Roland-
It is because some of your tip labels are formatted in such a way that R
cannot find their match in the row.names of ages.
For example, you have Sinocodon_sp., which corresponds to the tip label:
"'''Sinoconodon_sp.'''" These extra quotation marks are what's getting in
your way and making
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
Hi Roland!
ages should be a matrix, with row names and the ages in the first column.
On 7/21/11, Roland Sookias 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
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 wrote:
> Hi Roland,
>
> as I suspected, your ages list was not in the right format (has
> nothing to do with ape).
> Tr
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, metho
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 wrote:
> Dear Roland,
>
> it would be good if you add the
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 7/2
-phylo] Dating trees using date.phylo - ape problem?
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. Grae
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
