Dear Leonardo,
I think Mike's suggestion by running bayestraits mannually is a nice idea.
also, may i know which version of bayestraits you are using? there could be a
change in the requirement of the input format in its newest version (v4). That
said, you might wish to change to bayestraits v3 and see if it works. I see
others also report a similar problem. Error: Taxa ".." is not present in tree 1
/ error in BayesTrait v.4. Or would you pls mind sharing with everyone here or
with me your data so that we can take a closer look?
best,sishuo
On Friday, November 29, 2024 at 11:32:42 p.m. GMT+8, Leonardo Matheus
Servino <leonardomserv...@gmail.com> wrote:
Michael,
I checked and there is no mismatch between the trees and the dataset.
This is getting too much frustrating for me and for now, I think I'll give
up on that.
Anyway, I appreciate your help.
Em sex., 29 de nov. de 2024 às 09:43, Michael Zyphur <mzyp...@instats.org>
escreveu:
> Hi Leonardo
>
> There may be a mismatch between the taxa names in your dataset and those
> in your tree file. The taxa names in your dataset (final_data_bt) must
> match exactly the names in your tree (frog_newtree_50), meaning no extra
> space or different capitalizations or special characters/formatting
> differences. Try this:
>
> data_taxa <- final_data_bt[, 1]
> tree_taxa <- frog_newtree_50$tip.label
> mismatched_taxa <- setdiff(data_taxa, tree_taxa)
> print(mismatched_taxa)
> tree_only_taxa <- setdiff(tree_taxa, data_taxa)
> print(tree_only_taxa)
>
> Hopefully this shows where the issues might be coming from.
>
>
> Best wishes
>
> Michael Zyphur
> Director
> Institute for Statistical and Data Science
> *instats.org* <http://instats.org>
>
>
> On Fri, 29 Nov 2024 at 23:20, Leonardo Matheus Servino <
> leonardomserv...@gmail.com> wrote:
>
>> Michael,
>>
>> Thank you. Unfortunately I already tried to run in the terminal and got
>> errors as
>>
>> Error: Taxa Phyllomedusa_rohdei is not present in tree 1
>> Error: Taxa Phyllomedusa_ayeaye is not present in tree 1
>> Error: Taxa Phyllomedusa_megacephala is not present in tree 1
>> Error: Taxa Phyllomedusa_azurea is not present in tree 1
>> Error: Taxa Phyllomedusa_hypochondrialis is not present in tree 1
>> Error: Taxa Phyllomedusa_nordestina is not present in tree 1
>> Error: Taxa Agalychnis_dacnicolor is not present in tree 1
>> Error: Taxa Agalychnis_spurrelli is not present in tree 1
>> Error: Taxa Agalychnis_saltator is not present in tree 1
>> Error: Taxa Agalychnis_callidryas is not present in tree 1
>> Error: Taxa Agalychnis_annae is not present in tree 1
>> .
>> .
>> .
>> Basically, the program is not identifying my taxa in the trees. I
>> exported the data following the data format required and I don't know where
>> is the problem.
>>
>> Em sex., 29 de nov. de 2024 às 09:04, Michael Zyphur <mzyp...@instats.org>
>> escreveu:
>>
>>> Hi Leonardo
>>>
>>> Sorry, it looks like it doesn't support a debug mode - my mistake. Maybe
>>> try manually running BayesTraits. Export the data and tree files:
>>>
>>> write.table(final_data_bt, "data.txt", row.names = FALSE, col.names =
>>> TRUE, quote = FALSE) ape::write.tree(frog_newtree_50, file = "tree.txt")
>>>
>>> The run it through a terminal or command prompt:
>>>
>>> BayesTraits tree.txt data.txt
>>>
>>> then you should be able to input your commands manually when prompted.
>>> If it runs successfully, the issue is with how btw is interfacing with
>>> BayesTraits. If this doesn't work then maybe try checking the BayesTraits
>>> Path in btw
>>>
>>> results_1 <- bayestraits(
>>> data = final_data_bt,
>>> tree = frog_newtree_50,
>>> commands = command_vec1,
>>> bt_path = "/full/path/to/BayesTraits"
>>> )
>>>
>>> Replace "/full/path/to/BayesTraits" with the actual path to the
>>> BayesTraits executable.
>>>
>>> Hope this helps!
