adjust_pretest: Calculate pretest probability change over time

In covidprobability: Estimate the Unit-Wide Probability of COVID-19

Description

Calculates the pretest probability over time, assuming the individual does not develop symptoms, by taking into account the distribution of incubation periods (defined as the time from exposure to symptom onset).

Usage

adjust_pretest(pre0, asympt, days = 14, mu = 1.63, sigma = 0.5)

Arguments

pre0	Initial pretest probability (on day of exposure)
asympt	The proportion of positive patients who would be expected not to ever develop symptoms (true asymptomatic patients).
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

pretest probability by day (time series)

References

See McAloon et al. https://bmjopen.bmj.com/content/10/8/e039652/

covidprobability documentation built on Feb. 11, 2021, 5:08 p.m.