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Table 2 Experimental design

From: Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains

GY       
Experiment   2    3  
k t k μt k s ( μ tk ) t k μt k s ( μ tk )
1 0.0017 0.0045 5 0.1 0.2668 8
2 0.0032 0.0085 5 0.2 0.5337 9
3 0.0046 0.0124 5 0.3 0.8005 11
4 0.0061 0.0163 5 0.4 1.0674 12
5 0.0076 0.0202 5 0.5 1.3342 13
6 0.0090 0.0241 5 0.6 1.6010 14
7 0.0105 0.0281 6 0.7 1.8679 15
8 0.0120 0.0320 6 0.8 2.1347 15
9 0.0135 0.0359 6 0.9 2.4015 16
10 0.0150 0.0398 6 1.0 2.6684 17
GTR       
Experiment   5    6  
k t k μt k s(μt k ) t k μt k s(μt k )
1 0.1760 0.2668 8 0.1 0.1516 7
2 0.3520 0.5337 9 0.6 0.9098 11
3 0.5280 0.8005 11 1.1 1.6680 14
4 0.7039 1.0674 12 1.6 2.4262 16
5 0.8798 1.3342 13 2.1 3.1844 18
6 1.0558 1.6010 14 2.6 3.9426 20
7 1.2318 1.8679 15 3.1 4.7008 22
8 1.4077 2.1347 15 3.6 5.4590 24
9 1.5837 2.4015 16 4.1 6.2172 26
10 1.7597 2.6684 17 4.6 6.9754 27
UNR       
Experiment   7    8  
k t k μt k s(μ tk ) t k μt k s(μ tk )
1 0.0379 0.1516 7 0.1 0.4 9
2 0.2275 0.9098 11 0.6 2.4 16
3 0.4170 1.6680 14 1.1 4.4 21
4 0.6066 2.4262 16 1.6 6.4 26
5 0.7961 3.1844 18 2.1 8.4 30
6 0.9857 3.9426 20 2.6 10.4 34
7 1.1752 4.7008 22 3.1 12.4 38
8 1.3648 5.4590 24 3.6 14.4 42
9 1.5543 6.2172 26 4.1 16.4 45
10 1.7439 6.9754 27 4.6 18.4 49
  1. The table shows the time points t k , μ tk and the approximation of the Poission tail s(μt k ). For experiment 2, t k spanned the interval that contains the 10 longest branch lengths from the phylogeny of the 16 HIV pol sequences. In experiment 3 we started at 0.1 and ended at 1. We wished to design experiment 5 such that the corresponding s(μt k ) was the same as s(μt k ) from experiment 3. This allowed us to illustrate the relative performance of the methods when running on different sizes of the rate matrix. Experiment 6 was done on time points starting from 0.1 and ending at 4.6. As before, we wished to design experiment 7 such s(μt k ) corresponded to experiment 6. Experiment 8 used the same t k as experiment 6.