Add vignette describing user options

[epiverse-trace]

Add vignette describing user options

[thimotei]

Would also be useful to add an example with a linelist, converting it to a timeseries using incidence2. See also issue #7

[adamkucharski]

Perhaps clearer terminology for expanding window vs time-varying CFR (e.g. in x-axes) would be 'CFR on day X' vs 'CFR up to day X'

[pratikunterwegs]

Just checking whether this issue is still relevant, and if so how it might relate to the current contents of the vignettes? If I could get some pointers I can go ahead and make changes.

[adamkucharski]

The case study document @CarmenTamayo is working on should cover a lot of this - can then decide where content sits best among vignette/training/blog (as it also touches on wider issues about what 'ground truth' should be when evaluating different methods).

Think we've already added clarification to users about small vs big outbreaks for the static and time varying methods?

[pratikunterwegs]

Thanks - happy to integrate that as it comes up. I think we do have some documentation in the vignettes for small vs big outbreaks and the different methods. I think @avallecam is also going to take a look, so perhaps more focused issues would be better than adding a full vignette?

[pratikunterwegs]

Closing this as stale - seems focus for this has moved to case studies repo, happy to help there.