Hi Elvira, If you are interested in keeping the "surviving species" from phylogenies, it may be better to use a birth-death model to simulate the trees. There are 3 functions in ape to do this: they are documented in the same help page than drop.fossil() and they have options that make them quite flexible. If you really want to use rtree(), then, as rightly pointed out by Liam, the (default) uniform distribution may not be the right choice to generate branch lengths.
Best, Emmanuel ----- Le 26 Aoû 20, à 8:33, Elvira D`bastiani elviradbasti...@gmail.com a écrit : > Hi Liam, > > That, are branch lengths. I know that these NaNs correspond to the species > that have become extinct. > When I talk about 'delete' the NaNs, I want my newick not to have those > branches with NaNs. > > You helped me! > Thank you for talking about it with me! > > All the best, > > Em ter., 25 de ago. de 2020 às 22:14, Liam J. Revell <liam.rev...@umb.edu> > escreveu: > >> Hi Elvira. >> >> In your Newick string those NaN are branch lengths, not taxon labels. >> >> What do you mean by 'delete' the NaNs? You can set them to zero, as >> follows: >> >> tree$edge.length[is.na(tree$edge.length)]<-0 >> >> but then you get a tree that looks like this: >> >> http://www.phytools.org/blog/Elvira-tree.png >> >> so it's kind of hard to tell which taxa are extinct.... >> >> Sorry I can't be of more help! All the best, Liam >> >> Liam J. Revell >> University of Massachusetts Boston >> Universidad Católica de la Ssma Concepción >> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org >> >> Academic Director UMass Boston Chile Abroad: >> https://www.umb.edu/academics/caps/international/biology_chile >> >> On 8/25/2020 9:00 PM, Elvira D`bastiani wrote: >> > **[EXTERNAL SENDER] >> > >> > Hi Liam >> > >> > Also thank you for your informative answer. However, I don't want to >> > simulate trees. For example one of my trees looks like this: >> > >> > (2:17, (3: 258, (4: 1, (5: 1, ((7:47, (8:13, ((11: 1, (13: 46,9: 60): >> > 35): 35): 26, (10: 3, (12: 7, ((15: 4,14: 17): NaN, 6: NaN): - 904): >> > 53): 0): 34): 31): NaN, 1: NaN): - 621): 1): 138): 53); >> > >> > Here, I need to delete these NaN from the phylo file. >> > >> > I believe that with these functions I am unable to delete these NaN or >> > extract only the surviving species. >> > >> > Thank you for the help. >> > >> > Elvira. >> > >> > Em ter., 25 de ago. de 2020 às 17:33, Liam J. Revell >> > <liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>> escreveu: >> > >> > Dear Elvira. >> > >> > I'm not sure what's going on with the NaN values, but one issue that >> I >> > see with your example is that ape::drop.fossil identifies fossil >> > lineages by finding those that end before the present. Since rtree >> just >> > splits the tree randomly & samples the edge lengths from a uniform >> > distribution, this will leave you with only one lineage! >> > >> > To see how the function should work you could try something like: >> > >> > set.seed(99) >> > tree<-pbtree(n=15,b=1,d=0.2) >> > plotTree(tree) >> > plotTree(pruned<-drop.fossil(tree)) >> > >> > Hopefully this leaves things a bit clearer. >> > >> > For fun, also try: >> > >> > par(mfrow=c(1,1),mar=c(5.1,4.1,2.1,2.1),bty="n") >> > ltt(tree,lty="dashed",log.lineages=FALSE,log="y") >> > ltt(pruned,lty="solid",add=TRUE,log.lineages=FALSE, >> > log="y") >> > legend("topleft",c("observed","reconstructed"), >> > lty=c("dashed","solid"),bty="n") >> > >> > All the best, Liam >> > >> > Liam J. Revell >> > University of Massachusetts Boston >> > Universidad Católica de la Ssma Concepción >> > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615417539&sdata=5%2F1PtYD6DMW7gK7ef3QiRvXSeI0bozADU5lgrW9qPq0%3D&reserved=0 >> > >> > >> > Academic Director UMass Boston Chile Abroad: >> > https://www.umb.edu/academics/caps/international/biology_chile >> > >> > On 8/25/2020 4:21 PM, Elvira D`bastiani wrote: >> > > [EXTERNAL SENDER] >> > > >> > > Hi, >> > > >> > > I'm a beginner with phylogeny analysis. I'm having trouble >> > extracting only >> > > the surviving species from the phylogenies of my model. >> > > >> > > I used the drop.fossil (fPar) functions from ape and the >> drop.extinct >> > > (fPar) from geiger. But it is not deleting the way I need it. >> > > >> > > Running example correctly: >> > > my.tree = rtree (15, rooted = TRUE, tip.label = NULL, br = runif) >> > #random >> > > tree in phylo format >> > > class (my.tree) >> > > my.tree $ edge.length #I need this information without NaN. >> > > >> > >> my.tree$edge.length [1] 0.53879430 0.71471795 0.40579050 >> > 0.15278814 0.34023276 0.62665485 >> > > [7] 0.05737268 0.85166764 0.21264535 0.53946203 0.13648759 >> > 0.32486514 >> > > [13] 0.62107629 0.25598225 0.63487580 0.48567211 0.93817692 >> > 0.85750154 >> > > [19] 0.37088354 0.31420183 0.82853436 0.45184151 0.31587841 >> > 0.09780854 >> > > [25] 0.06490054 0.68945737 0.66805060 0.90454665 >> > > >> > > >> > > However in the same tree format (phylo format) in my analysis the >> > > edge.length comes out with NaN. Even after using the drop.fossil >> > (fPar) or >> > > drop.extinct (fPar) functions. It looks like this: >> > > >> > >> fPar$edge.length [1] 17 53 258 138 1 1 1 -621 >> > NaN 47 31 13 34 26 >> > > [15] 1 35 46 60 0 3 53 7 -904 NaN 4 17 >> > NaN NaN >> > > >> > > >> > > Is there any way to delete these NaN? >> > > >> > > >> > > Thanks in advance for the answer >> > > >> > > Best wishes >> > > >> > > e. >> > > >> > > -- >> > > >> > > *Elvira D'Bastiani*Doutoranda em Ecologia e Conservação >> > > Laboratório de Interações Biológicas >> > > Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brasil >> > > >> > * >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felviradbastiani.wixsite.com%2Fecoevo&data=02%7C01%7Cliam.revell%40umb.edu%7C40eeed8a082f4da7db1008d8493475c7%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637339836973837977&sdata=u5GV45faTYzUsRhhQpCQc9C5%2BSLDcrzE6mcyNlRNVUU%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felviradbastiani.wixsite.com%2Fecoevo&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615427534&sdata=sbljMhPeAIouSR2%2BKxEcRLpN34jrH99wtt5eOu3jLzY%3D&reserved=0 >> > >> > > >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felviradbastiani.wixsite.com%2Fecoevo&data=02%7C01%7Cliam.revell%40umb.edu%7C40eeed8a082f4da7db1008d8493475c7%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637339836973837977&sdata=u5GV45faTYzUsRhhQpCQc9C5%2BSLDcrzE6mcyNlRNVUU%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felviradbastiani.wixsite.com%2Fecoevo&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615427534&sdata=sbljMhPeAIouSR2%2BKxEcRLpN34jrH99wtt5eOu3jLzY%3D&reserved=0 >> >>* >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > _______________________________________________ >> > > R-sig-phylo mailing list - R-sig-phylo@r-project.org >> > <mailto:R-sig-phylo@r-project.org> >> > > >> > >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C40eeed8a082f4da7db1008d8493475c7%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637339836973837977&sdata=IdKD9kLK5Xh3yt1BDkA8n1srFFr5paq%2BSJAfivocP%2B4%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615437526&sdata=5cHozKE2yAxgIAicWfbSuoCPOTUDUJxnxzk62d2vDHo%3D&reserved=0 >> > >> > > Searchable archive at >> > >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C40eeed8a082f4da7db1008d8493475c7%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637339836973837977&sdata=5poPu09PsiPLuPYLC4itm9ouYfTXHC7ZNapkveNlkBU%3D&reserved=0 >> > < >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615457511&sdata=GWxl8BY1kA5Ub5wVDkvaZ1FqxZ7CWEnWpS5JHb4XcZQ%3D&reserved=0 >> > >> > > >> > >> > >> > >> > -- >> > *Elvira D'Bastiani >> > *Doutoranda em Ecologia e Conservação >> > Laboratório de Interações Biológicas >> > Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brasil >> > _https://elviradbastiani.wixsite.com/ecoevo >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felviradbastiani.wixsite.com%2Fecoevo&data=02%7C01%7Cliam.revell%40umb.edu%7Ce8848bf509ed41e5115408d8495b7db0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637340004615467512&sdata=BB8HoI1MISexdx94U14vY3K3ix8Tf6SA%2BZ9EZU0%2FLTM%3D&reserved=0 >> >_ >> > > > -- > > *Elvira D'Bastiani*Doutoranda em Ecologia e Conservação > Laboratório de Interações Biológicas > Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brasil > *https://elviradbastiani.wixsite.com/ecoevo > <https://elviradbastiani.wixsite.com/ecoevo>* > > [[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/ _______________________________________________ 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/
