Maximum duration (days): 365

# set custom openness
daedalus_npi(
  NA,
  "GBR", "sars_cov_1",
  openness = rep(0.1, 45)
)
#> <daedalus_npi/daedalus_response>
#> NPI strategy: custom
#> • Start time (days): 30
#> • End time (days): NA
#> • Openness (mean prop.): 0.1
#> • Maximum duration (days): 365

# time-limited NPI with multiple phases
daedalus_timed_npi(
  start_time = c(10, 20, 30),
  end_time = c(15, 25, 40),
  openness = list(
    rep(1, 45),
    rep(0.5, 45),
    rep(0.2, 45)
  ),
  country = "GBR"
)
#> <daedalus_npi/daedalus_response>
#> NPI strategy: custom_timed
#> • Start time (days): 10, 20, and 30
#> • End time (days): 15, 25, and 40
#> • Openness (mean prop.): 1, 0.5, and 0.2
#> • Maximum duration (days): NA