This repo provides a Bayesian model, immplemented in greta, to infer: infectiousness profiles, generation intervals, serial intervals, and incubation period distributions from the dates of infection, symptom onset, and isolation for infector/infectee pairs.
Just run simulation_estimation.R to get started.
This requires the latest version of the greta R package from GitHub: https://github.com/greta-dev/greta You can find help installing greta on the greta forum: https://forum.greta-stats.org/