get_degree: Find node degree for epicontacts objects

In epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts

Find node degree for epicontacts objects

Description

This function computes the number of contacts per cases in a epicontacts dataset. Whenever contacts are directed, the argument 'type' can be used to specify which kind of contact should be considered: 'in' (towards the case), 'out' (from the case), or 'both'.

Usage

get_degree(x, type = c("in", "out", "both"), only_linelist = FALSE)

Arguments

x	an epicontacts object
type	the type of degree to be computed (see description); if contacts are not directed, this will be forced to 'both'
only_linelist	a logical indicating if cases whose degree is computed should be from the linelist exclusively

Author(s)

Thibaut Jombart ([e-mail])

Examples

## make epicontacts object
if (require(outbreaks)) {
x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
                       id="case_id", to="case_id", from="infector",
                       directed=TRUE)
x

## compute in-degree
deg_in <- get_degree(x)
table(deg_in)

## compute out-degree
deg_out <- get_degree(x, "out")
barplot(table(deg_out), main = "Reproduction number distribution")
mtext(side = 3, "(based on case out-degree)")

}

epicontacts documentation built on March 31, 2023, 6:49 p.m.