empirical_incubation_dist function

Extract empirical incubation period distribution from linelist data

This function takes in a linelist data frame and extracts the empirical incubation period distribution and can take into account uncertainty in the dates of exposure.

empirical_incubation_dist(x, date_of_onset, exposure, exposure_end = NULL)

Arguments

• x: the linelist data (data.frame or linelist object) containing at least a column containing the exposure dates and one containing the onset dates.
• date_of_onset: the name of the column containing the onset dates (bare variable name or in quotes)
• exposure: the name of the column containing the exposure dates (bare variable name or in quotes)
• exposure_end: the name of a column containing dates representing the end of the exposure period. This is NULL by default, indicating all exposures are known and in the exposure column.

Returns

a data frame containing a column with the different incubation periods and a column containing their relative frequency

Note

For exposure dates, each element can be a vector containing several possible exposure dates. Note that if the same exposure date appears twice in the list it is given twice as much weight.

Examples

if (require(tibble)) {
random_dates <- as.Date("2020-01-01") + sample(0:30, 50, replace = TRUE)
x <- tibble(date_of_onset = random_dates)

# Linelist with a list column of potential exposure dates ------------------
mkexposures <- function(x) x - round(rgamma(sample.int(5, size = 1), shape = 12, rate = 3))
exposures <- sapply(x$date_of_onset, mkexposures)
x$date_exposure <- exposures

incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, date_exposure)
incubation_period_dist

# Linelist with exposure range ---------------------------------------------
start_exposure   <- round(rgamma(nrow(x), shape = 12, rate = 3))
end_exposure     <- round(rgamma(nrow(x), shape = 12, rate = 7))
x$exposure_end   <- x$date_of_onset - end_exposure
x$exposure_start <- x$exposure_end - start_exposure
incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, exposure_start, exposure_end)
incubation_period_dist
plot(incubation_period_dist,
     type = "h", lwd = 10, lend = 2, col = "#49D193",
     xlab = "Days since exposure",
     ylab = "Probability",
     main = "Incubation time distribution")
}

Author(s)

Flavio Finger, flavio.finger@lshtm.ac.uk , Zhian N. Kamvar