fit_gamma_incubation_dist: Fit discrite gamma distribution to incubation periods

In reconhub/epitrix: Small Helpers and Tricks for Epidemics Analysis

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,
  ...
)

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

Value

see [fit_disc_gamma()]

Author(s)

Flavio Finger, [e-mail]

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")

reconhub/epitrix documentation built on Feb. 5, 2023, 7:39 a.m.