Hi Sara.
Sorry for not replying directly to your PM.
I was able to read the file you sent me off-list with no problem, but
you may first want to remove all the spaces from the Newick string. You
can do this with any text editor search & replace. The spaces caused
problems for read.newick in phytools, but not for read.tree - but this
may not be true of earlier versions of ape.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/28/2016 7:32 PM, Sara Reese wrote:
Hi all,
I'm a senior Environmental Biology major at Colgate University in central
New York, and am working on a senior thesis that involves phylogenetically
weighting shrew body mass data. I used a Java program called TreeSnatcher
to produce a Newick expression from a phylogenetic tree image. I
successfully imported the Newick expression into R and reproduced the tree
using the ape package, but the tree that's produced from the Newick
expression has some errors in it. I've tried to edit the Newick expression
to fix them, but keep getting errors such as "Error in if (tp[3] != "")
obj$node.label <- tp[3] : missing value where TRUE/FALSE needed" when I do
so. There isn't much information about these types of errors, so I'm not
really sure what's going on. I'm wondering if anyone knows anything about
editing Newick expressions to correct branching. I can provide more detail
and any files if needed. Thank you!
Sara Reese
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