All distances between each pair of trees
CompareAllTrees(trees, exact = FALSE, slow = TRUE, verbose = FALSE)
| trees | List of bifurcating trees of class |
|---|---|
| exact | Logical specifying whether to calculate exact rearrangement distances. |
| slow | Logical specifying whether to report distance measures that are slow to calculate (quartet distance and maximum agreement subtree). |
| verbose | Logical specifying whether to report which calculation is presently being performed. |
Other pairwise tree distances:
AllDists(),
PairwiseDistances()
#> $pid #> 1 2 3 4 #> 2 0.8638710 #> 3 0.8765556 0.9393481 #> 4 0.8295972 0.9132010 0.5815350 #> 5 0.8446827 0.7062995 0.7776109 0.6929858 #> #> $msid #> 1 2 3 4 #> 2 0.5571818 #> 3 0.5945095 0.6140312 #> 4 0.5403198 0.4960348 0.3057217 #> 5 0.4871444 0.3824559 0.4106123 0.3434586 #> #> $cid #> 1 2 3 4 #> 2 0.8065354 #> 3 0.8070752 0.8766895 #> 4 0.7611890 0.8195411 0.5358147 #> 5 0.7893264 0.6319386 0.7244807 0.6291396 #> #> $qd #> [,1] [,2] [,3] [,4] [,5] #> [1,] 0.0000000 0.7571429 0.7000000 0.7285714 0.7142857 #> [2,] 0.7571429 0.0000000 0.8142857 0.7571429 0.5714286 #> [3,] 0.7000000 0.8142857 0.0000000 0.3857143 0.6285714 #> [4,] 0.7285714 0.7571429 0.3857143 0.0000000 0.5000000 #> [5,] 0.7142857 0.5714286 0.6285714 0.5000000 0.0000000 #> #> $nye #> 1 2 3 4 5 #> 1 0.0000000 0.5800000 0.5833333 0.5533333 0.5733333 #> 2 0.5800000 0.0000000 0.6366667 0.5866667 0.4533333 #> 3 0.5833333 0.6366667 0.0000000 0.4200000 0.5566667 #> 4 0.5533333 0.5866667 0.4200000 0.0000000 0.4666667 #> 5 0.5733333 0.4533333 0.5566667 0.4666667 0.0000000 #> #> $jnc2 #> 1 2 3 4 #> 2 0.8557778 #> 3 0.8737778 0.9360000 #> 4 0.8291111 0.9040000 0.6068889 #> 5 0.8335556 0.6680000 0.7790556 0.6943889 #> #> $jnc4 #> 1 2 3 4 #> 2 0.9591109 #> 3 0.9553738 0.9897600 #> 4 0.9428738 0.9846400 0.7266605 #> 5 0.9529047 0.7698800 0.9215405 0.8771234 #> #> $jco2 #> 1 2 3 4 #> 2 0.8113333 #> 3 0.8041667 0.8610556 #> 4 0.7846667 0.8195000 0.6068889 #> 5 0.8026667 0.6457778 0.7790556 0.6943889 #> #> $jco4 #> 1 2 3 4 #> 2 0.9541726 #> 3 0.9422743 0.9766605 #> 4 0.9379356 0.9579387 0.7266605 #> 5 0.9453156 0.7674109 0.9215405 0.8771234 #> #> $ms #> 1 2 3 4 #> 2 12 #> 3 10 12 #> 4 12 14 8 #> 5 11 11 11 9 #> #> $mast #> 1 2 3 4 5 #> 1 8 5 5 5 5 #> 2 5 8 5 4 5 #> 3 5 5 8 5 5 #> 4 5 4 5 8 5 #> 5 5 5 5 5 8 #> #> $masti #> 1 2 3 4 5 #> 1 13.343602 3.906891 3.906891 3.906891 3.906891 #> 2 3.906891 13.343602 3.906891 1.584963 3.906891 #> 3 3.906891 3.906891 13.343602 3.906891 3.906891 #> 4 3.906891 1.584963 3.906891 13.343602 3.906891 #> 5 3.906891 3.906891 3.906891 3.906891 13.343602 #> #> $nni_l #> 1 2 3 4 5 #> 1 5 5 5 5 #> 2 5 5 5 4 #> 3 5 5 4 5 #> 4 5 5 4 5 #> 5 5 4 5 5 #> #> $nni_L #> 1 2 3 4 5 #> 1 10 10 10 10 #> 2 10 10 10 7 #> 3 10 10 6 10 #> 4 10 10 6 10 #> 5 10 7 10 10 #> #> $nni_t #> 1 2 3 4 5 #> 1 10 10 10 10 #> 2 10 10 10 7 #> 3 10 10 6 10 #> 4 10 10 6 10 #> 5 10 7 10 10 #> #> $nni_U #> 1 2 3 4 5 #> 1 10 10 10 10 #> 2 10 10 10 7 #> 3 10 10 6 10 #> 4 10 10 6 10 #> 5 10 7 10 10 #> #> $nni_u #> 1 2 3 4 5 #> 1 18 18 18 18 #> 2 18 18 18 14 #> 3 18 18 10 18 #> 4 18 18 10 18 #> 5 18 14 18 18 #> #> $spr #> 1 2 3 4 5 #> 1 0 2 2 2 3 #> 2 2 0 3 3 2 #> 3 2 3 0 3 2 #> 4 2 3 3 0 2 #> 5 3 2 2 2 0 #> #> $tbr_l #> 1 2 3 4 5 #> 1 0 2 2 2 2 #> 2 2 0 2 2 2 #> 3 2 2 0 2 2 #> 4 2 2 2 0 2 #> 5 2 2 2 2 0 #> #> $tbr_u #> 1 2 3 4 5 #> 1 0 6 6 6 5 #> 2 6 0 6 6 5 #> 3 6 6 0 6 6 #> 4 6 6 6 0 6 #> 5 5 5 6 6 0 #> #> $rf #> 1 2 3 4 #> 2 10 #> 3 10 10 #> 4 10 10 8 #> 5 10 8 10 10 #> #> $icrf #> 1 2 3 4 #> 2 43.00456 #> 3 40.93417 43.00456 #> 4 43.00456 45.07494 32.91577 #> 5 41.41959 36.57112 41.41959 43.48998 #> #> $path #> 1 2 3 4 5 #> 1 0.000000 10.77033 9.165151 10.770330 9.746794 #> 2 10.770330 0.00000 11.135529 12.489996 10.344080 #> 3 9.165151 11.13553 0.000000 7.745967 9.110434 #> 4 10.770330 12.49000 7.745967 0.000000 8.888194 #> 5 9.746794 10.34408 9.110434 8.888194 0.000000 #>