Example to estimate incubation period
In epitrix: Small Helpers and Tricks for Epidemics Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=7,
  fig.height=5,
  fig.path="figs-overview/"
)

Description

This package contains two functions useful to compute the incubation period distribution from outbreak data. The inputs needed for each patient are given as a data.frame or linelist object and must contain:

the date of onset of symptoms
a list/vector of possible dates of exposure.

The function empirical_incubation_dist() computes the discrete probability distribution by giving equal weight to each patient. Thus, in the case of N patients, the n possible exposure dates of a given patient get the overall weight 1/(n*N). The function returns a data frame with column incubation_period containing the different incubation periods with a time step of one day and their relative_frequency.

The function fit_gamma_incubation_dist() takes the same inputs, but directly samples from the empirical distribution and fits a discrete gamma distribution to it by the means of fit_disc_gamma.

Example

Load environment:

library(magrittr)
library(epitrix)
library(distcrete)
library(ggplot2)

Make a linelist object containing toy data with several possible exposure dates for each case:

ll <- sim_linelist(15)

x <- 0:15
y <- distcrete("gamma", 1, shape = 12, rate = 3, w = 0)$d(x)
mkexposures <- function(i) {
  i - sample(x, size = sample.int(5, size = 1), replace = FALSE, prob = y)
}
exposures <- sapply(ll$date_of_onset, mkexposures)
ll$dates_exposure <- exposures

print(ll)

Empirical distribution:

incubation_period_dist <- empirical_incubation_dist(ll, date_of_onset, dates_exposure)
print(incubation_period_dist)

ggplot(incubation_period_dist, aes(incubation_period, relative_frequency)) +
  geom_col()

Fit discrete gamma:

fit <- fit_gamma_incubation_dist(ll, date_of_onset, dates_exposure)
print(fit)

x = c(0:10)
y = fit$distribution$d(x)
ggplot(data.frame(x = x, y = y), aes(x, y)) +
  geom_col(data = incubation_period_dist, aes(incubation_period, relative_frequency)) +
  geom_point(stat="identity", col = "red", size = 3) +
  geom_line(stat="identity", col = "red")

Note that if the possible exposure dates are consecutive for all patients then empirical_incubation_dist() and fit_gamma_incubation_dist() can take date ranges as inputs instead of lists of individual exposure dates (see help for details).