Hi Having another problem with the same function now. What you suggested worked for one tree, but for the attached tree and file it didn't...
I get:
> ttree<-date.phylo(tree, ages, rlen=10, method="equal")
Error: subscript out of bounds
> traceback()
1: date.phylo(tree, ages, rlen = 10, method = "equal")
On Thu, Jul 21, 2011 at 5:12 PM, Klaus Schliep <klaus.schl...@gmail.com> wrote:
> Hi Roland!
> ages should be a matrix, with row names and the ages in the first column.
>
> On 7/21/11, Roland Sookias <r.sook...@gmail.com> wrote:
>> 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
>>>
>>
>
>
> --
> Klaus Schliep
> Université Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
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therapsidtree.tre
Description: Binary data
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