[R-sig-phylo] problem with phylo.toBackbone

[Felipe Rossetto]

Hi everyone,

I am using the phylo.toBackbone function of phytools using an ultrametric
tree.
When I ran the command obj<-phylo.toBackbone(tree), a message ''Error in
match(x, table, nomatch = 0L) : argument "trans" is missing, with no
default'' appeared. Is the problem related to the fact I used an
ultrametric tree?

Many thanks in advance

felipe

Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7

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[Liam J. Revell]

Hi Felipe.

What version of phytools are you using? A very old phytools version did
not default to interactive mode if no translation table (trans) was
supplied.

Otherwise, I do not know - but it should not be because the tree is not
ultrametric.

All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

Post by Felipe Rossetto
Hi everyone,
I am using the phylo.toBackbone function of phytools using an ultrametric
tree.
When I ran the command obj<-phylo.toBackbone(tree), a message ''Error in
match(x, table, nomatch = 0L) : argument "trans" is missing, with no
default'' appeared. Is the problem related to the fact I used an
ultrametric tree?
Many thanks in advance
felipe
Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
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[Liam J. Revell]

Hi Felipe.

Yes, your phytools version is from late 2015 and I added the interactive
feature in summer 2016
(http://blog.phytools.org/2016/06/interactive-version-of-phylotobackbone.html).
To update all packages you can run (in a fresh R session without any
other sessions open):

update.packages()

however, if you have an older R version installed you may not get the
most recent package versions from this command.

Alternatively, you can install the development version of phytools from
GitHub using the package devtools. First install & load devtools from
within R and then run:

install_github("liamrevell/phytools")

I hope this is of some help. All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

Hi Laim,
the version is 0.5.10. maybe this verison does not support the functiom,
right?''
Is there a command for updating the version?
Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
Hi Felipe.
What version of phytools are you using? A very old phytools version
did not default to interactive mode if no translation table (trans)
was supplied.
Otherwise, I do not know - but it should not be because the tree is
not ultrametric.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
<http://faculty.umb.edu/liam.revell/>
Hi everyone,
I am using the phylo.toBackbone function of phytools using an ultrametric
tree.
When I ran the command obj<-phylo.toBackbone(tree), a message ''Error in
match(x, table, nomatch = 0L) : argument "trans" is missing, with no
default'' appeared. Is the problem related to the fact I used an
ultrametric tree?
Many thanks in advance
felipe
Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
<http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7>
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