linktree is a novel framework that estimates
group transmission assortativity from
transmission trees.
You can install the development version of linktree from GitHub with:
# install.packages("pak")
pak::pak("CyGei/linktree")library(linktree)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().
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.