get_si: Compute the serial interval (si) from transmission trees

In o2ools: Tools for 'outbreaker2'

Compute the serial interval (si) from transmission trees

Description

The serial interval is the time between the onset of symptoms in an infector-infectee pair. This function computes the serial interval statistics from a list of transmission trees.

Usage

get_si(
  trees,
  date_suffix = "date",
  stats = list(mean = mean, lwr = function(x) quantile(x, 0.025, na.rm = TRUE), upr =
    function(x) quantile(x, 0.975, na.rm = TRUE))
)

Arguments

trees	A list of data frames, generated by get_trees. It should contain information about the dates of onset.
date_suffix	A string indicating the suffix for date of onset columns. Default is "date", which means the columns should be named from_date and to_date.
stats	A list of functions to compute statistics. Default is: mean: the mean serial interval. lwr: the 2.5th percentile (lower quantile). upr: the 97.5th percentile (upper quantile). Each function should take a numeric vector as input and return a single numeric value.

Value

A data frame with serial interval statistic

See Also

get_trees for generating a list of transmission trees.

Examples

trees <- get_trees(out, date = linelist$onset)
si_stats <- get_si(trees)
str(si_stats)

o2ools documentation built on June 8, 2025, 10:18 a.m.