[R-sig-phylo] importing trees from birdtree.org into R

Discussion:

Agus Camacho

2018-02-13 22:11:47 UTC

Dear list,

I am puzzled with this error when importing a bird tree subset from
https://birdtree.org/subsets/ .

The subset is supposed to be in nexus format. However,

trees<-read.nexus("output.nex")

Error in if (tp[3] != "") obj$node.label <- tp[3] :

missing value where TRUE/FALSE needed

read.tree gives the same error
read.newick gets stuck, it never ends reading in the tree

I tried scanning the file and then several notes appear before the actual
trees Thus, I tried read.annotated.nexus from OutbreakTools.
But it gives another error:

Error in read.annotated.nexus("C:/Users/agusc/Dropbox/output.nex") :
.annotated.clado.build is not yet implemented.

I tried with several different subsets from different backbones and none
worked.
Here is one: https://www.dropbox.com/s/037u6pjr4006o6r/output.nex?dl=0

Somebody has reported this error previously in the internet, but it still
seems to be unsolved.

Thanks in advance and best regards.
Agus
--
Agustín Camacho Guerrero.
http://www.agustincamacho.com
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.

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Klaus Schliep

2018-02-14 00:51:26 UTC

Permalink

Dear Agustín,

the nexus file on dropbox does not contain any trees.
If you open it in an editor you see this:

#NEXUS

[Tree distribution from: The global diversity of birds in space and time;
W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
doi:10.1038/nature11631]
[Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ]
[Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]

BEGIN TREES;
TREE tree_4104 =
TREE tree_9438 =
...
TREE tree_1868 =
TREE tree_0011 =
END;

Looks like your download did not work and the error message from read.nexus
could improve.

Cheers,
Klaus

Post by Agus Camacho
Dear list,
I am puzzled with this error when importing a bird tree subset from
https://birdtree.org/subsets/ .
The subset is supposed to be in nexus format. However,
trees<-read.nexus("output.nex")
missing value where TRUE/FALSE needed
read.tree gives the same error
read.newick gets stuck, it never ends reading in the tree
I tried scanning the file and then several notes appear before the actual
trees Thus, I tried read.annotated.nexus from OutbreakTools.
.annotated.clado.build is not yet implemented.
I tried with several different subsets from different backbones and none
worked.
Here is one: https://www.dropbox.com/s/037u6pjr4006o6r/output.nex?dl=0
Somebody has reported this error previously in the internet, but it still
seems to be unsolved.
Thanks in advance and best regards.
Agus
--
Agustín Camacho Guerrero.
http://www.agustincamacho.com
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-

--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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Agus Camacho

2018-02-14 02:11:50 UTC

Permalink

Thanks for that, Klaus!
Regards
Agus

Post by Klaus Schliep
Dear Agustín,
the nexus file on dropbox does not contain any trees.
#NEXUS
[Tree distribution from: The global diversity of birds in space and time;
W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
doi:10.1038/nature11631]
[Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ]
[Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]
BEGIN TREES;
TREE tree_4104 =
TREE tree_9438 =
...
TREE tree_1868 =
TREE tree_0011 =
END;
Looks like your download did not work and the error message from
read.nexus could improve.
Cheers,
Klaus

--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

--
Agustín Camacho Guerrero.
http://www.agustincamacho.com
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.

[[alternative HTML version deleted]]

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Upham, Nathan

2018-02-14 02:33:10 UTC

Permalink

Hi Agus
I work next to the main developer for the birdtree.org<http://birdtree.org> site— glad to help figure the error if its on our end. I just downloaded a test file (Ericson sequenced, 100 trees) and it worked as intended including full trees. What species and settings did you choose for your download, and using what web browser?

Reply to me off list and we’ll get this sorted.

All the best
—nate

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nathan S. Upham, Ph.D.
Postdoctoral Associate, Yale University, Ecology and Evolutionary Biology
165 Prospect Street, OML 122, New Haven, CT, 06511, USA

personal web: Home<https://n8upham.github.io/> | Research Gate<https://www.researchgate.net/profile/Nathan_Upham> | Google Scholar<https://scholar.google.com/citations?user=zIn4NoUAAAAJ&hl=en>
lab pages: Jetz Lab<http://jetzlab.yale.edu/> | NSF VertLife grant<http://vertlife.org/>

Research Associate, Integrative Research Center, Field Museum of Natural History
Chair, Biodiversity Committee, American Society of Mammalogists
~> Check out the new Mammal Diversity Database<https://mammaldiversity.org/>
Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group

e: ***@yale.edu<mailto:***@yale.edu> | Skype: nate_upham | Twitter: @n8_upham

On Feb 13, 2018, at 9:11 PM, Agus Camacho <***@gmail.com<mailto:***@gmail.com>> wrote:

Thanks for that, Klaus!
Regards
Agus

2018-02-13 22:51 GMT-02:00 Klaus Schliep <***@gmail.com<mailto:***@gmail.com>>:

Dear Agustín,

the nexus file on dropbox does not contain any trees.
If you open it in an editor you see this:

#NEXUS

[Tree distribution from: The global diversity of birds in space and time;
W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
doi:10.1038/nature11631]
[Subsampled and pruned from birdtree.org<http://birdtree.org> on 2018-02-13T21:49:59Z ]
[Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]

BEGIN TREES;
TREE tree_4104 =
TREE tree_9438 =
...
TREE tree_1868 =
TREE tree_0011 =
END;

Looks like your download did not work and the error message from
read.nexus could improve.

