Calculate the probability of a missed infection given a test + quarantine strategy

get_prob_missed_infection(
  test_time,
  additional_quarantine_time = 0,
  shape_fnr = 2.33,
  rate_fnr = 0.24,
  max_sensitivity = 0.99,
  shape_exposure_to_threshold = 1.98,
  shape_threshold_to_symptoms = 2.16,
  rate = 0.72
)

Arguments

test_time	Numeric. Date post-exposure test sample is collected
additional_quarantine_time	Numeric. Additional days quarantined after test sample is collected. Default is 0
shape_fnr	Numeric. Shape of the gamma distribution used to estimate test sensitivity. Default is 2.33
rate_fnr	Numeric. Rate of the gamma distribution used to estimate test sensitivity. Default is 0.24
max_sensitivity	Numeric. Value between 0 and 1 indicating the maximum sensitivity. Default is 0.99.
shape_exposure_to_threshold	Numeric. Shape of the gamma distribution that describes the time from exposure to crossing the threshold of detection. Default is 1.98
shape_threshold_to_symptoms	Numeric. Shape of the gamma distribution that describes the time from crossing the threshold of detection to symptom onset. Default is 2.16
rate	Numeric. Rate of the gamma distributions that describe the time from exposure to crossing the threshold of detection and the time from crossing the threshold of detection to symptom onset. Default is 0.72.

Examples

## test sample collected 5 days post-exposure, quarantine until day 5
get_prob_missed_infection(5)
#> [1] 0.298666

## test sample collected 7 days post-exposure, quarantine until day 9
get_prob_missed_infection(7, 2)
#> [1] 0.06355525