Le 25/01/2019 à 00:14, Alina van dijk a écrit :
Hi everyone,
Thanks Emmanuel and Joseph for sharing your thoughts!
Emmanuel, today I tried multi2di and it works. But, if I understand
correctly, this function transforms the dichotomies with branches of
length zero. So for me, in fact, doesn't solve the politomy. Right?
To see what multi2di() does, try this code:
tr <- compute.brlen(stree(10), 1)
tr2 <- multi2di(tr)
par(mfcol = c(2, 2))
plot(tr)
plot(tr, use.edge.length = FALSE)
plot(tr2)
plot(tr2, use.edge.length = FALSE)
The internal branches that appear on the last plot have zero-length.
Note the option random = TRUE in multi2di().
I hope this can help you with your headache(s)...
Best,
Emmanuel
Joseph, I'm only a begginer with R and this program already gives me a
lot of headache.
It drives me crazy think in another program... hahahha
Just kidding! :)
But, nice to know that I have a plan B!
I will take a look!
Thanks in advance,
Best Regards,
Alina
Em qua, 23 de jan de 2019 às 16:29, Emmanuel Paradis
<emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> escreveu:
Hi Alina,
Did you try multi2di() to remove polytomies?
Best,
Emmanuel
Le 23/01/2019 à 17:41, Alina van dijk a écrit :
> Hi everyone,
>
> My name is Alina, I'm attending master degree in ecology and I have a
> little problem with my consensus phylogeny. I used 1000 phylogeny of
> birdtree to construct the consensus tree but now I need to insert
the dates
> in this consensus tree.
>
> To accomplish this idea, I tried different methods:
consensustree<-averageTree
> (tree,method="symmetric.difference") but the result is a
consensus tree in
> topology, binary and rooted but not ultrametric. For this problem
I used
> consensus_tree_ultrametric
> <-compute.brlen(consensustree,method="Grafen",power=1), but the edge
> lengths was altered.
>
> So, I used another method to make a consensus tree using phytools
> consensustree_another_method <- consensus.edges(multiphylo,method =
> "mean.edge") as a result, a ultrametric tree, rooted with
consensus edges
> lengths, but have polytomies :(
>
> I also tried using phylobase , proposed by Brian O'Meara in this
link:
>
https://grokbase.com/t/r/r-sig-phylo/12bn9x5gv4/why-no-branch-lengths-on-consensus-trees
> ,
> but as a result, my consensus tree wasn´t ultrametric and the
> transformation also altered the edge lengths.
>
> I only need to insert the dates based on the trees dated by Jetz
in this
> consensus tree and as result, an ultrametric tree, with consensus
edges
> lengths and no polytomy.
>
> Does anyone know how to solve that problem?
>
> Thanks in advance,
> Best Regards,
>
> Alina
>
> [[alternative HTML version deleted]]
>
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