Cheers,
Klaus

On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho <***@gmail.com<mailto:***@gmail.com>>
wrote:

Dear list,

I am puzzled with this error when importing a bird tree subset from
https://urldefense.proofpoint.com/v2/url?u=https-3A__birdtree.org_subsets_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=QCx_EErW5SnutNdxWnXm65RyRGtG1st3m0iAmNiulmU&e= .

The subset is supposed to be in nexus format. However,

trees<-read.nexus("output.nex")

Error in if (tp[3] != "") obj$node.label <- tp[3] :

missing value where TRUE/FALSE needed

read.tree gives the same error
read.newick gets stuck, it never ends reading in the tree

I tried scanning the file and then several notes appear before the actual
trees Thus, I tried read.annotated.nexus from OutbreakTools.
But it gives another error:

Error in read.annotated.nexus("C:/Users/agusc/Dropbox/output.nex") :
.annotated.clado.build is not yet implemented.

I tried with several different subsets from different backbones and none
worked.
Here is one: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_037u6pjr4006o6r_output.nex-3Fdl-3D0&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=BfBnKVjZjCJ1C8YumcqEIf2FGIDH2pRzLaqMU8gm01g&e=

Somebody has reported this error previously in the internet, but it still
seems to be unsolved.

Thanks in advance and best regards.
Agus
--
Agustín Camacho Guerrero.
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=jSdLapf5K-3pnA7_OTck6Zt-60GpMrs1IZ0AAh8B34E&e=
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.

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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phangorn.org_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=ZLALoSqYWiPRC_eOJCMWrhZgF0GgiIY5NOxGc-3IQCg&e=
--
Agustín Camacho Guerrero.
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=jSdLapf5K-3pnA7_OTck6Zt-60GpMrs1IZ0AAh8B34E&e=
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.

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Agus Camacho

2018-02-14 11:10:42 UTC

Permalink

Thanks Nathan,

I was right now able to figure out the problem. I noticed that the species
list I was using had one blank space after each species' epithet. It was
invisible at the original csv file, but after Klaus identified the trees
were not in the downloaded file, it made me think there was something wrong
with the species names. I deleted that blank space and now the trees work
fine.

Best regards,
Agus

Post by Upham, Nathan
Hi Agus
I work next to the main developer for the birdtree.org site— glad to help
figure the error if its on our end. I just downloaded a test file (Ericson
sequenced, 100 trees) and it worked as intended including full trees. What
species and settings did you choose for your download, and using what web
browser?
Reply to me off list and we’ll get this sorted.
All the best
—nate
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*Nathan S. Upham, Ph.D. *Postdoctoral Associate, Yale University, Ecology
and Evolutionary Biology
165 Prospect Street
<https://maps.google.com/?q=165+Prospect+Street&entry=gmail&source=g>,
OML 122, New Haven, CT, 06511, USA
personal web: Home <https://n8upham.github.io/> | Research Gate
<https://www.researchgate.net/profile/Nathan_Upham> | Google Scholar
<https://scholar.google.com/citations?user=zIn4NoUAAAAJ&hl=en>
lab pages: Jetz Lab <http://jetzlab.yale.edu/> | NSF VertLife grant
<http://vertlife.org/>
Research Associate, Integrative Research Center, Field Museum of Natural History
Chair, Biodiversity Committee, American Society of Mammalogists
~> Check out the new Mammal Diversity Database
<https://mammaldiversity.org/>
Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
Thanks for that, Klaus!
Regards
Agus
Dear Agustín,
the nexus file on dropbox does not contain any trees.
#NEXUS
[Tree distribution from: The global diversity of birds in space and time;
W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
doi:10.1038/nature11631]
[Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ]
[Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]
BEGIN TREES;
TREE tree_4104 =
TREE tree_9438 =
...
TREE tree_1868 =
TREE tree_0011 =
END;
Looks like your download did not work and the error message from
read.nexus could improve.
Cheers,
Klaus
Dear list,
I am puzzled with this error when importing a bird tree subset from
https://urldefense.proofpoint.com/v2/url?u=https-3A__
birdtree.org_subsets_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=
Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_
wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=QCx_
EErW5SnutNdxWnXm65RyRGtG1st3m0iAmNiulmU&e= .
The subset is supposed to be in nexus format. However,
trees<-read.nexus("output.nex")
missing value where TRUE/FALSE needed
read.tree gives the same error
read.newick gets stuck, it never ends reading in the tree
I tried scanning the file and then several notes appear before the actual
trees Thus, I tried read.annotated.nexus from OutbreakTools.
.annotated.clado.build is not yet implemented.
I tried with several different subsets from different backbones and none
worked.
Here is one: https://urldefense.proofpoint.com/v2/url?u=https-
3A__www.dropbox.com_s_037u6pjr4006o6r_output.nex-3Fdl-3D0&d=DwIFaQ&c=
cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_
wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=
BfBnKVjZjCJ1C8YumcqEIf2FGIDH2pRzLaqMU8gm01g&e=
Somebody has reported this error previously in the internet, but it still
seems to be unsolved.
Thanks in advance and best regards.
Agus
--
Agustín Camacho Guerrero.
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=
Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_
wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=jSdLapf5K-3pnA7_OTck6Zt-
60GpMrs1IZ0AAh8B34E&e=
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
phangorn.org_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=
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--
Agustín Camacho Guerrero.
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=
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60GpMrs1IZ0AAh8B34E&e=
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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