Hi all,
I forgot to copy my reply to Luke to the list - here's another solution in case
the question crops up again.
Cheers,
David
Begin forwarded message:
Date: 20 July 2011 11:57:46 GMT+01:00
To: Luke Matthews matth...@mednetworks.commailto:matth...@mednetworks.com
Subject: Re:
Hi Roland,
Just after the error, type:
traceback()
This will show you, hopefully, where the error happened.
Best,
Emmanuel
-Original Message-
From: Roland Sookias r.sook...@gmail.com
Sender: r-sig-phylo-boun...@r-project.org
Date: Thu, 21 Jul 2011 12:44:30
To:
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
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.comwrote:
Dear Roland,
it would be
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,
Hello,
Is it possible to use Ape Library to generate all possible evolutionary tree
structures given a fixed number of nodes? We're studying plant leaf evolutions
and we need to test each evolutionary tree on our models. We realize the number
of trees would be huge, so we'd chooce only the
Liutauras-
allTrees() in the phangorn package can calculate all possible trees for up
to 10 tips.
Cheers,
-Dave, UChicago
On Thu, Jul 21, 2011 at 10:20 AM, Liutauras Rusaitis
liutauras.rusai...@st-annes.ox.ac.uk wrote:
Hello,
Is it possible to use Ape Library to generate all possible
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.comwrote:
Hi Roland,
as I suspected, your ages list was not in the right format (has
nothing
And howmanytrees() in ape tells you how many trees there are for a given number
of tips (if it returns Inf, it's because this number is beyond the largest
representable number on your computer).
Best,
Emmanuel
-Original Message-
From: David Bapst dwba...@uchicago.edu
Sender:
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
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