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

[Agus Camacho]

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

2018-02-14 0:33 GMT-02:00 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
> ,
> OML 122, New Haven, CT, 06511, USA
>
> personal web: Home  | Research Gate
>  | Google Scholar
> 
> lab pages: Jetz Lab  | NSF VertLife grant
> 
>
> Research Associate, Integrative Research Center, Field Museum of Natural
> History
> Chair, Biodiversity Committee, American Society of Mammalogists
>  ~> Check out the new Mammal Diversity Database
> 
> Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
>
> e: nathan.up...@yale.edu | Skype: nate_upham | Twitter: @n8_upham
>
>
>
>
>
>
> On Feb 13, 2018, at 9:11 PM, Agus Camacho  wrote:
>
> Thanks for that, Klaus!
> Regards
> Agus
>
> 2018-02-13 22:51 GMT-02:00 Klaus Schliep :
>
> 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
>
>
> On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho 
> 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_=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=
> Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_
> wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=QCx_
> EErW5SnutNdxWnXm65RyRGtG1st3m0iAmNiulmU= .
>
> 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=DwIFaQ=
> cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_
> wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=
> BfBnKVjZjCJ1C8YumcqEIf2FGIDH2pRzLaqMU8gm01g=
>
> 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=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=
> Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_
> wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=jSdLapf5K-3pnA7_OTck6Zt-
> 60GpMrs1IZ0AAh8B34E=
> 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]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> 

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

[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, OML 122, New Haven, CT, 06511, USA

personal web: Home | Research 
Gate | Google 
Scholar
lab pages: Jetz Lab | NSF VertLife 
grant

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

e: nathan.up...@yale.edu | Skype: nate_upham | 
Twitter: @n8_upham






On Feb 13, 2018, at 9:11 PM, Agus Camacho 
> wrote:

Thanks for that, Klaus!
Regards
Agus

2018-02-13 22:51 GMT-02:00 Klaus Schliep 
>:

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


On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho 
>
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_=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=QCx_EErW5SnutNdxWnXm65RyRGtG1st3m0iAmNiulmU=
 .

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=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=BfBnKVjZjCJ1C8YumcqEIf2FGIDH2pRzLaqMU8gm01g=

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=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=jSdLapf5K-3pnA7_OTck6Zt-60GpMrs1IZ0AAh8B34E=
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]]

___
R-sig-phylo mailing list - 
R-sig-phylo@r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=KE5rlr3daja6JHbUqJvP2AlAphe78oeV_0vZiCCNRYw=
Searchable archive at 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2D=DwIFaQ=cjytLXgP8ixuoHflwc-poQ=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM=_wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU=szj7UYL8tC9dS7P9aTAKywcv5WlOuztpY7wJzVlAtQk=
sig-ph...@r-project.org/




--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, 

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

[Agus Camacho]

Thanks for that, Klaus!
Regards
Agus

2018-02-13 22:51 GMT-02:00 Klaus Schliep :

> 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
>
>
> On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho 
> wrote:
>
>> 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.
>>
>> [[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-ph...@r-project.org/
>>
>
>
>
> --
> 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]]

___
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] importing trees from birdtree.org into R

[Klaus Schliep]

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


On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho 
wrote:

> 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.
>
> [[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-ph...@r-project.org/
>



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

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

[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")

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.

[[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/