Real-Time Effective Reproduction Number Estimation and
Forecasting
Filtered (real-time/causal) and smoothed (retrospective)
estimation of the time-varying effective reproduction number (Rt)
from case-count time series, using the EpiFilter algorithm of
Parag (2021) , together with a
one-step-ahead in-sample prediction check, a genuine out-of-sample
one-step forecast with predictive intervals, elimination
probability P(Rt < 1), and forecast calibration metrics (mean
absolute error, mean squared error, root mean squared error,
empirical coverage, and the weighted interval score of Bracher
et al. (2021) ).
Disease-agnostic: works for any pathogen given a known generation
interval.