Great! It worked. What format should the file be in then? I thought I'd
followed the format specified.. Thanks very much indeed :)
On Thu, Jul 21, 2011 at 4:10 PM, Klaus Schliep <klaus.schl...@gmail.com>wrote:
> Hi Roland,
>
> as I suspected, your ages list was not in the right format (has
> nothing to do with ape).
> Try this:
>
> tmp = read.csv("agescut.csv", header=FALSE)
> ages = matrix(tmp[, 2], ncol=1)
> rownames(ages) = tmp[,1]
> tree = read.tree("archotreeresolved6.tre")
> ttree<-date.phylo(tree, ages, rlen=1, method="equal")
>
>
> Regards,
> Klaus
>
>
>
> On 7/21/11, Roland Sookias <r.sook...@gmail.com> wrote:
> > Hi
> >
> > Thanks guys.
> >
> > Attached are the two files (will these work via the list?)
> >
> > When I type trackback() all I get is 1: date.phylo(archotreeresolved,
> ages,
> > rlen = 1, method = "equal").
> >
> > Roland
> >
> >
> >
> > On Thu, Jul 21, 2011 at 1:24 PM, Klaus Schliep
> > <klaus.schl...@gmail.com>wrote:
> >
> >> Dear Roland,
> >>
> >> it would be good if you add the datasets, that one can reproduce your
> >> results (archotreeresolved, ages). I would guess from the error
> >> message that your ages list may has the wrong format.
> >> Also traceback() sometimes tells you where the error happens exactly.
> >>
> >> Kind regards
> >> Klaus
> >>
> >> On 7/21/11, Roland Sookias <r.sook...@gmail.com> wrote:
> >> > Hi all
> >> >
> >> > I'm trying to assign lengths to branches in a tree using the Ruta et
> al.
> >> > 2008 method via Graeme Lloyd's date.phylo() function (see
> >> > http://www.graemetlloyd.com/methdpf.html). I keep coming up against
> an
> >> error
> >> > for some reason. Graeme himself does exactly the same thing seemingly
> on
> >> his
> >> > Mac (I'm using Windows 7, R 2.13.1, Ape 2.7-2 - Graeme has Ape 2.7-1)
> >> > and
> >> it
> >> > works. I've tried various permutations of the tree, with and without a
> >> > rooted symbol [&r], and there are no special characters etc., the
> names
> >> in
> >> > tree and ages list are the same. I still keep getting:
> >> >
> >> > ttree<-date.phylo(archotreeresolved, ages, rlen=1, method="equal")
> >> > Error in ages[tree$tip.label[find.descendants(nodes[i], tree)], 1] :
> >> > incorrect number of dimensions
> >> >
> >> > Any help, or advice what to try/look into much appreciated. Graeme
> >> > thinks
> >> > it's something with ape not date.phylo...
> >> >
> >> > Very best
> >> >
> >> > Roland
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > R-sig-phylo mailing list
> >> > R-sig-phylo@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >> >
> >>
> >>
> >> --
> >> Klaus Schliep
> >> Université Paris 6 (Pierre et Marie Curie)
> >> 9, Quai Saint-Bernard, 75005 Paris
> >>
> >
>
>
> --
> Klaus Schliep
> Université Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
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