EpiNow2: Stan code review

[benjaminortizulloa]

please edit in outline from the previous task (no local copy - oops)

EpiNow2 makes use of stan to define and fit its model. This code is complex and requires independent review. There may also be areas that could benefit from optimisation or simple model changes that may drastically increase performance. This task could extend to recommendations on model structure or be limited to the functionality of the code.

• Review all code in the inst/stan folder based on stan best practice and suggest improvements
• Review interface R code (mainly in R/estimate_infections.R) and suggest improvements
• Check testing of stan code (tests/testthat/test-stan......R) and suggest improvements
• Review prior usage and initialisation
• Review overall model structure

[impact: please edit in from previous task (no local copy -oops)]
[originally proposed by @seabbs]
[suggested repo: https://github.com/epiforecasts/EpiNow2 | @seabbs]
[additional notes: ]