Plot the trajectory posteriors from a raw EpiFusion object separated by chain — plot_chainwise

Plots the trajectory posteriors from a raw EpiFusion object, separated by chain to allow assessment of convergence. You can specify the trajectory type (infection, Rt, cumulative infection) using the type parameter, or the function will plot each type by default. You may specify a proportion of each chain to discard as burn-in with the burn_in parameter.

plot_chainwise_trajectories(raw_epifusion, burn_in, type = NA)

Arguments

raw_epifusion: raw EpiFusion object
burn_in: proportion (as a decimal) of each chain to discard as burn in
type: (optional) "infection" "rt" or "cumulativeinfection"