The probability that an individual has COVID-19 will change over time as new information is gleaned. The initial probability is the pretest probability (pre0) associated with the nature of the interaction/exposure. This probability will decrease with each passing day that the individual does not develop symptoms. When a test is done, the probability is the posttest probability; this reduces the probability based on the test characteristics at the time of testing. Subsequently, the probability will continue to decrease with each passing day that no symptoms develop. This function returns a time series including those 3 phases.

individual_probability(test_day, pre0, sens, spec, asympt, days, mu, sigma)

Arguments

test_day

Day of PCR test (days since exposure)

pre0

Pre-test probability of person on day of exposure

sens

A vector of sensitivities by day since exposure

spec

The specificity of the PCR test

asympt

The proportion of infected patients expected to remain asymptomatic throughout the course of infection

days

Days since exposure for calculation range

mu

The mean of a lognormal distribution that approximates the incubation period for COVID-19. E.g. 1.63 (see reference).

sigma

The standard deviation of a lognormal distribution that approximates the incubation period for COVID-19. E.g. 0.5 (see reference).

Value

A time series of probabilities