Standardize on \mathcal{R}(t) for the time-varying reproduction number in the docs

Propose $\mathcal{R}$ over $R$ to disambiguate the reproduction number from the recovered compartment in SIR-family models.
Propose $\mathcal{R}(t)$ over $\mathcal{R}_t$ to reflect that the reproduction number is a function of time is a latent quantity, not a datapoint.

I think this should wait for #650 to land. After that, it might be a good task for a coding agent.

Note that GH renders $\mathcal{R}$ in markdown identically to $R$ (at least for me), but they render differently in our docs (which use katex).

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