>>>
>>>
>>> Best wishes
>>>
>>> Michael Zyphur
>>> Director
>>> Institute for Statistical and Data Science
>>> *instats.org* <http://instats.org>
>>>
>>>
>>> On Fri, 29 Nov 2024 at 22:00, Leonardo Matheus Servino <
>>> leonardomserv...@gmail.com> wrote:
>>>
>>>> Dear Michael,
>>>>
>>>> Thanks for your answer. I tried to run in debug mode, but the console
>>>> simply gave me another error message:
>>>>
>>>> Error in bayestraits(data = final_data_bt, tree = frog_newtree_50,
>>>> commands = command_vec1, :
>>>> unused argument (debug = TRUE)
>>>>
>>>>
>>>> Em qui., 28 de nov. de 2024 às 21:43, Michael Zyphur <
>>>> mzyp...@instats.org> escreveu:
>>>>
>>>>> Hi Leonardo
>>>>>
>>>>> The "btw can't find a log file" error is common with the btw package
>>>>> when the underlying BayesTraits executable fails to run properly or save
>>>>> its output. Assuming that 1) the BayesTraits installation is fine, 2) the
>>>>> file and path permissions are all ok, and 3) your input data format is
>>>>> appropriate given the requirements, then you can try running it in debug
>>>>> mode to troubleshoot the problem with something like:
>>>>>
>>>>> results_1 <- bayestraits(
>>>>> data = final_data_bt,
>>>>> tree = frog_newtree_50,
>>>>> commands = command_vec1,
>>>>> debug = TRUE
>>>>> )
>>>>>
>>>>> This may provide clues about where the process is failing.
>>>>>
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Michael Zyphur
>>>>> Director
>>>>> Institute for Statistical and Data Science
>>>>> *instats.org* <http://instats.org>
>>>>>
>>>>>
>>>>> On Fri, 29 Nov 2024 at 04:50, Leonardo Matheus Servino <
>>>>> leonardomserv...@gmail.com> wrote:
>>>>>
>>>>>> Dear group,
>>>>>>
>>>>>> Anyone here is familiar with package btw?I'm trying to perform some
>>>>>> analysis with my dataset, but I got the following error message:
>>>>>>
>>>>>> command_vec1 <- c("3", "2")
>>>>>>
>>>>>>
>>>>>> results_1 <- bayestraits(data = final_data_bt, tree = frog_newtree_50,
>>>>>> commands = command_vec1)
>>>>>>
>>>>>> Error in bayestraits(data = final_data_bt, tree = frog_newtree_50,
>>>>>> commands = command_vec1) :
>>>>>> Something went wrong: btw can't find a log file
>>>>>>
>>>>>>
>>>>>> Has anyone here ever faced this error?
>>>>>>
>>>>>> Cheers
>>>>>> --
>>>>>> Leonardo Matheus Servino
>>>>>> Pós-graduação em Ecologia
>>>>>>
>>>>>> Departamento de Ecologia
>>>>>> Universidade de São Paulo
>>>>>> Rua do Matão, Trav. 14, n˚ 101
>>>>>> Cid. Universitária - São Paulo, SP
>>>>>> 05508-090
>>>>>> Brasil
>>>>>>
>>>>>> *Lattes <http://lattes.cnpq.br/3993528079964952> - **ResearchGate
>>>>>> <https://www.researchgate.net/profile/Leonardo_Servino> - ORCID
>>>>>> <https://orcid.org/0000-0002-6772-376X> - LinkedIn
>>>>>> <https://www.linkedin.com/in/leonardo-matheus-servino-8379ba1b2>*
>>>>>>
>>>>>> [[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/
>>>>>>
>>>>>
>>>>
>>>> --
>>>> Leonardo Matheus Servino
>>>> Pós-graduação em Ecologia
>>>>
>>>> Departamento de Ecologia
>>>> Universidade de São Paulo
>>>> Rua do Matão, Trav. 14, n˚ 101
>>>> Cid. Universitária - São Paulo, SP
>>>> 05508-090
>>>> Brasil
>>>>
>>>> *Lattes <http://lattes.cnpq.br/3993528079964952> - **ResearchGate
>>>> <https://www.researchgate.net/profile/Leonardo_Servino> - ORCID
>>>> <https://orcid.org/0000-0002-6772-376X> - LinkedIn
>>>> <https://www.linkedin.com/in/leonardo-matheus-servino-8379ba1b2>*
>>>>
>>>
>>
>> --
>> Leonardo Matheus Servino
>> Pós-graduação em Ecologia
>>
>> Departamento de Ecologia
>> Universidade de São Paulo
>> Rua do Matão, Trav. 14, n˚ 101
>> Cid. Universitária - São Paulo, SP
>> 05508-090
>> Brasil
>>
>> *Lattes <http://lattes.cnpq.br/3993528079964952> - **ResearchGate
>> <https://www.researchgate.net/profile/Leonardo_Servino> - ORCID
>> <https://orcid.org/0000-0002-6772-376X> - LinkedIn
>> <https://www.linkedin.com/in/leonardo-matheus-servino-8379ba1b2>*
>>
>
--
Leonardo Matheus Servino
Pós-graduação em Ecologia
Departamento de Ecologia
Universidade de São Paulo
Rua do Matão, Trav. 14, n˚ 101
Cid. Universitária - São Paulo, SP
05508-090
Brasil
*Lattes <http://lattes.cnpq.br/3993528079964952> - **ResearchGate
<https://www.researchgate.net/profile/Leonardo_Servino> - ORCID
<https://orcid.org/0000-0002-6772-376X> - LinkedIn
<https://www.linkedin.com/in/leonardo-matheus-servino-8379ba1b2>*
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