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Update model definition with new prior on infection feedback
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kaitejohnson authored Dec 17, 2024
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Expand Up @@ -265,7 +265,7 @@ We use informative priors for parameters that have been well characterized in th
| Total genomes shed per infected individual | $\log_{10}[G] \sim \mathrm{Normal}(9, 2)$ | Watson et al 2023[^Watson] |
| Initial infections per capita $I_0$ | $I_0 \sim \mathrm{Beta}(1 + k i_\mathrm{est}, 1 + k (1-i_\mathrm{est}))$ | where $i_\mathrm{est}$ is the sum of the last 7 days of hospital admissions, divided by jurisdiction population, and divided by the prior mode for $p_\mathrm{hosp}$, and $k = 5$ is a parameter governing the informativeness ("certainty") of the Beta distribution |
| Initial exponential growth rate | $r \sim \mathrm{Normal}(0, 0.01)$ | Chosen to assume flat dynamics prior to observations |
| Infection feedback term | $\gamma \sim \mathrm{logNormal}(6.37, 0.4)$ | Weakly informative prior chosen to have a mode of 500 in natural scale, based on posterior estimates of peaks from prior seasons in a few jurisdictions |
| Infection feedback term | $\gamma \sim \mathrm{logNormal}(4.50, 0.64)$ | Weakly informative prior chosen to have a mode of 90 in natural scale, based on posterior estimates of the infection feedback fit to the peak in the 2023-24 epidemic season in a few jurisdictions |
| Day of the week effects | $\frac{\vec{\omega}}{7} \sim \mathrm{Dirichlet}(5, 5, 5, 5, 5, 5, 5)$ | Weakly informative prior with a mode at even daily reporting (no effects) |
| Standard deviation of the log of the site-lab level multiplier $M_{ij}$ | $\sigma_m \sim \mathrm{Normal}(0, 0.25) $ | Weakly informative prior chosen to allow average magnitude of concentrations to be either similar or different among individual sites, depending on data |
| Modal site-level observation standard deviation | $\hat{\sigma}\_c \sim \mathrm{Normal}(1,1)$ | Weakly informative prior chosen to allow the mode to be either small or large |
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