Hi Jonathan.
The function won't evaluate if there are no edge lengths, so if you have
a result, your tree must have edge lengths. If they are all set to 1,
then this would indeed be the number of edges between the two species
(or the number of speciation events in a completely sampled pure-birth
tree plus one).
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 10/3/2015 2:53 PM, Jonathan Greenberg wrote:
Thanks! Liam, what would be the intrepretation of your function if branch
lengths are not included? Just how many "segments" it takes to get between
species? As a generality, the larger this number, the more distantly
related two species might be? Or without lengths can I not make any
generalizations?
--j
P.S. This function worked great on that big tree.
On Fri, Oct 2, 2015 at 8:06 PM Joseph W. Brown <[email protected]> wrote:
There are no branch lengths in the OpenTree synthetic tree (yet).
Joseph.
________________________________________
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
[email protected]
On 2 Oct, 2015, at 17:12, Jonathan Greenberg <[email protected]> wrote:
Folks:
Pardon the newbish question, I'm an outsider joining the world of
phylogenetic analysis. Given a large newick tree e.g. from the new open
tree of life:
http://files.opentreeoflife.org/trees/v3subtrees/chloroplastida.tre.gz
<https://urldefense.proofpoint.com/v2/url?u=http-3A__files.opentreeoflife.org_trees_v3subtrees_chloroplastida.tre.gz&d=AwMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=rVZB6fYleVUDfV0TxTbBZKqFxQKdA_ifFsqsiwLwxio&m=D2gcT4_WJlt0zVaULXs8lCrMTpWpkKRXwBWy7MVXq9I&s=vaQnh80A72P-Q_9k048juaiepUbudvuDFS_N-azw8bM&e=>
(304959 tips)
I want to calculate a pairwise distance between a small subset of species.
The tricks I've seen so far using the ape package do no work on a tree of
that size:
MyTree <- read.tree("pathto/chloroplastida.tre")
pairwise_distance <- cophenetic(MyTree)
Error in double(nm * nm) : vector size cannot be NA
In addition: Warning message:
In nm * nm : NAs produced by integer overflow
pairwise_distance <- cophenetic(MyTree)["Abies concolor","Pinus jeffreyi"]
Error in double(nm * nm) : vector size cannot be NA
In addition: Warning message:
In nm * nm : NAs produced by integer overflow
This is due to the matrix having more cells than allowed
by .Machine$integer.max
My question is thus: I want to determine either single species to single
species distances without having an algorithm attempt to calculate the
distance for all possible species (which is what ape is doing). Is there a
package/trick to accomplish this? Thanks!
--j
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