Read MCMCtree output tree into R
readMCMCTree.RdRead MCMCtree output tree into R to produce time-scaled tree in APE format, and a table of the mean and 95
Examples
data(MCMCtree.output)
#> Warning: data set ‘MCMCtree.output’ not found
attach(MCMCtree.output)
#> The following objects are masked from MCMCtree.output (pos = 4):
#>
#> MCMCtree.phy, MCMCtree.posterior
#> The following objects are masked from MCMCtree.output (pos = 6):
#>
#> MCMCtree.phy, MCMCtree.posterior
# tree and node ages
readMCMCtree(MCMCtree.phy, from.file=FALSE)
#> $apePhy
#>
#> Phylogenetic tree with 103 tips and 102 internal nodes.
#>
#> Tip labels:
#> Dioscorea_villosa, Colchicum_autumnale, Smilax_bona-nox, Sorghum_bicolor, Zea_mays, Oryza_sativa, ...
#>
#> Rooted; includes branch lengths.
#>
#> $nodeAges
#> mean 95%_lower 95%_upper
#> 104 7.767503 6.651 9.296
#> 105 7.306332 6.337 8.634
#> 106 6.644847 5.906 7.652
#> 107 6.228787 5.607 7.012
#> 108 5.944306 5.403 6.633
#> 109 5.554283 5.118 6.145
#> 110 5.001146 4.766 5.149
#> 111 4.466497 4.367 4.509
#> 112 4.272271 4.131 4.405
#> 113 3.515712 3.311 3.651
#> 114 2.329351 2.068 2.467
#> 115 2.114190 1.853 2.341
#> 116 1.913382 1.671 2.174
#> 117 1.661844 1.474 1.893
#> 118 1.242075 1.151 1.285
#> 119 1.048606 0.926 1.175
#> 120 0.959314 0.847 1.091
#> 121 0.680444 0.365 0.913
#> 122 0.895020 0.767 1.029
#> 123 0.783066 0.624 0.930
#> 124 0.481127 0.319 0.653
#> 125 0.208725 0.090 0.386
#> 126 0.348893 0.194 0.536
#> 127 1.544019 1.390 1.759
#> 128 1.423139 1.282 1.642
#> 129 1.311295 1.190 1.538
#> 130 1.182058 1.109 1.388
#> 131 0.761427 0.513 1.050
#> 132 1.261988 1.210 1.286
#> 133 1.152143 1.047 1.226
#> 134 1.069097 0.949 1.168
#> 135 0.965804 0.834 1.089
#> 136 0.861304 0.698 1.001
#> 137 0.756563 0.556 0.920
#> 138 0.576249 0.352 0.782
#> 139 0.866342 0.689 1.005
#> 140 0.736447 0.503 0.913
#> 141 1.070807 0.943 1.170
#> 142 0.972898 0.837 1.089
#> 143 0.886580 0.741 1.015
#> 144 0.760147 0.583 0.908
#> 145 0.666530 0.483 0.834
#> 146 0.362568 0.186 0.573
#> 147 0.455096 0.229 0.727
#> 148 1.014444 0.782 1.180
#> 149 0.783065 0.472 1.019
#> 150 3.177954 3.084 3.372
#> 151 2.886741 2.660 3.182
#> 152 0.952532 0.426 1.932
#> 153 0.209907 0.067 0.511
#> 154 2.438058 1.701 3.048
#> 155 2.114159 1.425 2.791
#> 156 0.630082 0.186 1.268
#> 157 1.252099 0.835 1.883
#> 158 0.893094 0.507 1.322
#> 159 1.139416 0.794 1.627
#> 160 0.952772 0.631 1.329
#> 161 0.684231 0.364 1.029
#> 162 0.346178 0.135 0.684
#> 163 4.042667 3.923 4.196
#> 164 3.572424 3.215 3.938
#> 165 2.694457 1.069 3.563
#> 166 3.906610 3.848 4.040
#> 167 1.157836 0.498 2.476
#> 168 4.089600 3.927 4.322
#> 169 1.262264 0.751 2.345
#> 170 0.880515 0.427 1.586
#> 171 0.118091 0.041 0.278
#> 172 4.870626 4.632 5.065
#> 173 4.671717 4.397 4.916
#> 174 3.997939 3.494 4.493
#> 175 3.397905 2.994 3.957
#> 176 2.823961 2.685 3.177
#> 177 1.778637 0.972 2.746
#> 178 1.043410 0.699 1.538
#> 179 0.864497 0.545 1.262
#> 180 0.290700 0.161 0.498
#> 181 0.224755 0.098 0.429
#> 182 0.228450 0.104 0.426
#> 183 0.323686 0.126 0.642
#> 184 4.184525 4.053 4.461
#> 185 2.726547 2.283 3.621
#> 186 1.227128 0.707 2.209
#> 187 0.794258 0.332 1.346
#> 188 2.439996 0.792 3.922
#> 189 0.164268 0.053 0.382
#> 190 4.971913 4.089 5.802
#> 191 4.515646 3.554 5.409
#> 192 4.064539 2.936 5.021
#> 193 3.347874 2.004 4.445
#> 194 2.066850 0.860 3.533
#> 195 4.470035 3.452 5.384
#> 196 3.595206 2.097 4.690
#> 197 3.075275 1.413 4.250
#> 198 4.738018 3.116 6.056
#> 199 3.176621 1.125 4.842
#> 200 4.686395 2.547 6.542
#> 201 5.884835 3.952 7.700
#> 202 4.184454 2.113 6.224
#> 203 6.680455 5.025 8.412
#> 204 5.843148 4.500 7.406
#> 205 4.869119 3.227 6.683
#>
#> attr(,"class")
#> [1] "MCMCtreer"