Estimate Transmission Assortativity Coefficients

Estimates group transmission assortativity coefficients from transmission trees. Group transmission assortativity coefficients measure the tendency for individuals to transmit within their own group (e.g. age group, vaccination status, or location) compared to other groups. The package requires information on who infected whom, group membership for all individuals, and the relative sizes of each group in the population. For more details see Geismar et al. (2024) .

linktree

linktree is a novel framework that estimates group transmission assortativity from transmission trees.

Installation

You can install the development version of linktree from GitHub with:

# install.packages("pak")
pak::pak("CyGei/linktree")

library(linktree)

Definition

Group transmission assortativity quantifies the extent to which individuals transmit within their own group compared to others. The methodology is described in our paper, and briefly discussed on YouTube.

The $\gamma$ coefficient ranges from 0 to $\infty$. It describes the excess propability of transmitting within your own group versus other groups. See get_gamma().

We can rescale $\gamma$ to the $\delta$ coefficient, which ranges from -1 to 1 using get_delta().

Documentation

linktree requires that you have transmission chain data (i.e. who infected whom) and group membership for each individual in the transmission chain.

For more information, check the dedicated vignette.