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 <liam.rev...@umb.edu>
escreveu:
> 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
> distribution, this will leave you with only one lineage!
>
> To see how the function should work you could try something like:
>
> set.seed(99)
> tree<-pbtree(n=15,b=1,d=0.2)
> plotTree(tree)
> plotTree(pruned<-drop.fossil(tree))
>
> Hopefully this leaves things a bit clearer.
>
> For fun, also try:
>
> par(mfrow=c(1,1),mar=c(5.1,4.1,2.1,2.1),bty="n")
> ltt(tree,lty="dashed",log.lineages=FALSE,log="y")
> ltt(pruned,lty="solid",add=TRUE,log.lineages=FALSE,
> log="y")
> legend("topleft",c("observed","reconstructed"),
> lty=c("dashed","solid"),bty="n")
>
> All the best, Liam
>
> Liam J. Revell
> University of Massachusetts Boston
> Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad:
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 8/25/2020 4:21 PM, Elvira D`bastiani wrote:
> > [EXTERNAL SENDER]
> >
> > 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:
> > my.tree = rtree (15, rooted = TRUE, tip.label = NULL, br = runif) #random
> > tree in phylo format
> > class (my.tree)
> > my.tree $ edge.length #I need this information without NaN.
> >
> >> my.tree$edge.length [1] 0.53879430 0.71471795 0.40579050 0.15278814
> 0.34023276 0.62665485
> > [7] 0.05737268 0.85166764 0.21264535 0.53946203 0.13648759 0.32486514
> > [13] 0.62107629 0.25598225 0.63487580 0.48567211 0.93817692 0.85750154
> > [19] 0.37088354 0.31420183 0.82853436 0.45184151 0.31587841 0.09780854
> > [25] 0.06490054 0.68945737 0.66805060 0.90454665
> >
> >
> > However in the same tree format (phylo format) in my analysis the
> > edge.length comes out with NaN. Even after using the drop.fossil (fPar)
> or
> > drop.extinct (fPar) functions. It looks like this:
> >
> >> fPar$edge.length [1] 17 53 258 138 1 1 1 -621 NaN 47
> 31 13 34 26
> > [15] 1 35 46 60 0 3 53 7 -904 NaN 4 17 NaN
> NaN
> >
> >
> > Is there any way to delete these NaN?
> >
> >
> > Thanks in advance for the answer
> >
> > Best wishes
> >
> > e.
> >
> > --
> >
> > *Elvira D'Bastiani*Doutoranda em Ecologia e Conservação
> > Laboratório de Interações Biológicas
> > Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brasil
> > *
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--
*Elvira D'Bastiani*Doutoranda em Ecologia e Conservação
Laboratório de Interações Biológicas
Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brasil
*https://elviradbastiani.wixsite.com/ecoevo
<https://elviradbastiani.wixsite.com/ecoevo>*
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