Speed up renewal

[seabbs]

The renewal code can be sped up using a dot product vs its current implementation. This a core part of the simulation code and so would give a good speed up. However, if planning on using thee EpiNow2 simulation model then this change is not needed as this part of the code base will be depreciated I would imagine.

EpiSoon/R/predict.R

Line 111 in d8a5531

~ sum(cases$cases * draw_from_si_prob(

[sbfnk]

Yes, making EpiNow2 a dependency and fully basing it on that probably makes sense.

[seabbs]

The cost is of course the terrifying requirement for stan and the dreaded maybe having to compile something. There could be an easy argument for having a duplicate R based simulator in this package (which wouldn't need to have feature parity) and making it optional for the user.

The dependency structure would get complicated but that could also have utility in EpiNow2 (this was how EpiNow and the forecasting component of EpiNow2 worked before being depreciated.

The other option is pulling out or resuing some of the epinowcast R code that makes doing this stuff more matrix focused.

The final options is depending on an external package, for example projections, but that seems like a risky dependency and has made some design decisions that could make its use tricky for us.