Hi Liam,
That, are branch lengths. I know that these NaNs correspond to the species
that have become extinct.
When I talk about 'delete' the NaNs, I want my newick not to have those
branches with NaNs.
You helped me!
Thank you for talking about it with me!
All the best,
Em ter., 25 de ago. de
Hi Elvira.
In your Newick string those NaN are branch lengths, not taxon labels.
What do you mean by 'delete' the NaNs? You can set them to zero, as follows:
tree$edge.length[is.na(tree$edge.length)]<-0
but then you get a tree that looks like this:
Dear Liam,
Thanks for your answer. It got a little clearer. But I still can't resolve
my error ;(
Thanks
Best regards
Elvira
Em ter., 25 de ago. de 2020 às 17:33, Liam J. Revell
escreveu:
> Dear Elvira.
>
> I'm not sure what's going on with the NaN values, but one issue that I
> see with
Dear Elvira.
I'm not sure what's going on with the NaN values, but one issue that I
see with your example is that ape::drop.fossil identifies fossil
lineages by finding those that end before the present. Since rtree just
splits the tree randomly & samples the edge lengths from a uniform
Hi,
I'm a beginner with phylogeny analysis. I'm having trouble extracting only
the surviving species from the phylogenies of my model.
I used the drop.fossil (fPar) functions from ape and the drop.extinct
(fPar) from geiger. But it is not deleting the way I need it.
Running example correctly:
