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 < [email protected]> 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 <[email protected]> > 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 < >> [email protected]> 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 < >>> [email protected]> 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 < >>>> [email protected]> 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 - [email protected] >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>>> Searchable archive at >>>>> http://www.mail-archive.com/[email protected]/ >>>>> >>>> >>> >>> -- >>> 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>* > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
