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Table 1 Performance of subsampling strategies and the scenario in which all available genetic samples were used (“All” strategy) in the phylodynamic analysis

From: Assessing biases in phylodynamic inferences in the presence of super-spreaders

Strategy Percent bias Percent error HPD size Coverage (%) Convergence (%)
All 0.05 (−7.7, 6.6) 6.87 (0.23, 30.6) 37.5 (10.3, 77.5) 91 59
Equal −1.66 (−10.5, 6.4) 8.13 (0.6, 24.7) 52.0 (20.0, 93.3) 98 93
Random −1.54 (−8.2, 4.3) 6.94 (0.28, 29.2) 56.9 (19.5, 100.3) 99 92
Herd infected 0.58 (−7.0, 4.9) 5.84 (0.34, 22.6) 58.8 (25.4, 88.5) 99 95
Herd 0.02 (−10.0, 4.9) 7.22 (0.21, 26.5) 55.7 (24.2, 91.8) 99 93
  1. Coverage indicates the proportion of 95% HPD that contained the true value of the last sampling time out of 100 iterations. Convergence metric is a rudimentary measure to indicate how many iterations failed to converge within 50 000 000 MCMC iterations. A longer chain was run if a convergence did not occur to obtain TMRCA estimates.