Growth estimators

[adrian-lison]

Description

This PR closes #768.

The PR adds a new option to calculate the growth rate in estimate_infections() and simulate_infections() that is based on an estimator by Parag et al. 2022.

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
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After the initial Pull Request

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[adrian-lison]

@seabbs @sbfnk

Just opened a draft PR while working on this. I have drafted the basic stan code, but couldn't test it locally yet because of issues with my rstan installation ^^

I have for now added an argument growth_method to the rt_opts(), because I didn't find it justified to create a completely new opts type. There are a couple of open questions to discuss, in particular how much of a problem it is that with the alternaitve approach the most recent growth rates are undefined due to the shift applied.

Will get back with more details soonish.

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if f15d0d6 is merged into main:

• ✔️default: 22.8s -> 23.3s [-7.84%, +12.97%]
• ✔️no_delays: 23.1s -> 29.2s [-26.06%, +78.93%]
• ✔️random_walk: 8.83s -> 9.37s [-2.79%, +14.91%]
• ✔️stationary: 15.8s -> 11.2s [-94.64%, +36.65%]
• ✔️uncertain: 35.7s -> 34.1s [-14.02%, +5.17%]
  Further explanation regarding interpretation and methodology can be found in the documentation.