fit_gamma_incubation_dist function

Fit discrite gamma distribution to incubation periods

A wrapper around fit_disc_gamma to fit a discrete gamma distribution to incubation periods derived from exposure and onset dates. Can take into account uncertain dates of exposure.

fit_gamma_incubation_dist(
  x,
  date_of_onset,
  exposure,
  exposure_end = NULL,
  nsamples = 1000,
  ...
)

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.
• nsamples: The number of samples to draw from the empirical distribution to fit on (dafaults to 1000)
• ...: passed to fit_disc_gamma

Returns

see [fit_disc_gamma()]

Examples

random_dates <- as.Date("2020-01-01") + sample(0:30, 50, replace = TRUE)
x <- data.frame(date_of_onset = random_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

fit <- fit_gamma_incubation_dist(x, date_of_onset, date_exposure)
plot(0:20, fit$distribution$d(0:20),
     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