epitrix (version 0.4.0)

fit_gamma_incubation_dist: Fit discrite gamma distribution to incubation periods

Description

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.

Usage

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

Value

see [fit_disc_gamma()]

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

Author

Flavio Finger,

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")