rtestim: Time-varying reproduction number estimation with trend filtering
Fig 7
Estimated instantaneous reproduction number based on Covid-19 daily confirmed incident cases.
The epidemic is between January 23rd, 2020 and June 28th, 2023 in Canada. The left panels show estimates corresponding to 50 tuning parameters. The right panels show the CV-tuned estimate along with approximate 95% confidence bands. The top, middle and bottom panels show the estimated using the Poisson trend filtering in Eq (5) with degrees k = 1, 2, 3 respectively. All estimates use a constant serial interval distribution, which is the weighted sum of probabilities of the 4 dominant variants used in Fig 1.