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 > [[alternative HTML version deleted]]
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