Change to Rt calculation to fix discretisation error

Chris Jewell requested to merge fix-rt-discretisation-error into master

Investigation showed that the high rate of cases in the UK in January caused a significant discretisation error between the chain binomial model and continuous time analogues. The previous Rt calculation made use of a continuous time approximation, and so gave biased estimates of Rt.

The new implementation calculates Rt using expectations of the chain binomial model in terms of transition probabilities, not rates as previously.

Merge request reports