Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'
Hi Anna. Your attached file with extension .nwk is also a Nexus style file so it cannot be read with read.tree or read.newick. read.tree and read.newick read a simple Newick style text string, or a set of such strings on separate lines in a file. It looks like the problem with your Nexus file, extension .nex, is that there are line breaks or spaces within the Newick string. The problem with your Nexus file of extension .nwk is probably the figtree block (although this is just a guess). Try this: obj-readLines(IndTree.nwk) ii-grep(tree_1,obj) x-strsplit(obj[ii], )[[1]] tree-read.tree(text=x[length(x)]) All the best, Liam Liam J. Revell, Assistant 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 8/15/2014 9:56 AM, Anna Bastian wrote: Dear list members, I am trying to read a tree into R (‘ape’ package). I downloaded the latest versions. The tree has many polytomies and that might be the problem. It contains ten species and each species contains of a different number of individuals (those are the polytomies). I attached it here. I tried read.nexus …and get:Error in trees[[i]] : subscript out of bounds I tried read.tree #using a newick format for the tree) …and get:Error in if (tp[3] != ) obj$node.label - tp[3] : missing value where TRUE/FALSE needed I came across a “Robust Newick tree reader” by Liam Revell and tied the code he provides (http://www.phytools.org/read.newick/v0.5/read.newick.R) but I can’t make it work. Can somebody get the tree into R? Please let me know if you know what’s wrong Thanks a lot Anna ** ** * * * * * * * * * * * ** *University of Cape Town* /Animal Evolution and Systematics Group/ Department of Biological Sciences Room 3.32 Tel: +27 (0)21 6502405 Fax: +27 (0)21 6502718 UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'
Great, François. Now I have the tree in R and can continue with the next steps. Thanks a lot for your help Anna From: François Michonneau [mailto:francois.michonn...@gmail.com] Sent: Freitag, 15. August 2014 16:07 To: Anna Bastian Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape' Hi Anna, I can read your tree using the package phylobase: tr - readNexus(file=IndTree.nex) If you need it in the phylo format to use with other functions in ape, you can convert it with: as(tr, phylo) cheers, -- François On Fri, Aug 15, 2014 at 9:56 AM, Anna Bastian anna.bast...@uct.ac.zamailto:anna.bast...@uct.ac.za wrote: Dear list members, I am trying to read a tree into R (‘ape’ package). I downloaded the latest versions. The tree has many polytomies and that might be the problem. It contains ten species and each species contains of a different number of individuals (those are the polytomies). I attached it here. I tried read.nexus …and get: Error in trees[[i]] : subscript out of bounds I tried read.tree #using a newick format for the tree) …and get: Error in if (tp[3] != ) obj$node.label - tp[3] : missing value where TRUE/FALSE needed I came across a “Robust Newick tree reader” by Liam Revell and tied the code he provides (http://www.phytools.org/read.newick/v0.5/read.newick.R) but I can’t make it work. Can somebody get the tree into R? Please let me know if you know what’s wrong Thanks a lot Anna * * * * * * * * * * * University of Cape Town Animal Evolution and Systematics Group Department of Biological Sciences Room 3.32 Tel: +27 (0)21 6502405tel:%2B27%20%280%2921%206502405 Fax: +27 (0)21 6502718tel:%2B27%20%280%2921%206502718 UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111tel:%2B27%2021%20650%209111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto:R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'
Hi Liam,
Thanks for explaining what is wrong with the format of the newick tree file.
I will work in understanding and re-writing the tree with the correct
formatting.
Your script worked fine and the tree is finally in R!
Thanks a lot. I appreciate your help
Regards,
Anna
-Original Message-
From: Liam J. Revell [mailto:liam.rev...@umb.edu]
Sent: Freitag, 15. August 2014 16:48
To: Anna Bastian; r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'
Hi Anna.
Your attached file with extension .nwk is also a Nexus style file so it cannot
be read with read.tree or read.newick. read.tree and read.newick read a simple
Newick style text string, or a set of such strings on separate lines in a file.
It looks like the problem with your Nexus file, extension .nex, is that there
are line breaks or spaces within the Newick string. The problem with your Nexus
file of extension .nwk is probably the figtree block (although this is just a
guess).
Try this:
obj-readLines(IndTree.nwk)
ii-grep(tree_1,obj)
x-strsplit(obj[ii], )[[1]]
tree-read.tree(text=x[length(x)])
All the best, Liam
Liam J. Revell, Assistant 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 8/15/2014 9:56 AM, Anna Bastian wrote:
Dear list members,
I am trying to read a tree into R ('ape' package). I downloaded the
latest versions.
The tree has many polytomies and that might be the problem.
It contains ten species and each species contains of a different
number of individuals (those are the polytomies).
I attached it here.
I tried read.nexus
...and get:Error in trees[[i]] : subscript out of bounds
I tried read.tree #using a newick format for the tree)
...and get:Error in if (tp[3] != ) obj$node.label - tp[3] :
missing value where TRUE/FALSE needed
I came across a Robust Newick tree reader by Liam Revell and tied
the code he provides
(http://www.phytools.org/read.newick/v0.5/read.newick.R) but I can't
make it work.
Can somebody get the tree into R?
Please let me know if you know what's wrong
Thanks a lot
Anna
**
** * * * * * * * * * * *
**
*University of Cape Town*
/Animal Evolution and Systematics Group/
Department of Biological Sciences
Room 3.32
Tel: +27 (0)21 6502405
Fax: +27 (0)21 6502718
--
--
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mail disclaimer
published on our website at
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
from
+27 21 650 9111. This e-mail is intended only for the person(s) to
+whom
it is addressed. If the e-mail has reached you in error, please notify
the author. If you are not the intended recipient of the e-mail you
may not use, disclose, copy, redirect or print the content. If this
e-mail is not related to the business of UCT it is sent by the sender
in the sender's individual capacity.
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