Table 3.
Results from simulation scenarios 4–6. Transmission rate ratio and sampling proportions were jointly estimated for transmission trees belonging to the same tree class. For Bayesian inference, rλ,1 was fixed to its true value (rλ,1 = 1.0). For scenarios 4 and 5, all simulation replicates yielded ESS > 200 for all estimated parameters. For scenario 6, in total 98 replicates yielded ESS > 200 for all the parameters.
| Scenario | Parameter | Truth | Median | Relative error | Relative bias | Relative HPD width | 95% HPD accuracy |
|---|---|---|---|---|---|---|---|
| 4 | Rbase | 3.0 | 2.983 | 0.032 | −0.006 | 0.174 | 95 |
| rλ,1 | 1.0 | 1.0 (fixed) | – | – | – | – | |
| rλ,2 | 1.666 | 1.630 | 0.046 | −0.022 | 0.246 | 97 | |
| s1,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s1,2 | 0.01 | 0.012 | 0.227 | 0.206 | 1.082 | 99 | |
| s2,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s2,2 | 0.01 | 0.010 | 0.122 | 0.005 | 1.080 | 100 | |
| 5 | Rbase | 3.0 | 2.983 | 0.051 | −0.006 | 0.233 | 95 |
| rλ,1 | 1.0 | 1.0 (fixed) | – | – | – | – | |
| rλ,2 | 1.666 | 1.598 | 0.071 | −0.041 | 0.311 | 91 | |
| s1,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s1,2 | 0.01 | 0.013 | 0.263 | 0.259 | 1.212 | 100 | |
| s2,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s2,2 | 0.01 | 0.010 | 0.082 | −0.019 | 1.120 | 100 | |
| 6 | Rbase | 3.0 | 2.694 | 0.102 | −0.102 | 0.191 | 44 |
| rλ,1 | 1.0 | 1.0 (fixed) | – | – | – | – | |
| rλ,2 | 1.666 | 1.6137 | 0.062 | −0.031 | 0.297 | 93 | |
| s1,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s1,2 | 0.01 | 0.012 | 0.169 | 0.157 | 1.127 | 100 | |
| s2,1 | 0.0 | 0.0 (fixed) | – | – | – | – | |
| s2,2 | 0.01 | 0.009 | 0.129 | −0.113 | 1.054 | 100 |