Represent vaccine investment scenarios for DAEDALUS — class

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

Usage

daedalus_vaccination(
  name,
  country,
  start_time = NULL,
  rate = NULL,
  uptake_limit = NULL,
  efficacy = 50,
  waning_period = 180
)

is_daedalus_vaccination(x)

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

Arguments

name

A vaccination investment scenario name as a string. Passing a name from among daedalus.data::vaccination_scenario_names leads to any optional parameters (see below) being drawn from pre-canned scenarios. These are stored as packaged data in daedalus.data::vaccination_scenario_data.

Passing a name that is not among pre-canned scenarios causes all following parameters to become compulsory and non-optional.

country

A <daedalus_country> object or a 2- or 3-character string that can be coerced to a <daedalus_country> (e.g. "GBR" for the United Kingdom). Used to determine when vaccination should end.

start_time

The number of days after the start of the epidemic that vaccination begins. Must be a single number. Defaults to NULL and is optional if name is a pre-canned strategy. If so, the start time is taken from the vaccination scenarios specified by name. Passed to the time_on argument in new_daedalus_response() via the class constructor new_daedalus_vaccination().

rate

A single number for the percentage of the total population that can be vaccinated each day. This is converted into a proportion automatically within daedalus(). Defaults to NULL and is optional if name is a pre-canned strategy; if so rate is taken from pre-canned scenario data.

uptake_limit

A single number giving the upper limit for the percentage of the population that can be vaccinated. When this limit is reached, vaccination ends. Passed to the value_state_off argument in new_daedalus_response() via the class constructor new_daedalus_vaccination(). Defaults to NULL and is optional if name is a pre-canned strategy in which case uptake_limit is taken from pre-canned scenario data.

efficacy

A single number in the range [0, 100] giving the efficacy of vaccination in preventing infection. A value of 0 indicates that vaccinated individuals are as susceptible to infection as unvaccinated ones, while 100 would indicate completely non-leaky vaccination that completely protects against infection. Defaults to 50%.

waning_period

A single number representing the number of days over which the average individual wanes out of the vaccinated stratum to the unvaccinated stratum. Only individuals in the susceptible and recovered compartments can wane out of being vaccinated. Defaults to 180 days.

x

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

...

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

Details

Note that vaccination once ended by reaching the uptake_limit does not restart once individuals wane out of the vaccinated compartment.

Examples

# for no advance vaccine investment in the UK
daedalus_vaccination("none", "GBR")
#> <daedalus_vaccination/daedalus_response>
#> Vaccine investment scenario: none
#> • Start time (days): 365
#> • Rate (% per day): 0.143
#> • Uptake limit (%): 40
#> • Efficacy (%): 50
#> • Waning period (mean, days): 180

# modifying parameters for pre-defined strategies during initialisation
# set daily vaccination rate to 1.5% of population
daedalus_vaccination("low", "GBR", rate = 1.5)
#> <daedalus_vaccination/daedalus_response>
#> Vaccine investment scenario: low
#> • Start time (days): 300
#> • Rate (% per day): 1.5
#> • Uptake limit (%): 50
#> • Efficacy (%): 50
#> • Waning period (mean, days): 180

# a fully customised strategy
daedalus_vaccination(
  "custom", "GBR", start_time = 100, rate = 1.5, uptake_limit = 70
)
#> <daedalus_vaccination/daedalus_response>
#> Vaccine investment scenario: custom
#> • Start time (days): 100
#> • Rate (% per day): 1.5
#> • Uptake limit (%): 70
#> • Efficacy (%): 50
#> • Waning period (mean, days): 180