Finland COVID-19 R-value estimate March - August

<p>This dataset contains the time-dependent effective&nbsp;reproduction number&nbsp;R_t&nbsp;of the COVID-19 epidemic in Finland for the period Feb 27th&nbsp;2020 - August 14th 2020. The reproduction number was&nbsp;estimated using the daily new coronavirus cases in <a href="https://thl.fi/en/web/thlfi-en/statistics/statistical-databases/open-data/confirmed-corona-cases-in-finland-covid-19-">the infectious diseases registry of&nbsp;Finland</a>&nbsp;with an unscented RTS smoother and the SEIR epidemic&nbsp;model.</p> <p>The SEIR model was defined as<br> <span class="math-tex">\(S(t+1) = S(t) - \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} + \omega_{S}\\ E(t+1) = E(t) + \frac{R_t(t)}{T_i} I(t) \frac{S(t)}{N} - \frac{E(t)}{T_e} + \omega_{E}\\ I(t+1) = I(t) + \frac{E(t)}{T_e}-\frac{I(t)}{T_i} + \omega_{I} \\ R_t(t+1) = R_t(t) + \omega_{R_t}\)</span></p> <p>with S, E, and I&nbsp;being the susceptible, exposed, and&nbsp;infective populations, R_t&nbsp;the time-dependent effective reproduction number, and&nbsp;&omega;s are normally distributed random numbers with zero mean and small (1e-8) variance except for&nbsp;&omega;_Rt whose variance was set to 0.00025. The exposed state duration was set to&nbsp;T_e=3 days and infective state duration T_i=5 days.</p> <p>The measurement model (from the SEIR state to observed daily new cases)&nbsp;was defined as<br> <span class="math-tex">\(P_\text{new cases}(k) \propto \mathcal{N}\left[ \alpha \frac{R_t(t-5 days)}{T_i}I(t-5\text{days}) \frac{S(t-5\text{days})}{N}, \sigma_\text{new cases}^2(t) \right]\)</span>, i.e., via a time-delayed gaussian process whose variance was computed by the observed daily new cases with a 7-day rolling mean. Here the detection rate&nbsp;&alpha; is set to 10%, but has no significant affect on the computed R-values.</p> <p>&nbsp;</p> <p>The data is a CSV-format file with the columns</p> <ul> <li>date = ISO 8601 date string</li> <li>Rt = maximum a posteriori estimate of R_t</li> <li>Rt_lower50 = lower limit&nbsp;of the 50% credible interval for R_t</li> <li>Rt_upper50 = upper limit of the 50% credible interval for R_t</li> <li>Rt_lower90 = lower limit&nbsp;of the 90% credible interval for R_t</li> <li>Rt_upper90 = upper limit of the 90% credible interval for R_t</li> </ul>