我试图用ape软件包在R中绘制一棵推断出的桉树系统发育树.
我得到以下错误:
> plot(euc.tr)
Error in plot.phylo(euc.tr) : tree badly conformed; cannot plot. Check the edge matrix.
我试着看euc.tr$edge想看看我是否能找到任何错误,但我很难理解矩阵中的数字应该如何与树对应,而且我不确定"严重一致"是什么意思,即使在搜索了谷歌和ape手册之后也是如此.
当我在Mesquit而不是R中打开nexus文件时,我看不到这棵树有任何异常.
R中的系统发育树对象摘要:
> summary(euc.tr)
Phylogenetic tree: euc.tr
Number of tips: 674
Number of nodes: 568
Branch lengths:
mean: 2.436121
variance: 23.99677
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.000728 0.118585 0.477268 2.297975 50.513412
No root edge.
First ten tip labels: Angophora_bakeri
Angophora_costata
Angophora_exul
Angophora_floribunda
Angophora_hispida
Angophora_inopina
Angophora_melanoxylon
Angophora_robur
Angophora_subvelutina
Angophora_woodsiana
No node labels.
边缘矩阵的头部(共1241行):
> head(euc.tr$edge)
[,1] [,2]
[1,] 675 676
[2,] 676 677
[3,] 677 678
[4,] 678 6240
[5,] 678 679
[6,] 679 680