Thanks a lot Brian!
Took me the whole day but finally treePL works fine although there were some
difficulties with Yosemite and the version of c++.
The "tree <- reorder(tree)" trick didn't do the trick.
Cheers,
Franz
> Brian O'Meara <omeara.br...@gmail.com> hat am 30. Dezember 2014 um 19:56
> geschrieben:
>
>
> The programs r8s, pathd8, and treepl can all take a phylogram and return a
> chronogram, but they're not within R (though they could be wrapped). You
> could also infer a chronogram from the start using Beast or MrBayes, though
> the large size of the tree may make it difficult.
>
> One simple thing to try before all this, though, is pass your tree through
> a reorder() function call (using default arguments) before passing it to
> chronos: (i.e.,
>
> tree <- read.tree("full_Cipres_Data/RAxML_bestTree.tre")
>
> *tree <- reorder(tree)
tree <- chronos(tree, lambda = 1, model =
> "correlated", quiet = FALSE,
> calibration = makeChronosCalib(tree),
> control = chronos.control())
>
> Sometimes the imported tree structure, while valid, can be an issue for
> ape and I find doing this reordering can fix weird errors.
>
> Best,
> Brian
>
> _______________________________________
> Brian O'Meara
> Assistant Professor
> Dept. of Ecology & Evolutionary Biology
> U. of Tennessee, Knoxville
> http://www.brianomeara.info
>
> Postdoc collaborators wanted: http://nimbios.org/postdocs/
> Calendar: http://www.brianomeara.info/calendars/omeara
>
> On Tue, Dec 30, 2014 at 4:18 AM, Franz Krah <f.k...@mailbox.org> wrote:
>
> > Dear all,
> >
> > I used chronos to make a large phylogeny (~3600 species) ultrametric.
> > The tree is rooted and binary.
> >
> > With the following code I get the error:
> >
> > tree <- read.tree("full_Cipres_Data/RAxML_bestTree.tre")
> > tree <- chronos(tree, lambda = 1, model = "correlated", quiet = FALSE,
> > calibration = makeChronosCalib(tree),
> > control = chronos.control())
> >
> >
> > Error:
> >
> > In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) :
> > NA/NaN function evaluation
> >
> > This error was posted before some times but I didn't find a satisfying
> > answer.
> >
> > I tried out some things but didn't helped: altering the root in different
> > ways,
> > altering the model, altering lambda. The functions worked fine with smaller
> > phylogenies before!
> >
> > Hope someone found a solution!
> > Are there other ways of making my tree ultrametric?
> >
> > Cheers, Franz
> >
> > _______________________________________________
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> > http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
