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Table 1 Parameter inference simulations. Results from pairwise MAP runs on 100 generated tree topologies using the combined method, the r × t-method, and the l-method.

From: Birth-death prior on phylogeny and speed dating

Tree size Method1 MAP value MAP diff2 Rates diff3 Times diff4 Comp time5
   average average worst average worst average worst relative
10 leaves combined -8046.54 0.48 3.39 0.58 1.46 0.26 0.72 1
  r × t -8046.72 0.32 13.03 0.36 4.61 0.17 1.73 2
  l -8049.34 0.012 0.20 0.00068 0.0084 0.0015 0.05 1
100 leaves combined -65249.12 1.61 8.60 4.72 10.64 1.24 3.39 2
  r × t -65257.40 4.66 23.10 14.08 21.66 5.11 9.19 10
  l -65258.41 0.16 1.54 0.034 0.071 0.060 0.41 1
  1. 1The combined method and the r × t-method infer optimal substitution rates and divergence times. The l-method infer optimal branch lengths which are subsequently partitioned into rates and times. The latter problem is much easier and the inferred rates and times less optimal.
  2. 2Difference in log-likelihood between two MAP runs on the same tree.
  3. 3Difference in substitution rate norm between two MAP runs on the same tree.
  4. 4Difference in divergence time norm between two MAP runs on the same tree.
  5. 5Approximate computation time relative to the l-method.