Table 1.
Estimates of key epidemiological parameters. These estimates are aggregated over 300 500-member ensemble runs and shown as mean and standard deviation (parentheses). The SEIR-network-EAKF updated the estimates each week as new weekly incidence data were assimilated; consequently, parameter estimates are shown at four different time points: (i) the onset, defined as the first of three consecutive weeks with non-decreasing numbers of cases; (ii) self-sustained transmission (Tss), defined as the first week during which over 80% of cases are infected locally; (iii) the maximum epidemic forcing, defined as the week with the highest effective reproductive number Re; and (iv) the week ending 25 January 2015. Re was treated as an independent parameter for each district, whereas other parameters were treated as common parameters for all districts. The three time points vary by district; common parameters were estimated at the time points as defined for Western Area Urban. The times for each district are available in the electronic supplementary material, table S2.
| onset | self-sustained (Tss) | maximum epidemic forcing | 25 Jan 2015 | |
|---|---|---|---|---|
| Re: Bo | 1.26 (0.10) | 1.31 (0.15) | 1.65 (0.17) | 1.08 (0.12) |
| Re: Bombali | 1.03 (0.09) | 1.10 (0.11) | 1.87 (0.12) | 0.76 (0.13) |
| Re: Bonthe | 0.79 (0.16) | — | 0.85 (0.20) | 0.85 (0.20) |
| Re: Kailahun | 1.38 (0.05) | 1.56 (0.10) | 1.89 (0.18) | 0.88 (0.15) |
| Re: Kambia | 0.96 (0.13) | 1.11 (0.21) | 1.25 (0.21) | 1.25 (0.21) |
| Re: Kenema | 1.29 (0.11) | 1.92 (0.29) | 2.16 (0.19) | 0.98 (0.17) |
| Re: Koinadugu | 1.07 (0.11) | 1.33 (0.11) | 1.33 (0.11) | 0.78 (0.12) |
| Re: Kono | 1.00 (0.1) | 1.12 (0.13) | 1.56 (0.20) | 0.96 (0.16) |
| Re Moyamba | 1.06 (0.15) | 1.17 (0.17) | 1.32 (0.29) | 0.44 (0.20) |
| Re: Port Loko | 1.07 (0.09) | 1.21 (0.14) | 1.82 (0.11) | 0.90 (0.23) |
| Re: Pujehun | 1.05 (0.11) | 0.93 (0.12) | 1.11 (0.15) | 0.83 (0.14) |
| Re: Tonkolili | 1.08 (0.10) | 1.18 (0.13) | 1.56 (0.13) | 0.89 (0.12) |
| Re: Western Area Rural | 0.95 (0.10) | 0.95 (0.10) | 1.85 (0.38) | 0.81 (0.11) |
| Re: Western Area Urban | 1.00 (0.10) | 1.00 (0.10) | 2.22 (0.09) | 0.71 (0.25) |
| incubation period (days) | 14.27 (0.94) | 14.27 (0.94) | 9.64 (1.06) | 10.72 (1.11) |
| infectious period (days) | 12.35 (0.79) | 12.35 (0.79) | 11.32 (0.98) | 10.92 (2.53) |
| gravity model: τ1 | 0.47 (0.03) | 0.47 (0.03) | 0.46 (0.04) | 0.49 (0.08) |
| gravity model: τ2 | 0.50 (0.03) | 0.50 (0.03) | 0.50 (0.04) | 0.51 (0.06) |
| gravity model: ρ | 8.04 (0.37) | 8.04 (0.37) | 7.93 (0.79) | 7.13 (1.28) |