Hi Leonardo Best of luck and hopefully you can find a solution that works. If you have a colleague who is able to run bayestraits with no errors, then perhaps try your own data and code with them.
Best wishes Michael Zyphur Director Institute for Statistical and Data Science *instats.org* <http://instats.org> On Sat, 30 Nov 2024 at 00:03, Leonardo Matheus Servino < [email protected]> 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 <[email protected]> > 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 < >> [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>* >>> >> > > -- > 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]/
