[tunesmith]

Some combination of death, natural immunity, vaccination, distancing, mask use, etc. What other forces are you suggesting?

Note that the more populous counties probably increased vaccination at a greater rate, like Miami-Dade went from 56% to 72% over the same time range.

[angelzen]

Natural immunity as a direct effect of an infection wave is my first guess. In some circles 'natural immunity' has become a dirty word :/

The assumptions between the equation rt = r0 * (1 - (vacRate * eff)) are too simplistic and unable to explain Florida infection wave behavior. There are more variables that we ignore when focusing only on Rt and vaccines.

The silver lining: At some point the whole population would have been exposed to covid, either through vaccines, infection or both. At that point the whole vaccination rate / effectiveness discussion becomes moot. Perhaps I wish the public discourse would keep an eye on 'estimated population fraction exposed to covid' that includes all plausible factors.

[tunesmith]

Yes, I brought up that equation merely to illustrate how vaccination alone can impact Rt downward - for a while it was unclear to me exactly how "partial vaccination" (before herd immunity) was a benefit; that helped me see that it really just mean it slows down the doubling rate until you get to Rt=1. But overall, Rt is impacted by all forms of mitigation including natural immunity.

The way I actually use that equation in my personal dashboards is to estimate what Rt "would" be, at today's mitigation levels, if no one had gotten vaccinated. So for instance, Portland's Rt is currently 0.92 (according to one model). By plugging in Portland's vaccination rate and efficacy estimates, you can estimate that Portland's Rt would be around 2 today if not for the vaccinations, if all other mitigation were the same.

On the one hand, 2 is a lot better than those estimates of 5 to 9.5, which means that we're impacted a lot by current mitigation practices (masks, distancing) and natural immunity. On the other hand, 2 is huge! Given estimates on infectious periods, that means that currently our cases halve every 90 days or so, but 2 would mean cases would be doubling every week or so. Gargantuan difference. So just an illustration that vaccination has a big impact and matters a lot.