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>* [[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/
