Hello,
I am looking the correct way to use the function which.edge {ape} and to
understand what it returns…
which.edge(phy, group)
so I use as phy an object I get like that:
as.phylo(dendroIcscan)
summary(as.phylo(dendroIcscan))
Phylogenetic tree: as.phylo(dendroIcscan)
Number of tips: 169
Number of nodes: 168
Branch lengths:
mean: 0.1140614
variance: 0.006095345
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.005061 0.047450 0.093750 0.175000 0.361100
No root edge.
First ten tip labels: B-40-2x-T
B-41-2x-T
B-43-2x-T
B-47-2x-T
B-52-2x-T
B-72-3x-T
B-73-2x-A
B-75-4x-T
B-83-4x-A
B-84-4x-NA
No node labels.
and as group, I get an object:
ColPloIcscan
[1] 2 2 2 2 2 3 2 4 4 4 4 4 4 2 4 2 2 4 2 4 2 4 2 4 2 4 2 4 2 3 2 3 2 4 2 3 2
4 2 4 3 3 4 2 4 2 4 2 4 3 4 2 4 2 4 2 4 2 3 4 4 2 3 4 2 4 3 3 2 4 2 4 2 4 4 4 4
2 4 2 4 4 3 4 4 4
[87] 2 3 4 2 4 4 2 4 2 2 3 2 4 2 4 2 4 2 4 4 2 2 4 3 4 4 4 4 4 4 4 4 4 4 4 2 2
3 2 2 4 3 4 2 4 4 2 2 4 3 4 2 4 4 2 4 3 2 3 2 4 2 4 2 4 4 4 2 2 2 4 2 2 4 2 4 2
2 4 4 4 4 2
with everything in the same order than in the phylogenetic tree.
As there is no exemple, I try around with several commande :
> which.edge(as.phylo(dendroIcscan), ColPloIcscan)
[1] 10 50 68 69 71 72 73 74 79 80 110 120 121 122
> which.edge(as.phylo(dendroIcscan), ColPloIcscan==2)
[1] 9 10 50 68 69 70
> which.edge(as.phylo(dendroIcscan), ColPloIcscan==3)
[1] 9 10 50 68 69 70
> which.edge(as.phylo(dendroIcscan), ColPloIcscan==4)
[1] 8 9 10 50 68 69 70
There is no exemple, and it doesn't make sens in itself… who could help me with
that?
Benjamin
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