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Merge branch 'prod' into update-model-defn
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kaitejohnson authored Mar 26, 2024
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Expand Up @@ -231,15 +231,13 @@ The subpopulation $\mathcal{R}_{k}(t)$ is subject to the infection feedback desc
```math
\mathcal{R}_k(t) = \mathcal{R}^\mathrm{u}_k(t) \exp \left(-\gamma \sum_{\tau = 1}^{T_f} I_k(t-\tau) g(\tau) \right)
```

From $\mathcal{R}_{k}(t)$, we generate values of the supopulation-level _expected_ latent incident infections per capita $I_k(t)$ using the renewal process described in [the infection component](#infection-component).

To obtain the number of statewide infections per capita $I(t)$, we sum the $K_\mathrm{total}$ subpopulation per capita infection counts $I_k(t)$ weighted by their population sizes:

```math
I(t) = \frac{1}{\sum\nolimits_{k=1}^{K_\mathrm{total}} n_k} \sum_{k=1}^{K_\mathrm{total}} n_k I_k(t)
```

We infer the site level initial per capita incidence $I_k(0)$ hierarchically. Specifically, we treat $\mathrm{logit}[I_k(0)]$ as Normally distributed about the corresponding state-level value $\mathrm{logit}[I(0)]$, with an estimated standard deviation $\sigma_{i0}$:

$$
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