Plot the forecast reproduction number over the forecast horizon - #639
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The forecast model computed the reproduction number over the forecast horizon (f_R) in generated quantities but only returned the forecast onsets, so gather_draws(R[day]) on the forecast fit stopped at the cutoff and the forecast Rt was never plotted past the vertical line. Output forecast_R from the model and append it to the forecast Rt trajectory so it extends across the forecast horizon. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
seabbs
enabled auto-merge
June 21, 2026 15:33
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Confirming this fixes the docs issue |
sbfnk
approved these changes
Jun 21, 2026
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In the forecasting concepts session, the plot under "We can now plot the forecast and estimated reproduction numbers" did not show the forecast Rt extending past the cutoff.
Cause: the forecast model (
estimate-inf-and-r-rw-forecast.stan) computes the reproduction number over the forecast horizon (f_R) ingenerated quantities, but only returned the forecast onsets. Sogather_draws(R[day])on the forecast fit only covered days up to the cutoff, and the blue forecast Rt line stopped at the vertical dashed line.Fix:
forecast_R(the reproduction number over the forecast horizon) from the model.extract-Rtchunk (shifted bycutoff) so the forecast extends across the horizon, matching the onset forecast plots.Verified locally: the model compiles, and an end-to-end fit confirms
forecast_Rnow spans the full 28-day horizon (days 72–99) with finite values._freeze/is gitignored so CI renders fresh. The model is only used in this session.🤖 Generated with Claude Code