Create a list of intervention settings to run the ringbp model

Usage

intervention_opts(quarantine = FALSE, test_sensitivity = 1)

Arguments

quarantine

a logical scalar: whether quarantine is in effect. If TRUE, traced contacts are isolated when their infector is isolated, regardless of their own symptom status (so they may be isolated before symptom onset, and asymptomatic traced contacts are isolated too). If FALSE, only symptomatic traced contacts are isolated, no earlier than their own symptom onset. Defaults to FALSE

test_sensitivity

a numeric scalar probability (between 0 and 1 inclusive), or a function of time returning probabilities in [0, 1]: the test sensitivity (i.e. probability that a true positive tests positive).

A scalar is treated as a constant test sensitivity over the whole simulation. A function accepts a numeric vector of times (symptom onset time in days since the exposure of the initial cases on day 0) and returns a numeric vector of probabilities of the same length, allowing the test sensitivity to vary with time. For example, \(t) ifelse(t < 30, 0, 0.8) represents a testing programme that activates on day 30 with sensitivity 0.8.

Only symptomatic individuals that do not self-isolate are tested; a false-negative result means the case is not isolated via the testing pathway (see outbreak_step() for how isolation times are assigned). Default is 1, which assumes all tested individuals get a positive test result.

Value

A list with class <ringbp_intervention_opts>.

Examples

# quarantine is not active (default)
intervention_opts(quarantine = FALSE)
#> $quarantine
#> [1] FALSE
#> 
#> $test_sensitivity
#> function (t) 
#> rep(x, length(t))
#> <bytecode: 0x558feff3d538>
#> <environment: 0x558fecc9c918>
#> 
#> attr(,"class")
#> [1] "ringbp_intervention_opts"

# quarantine is active
intervention_opts(quarantine = TRUE)
#> $quarantine
#> [1] TRUE
#> 
#> $test_sensitivity
#> function (t) 
#> rep(x, length(t))
#> <bytecode: 0x558feff3d538>
#> <environment: 0x558fef9fda10>
#> 
#> attr(,"class")
#> [1] "ringbp_intervention_opts"

# 20% of tests return a false-negative
intervention_opts(test_sensitivity = 0.8)
#> $quarantine
#> [1] FALSE
#> 
#> $test_sensitivity
#> function (t) 
#> rep(x, length(t))
#> <bytecode: 0x558feff3d538>
#> <environment: 0x558fee55b398>
#> 
#> attr(,"class")
#> [1] "ringbp_intervention_opts"

# time-varying test sensitivity, in the first 30 days of the outbreak
# sensitivity is 0.5, then after 30 days, sensitivity improves to 0.8
intervention_opts(
  test_sensitivity = \(t) ifelse(t > 30, yes = 0.8, no = 0.5)
)
#> $quarantine
#> [1] FALSE
#> 
#> $test_sensitivity
#> function (t) 
#> ifelse(t > 30, yes = 0.8, no = 0.5)
#> <environment: 0x558feda7d270>
#> 
#> attr(,"class")
#> [1] "ringbp_intervention_opts"