[R-sig-phylo] utilise more data by making polytomies
Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add those tips in as a polytomy with their congenerics present on the tree. Is there a method in R that would help me to do this? Many thanks Henry [[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/
Re: [R-sig-phylo] utilise more data by making polytomies
Something similar to this is in phytools (http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html), though not yet on CRAN. Let me know if this is what you're thinking of. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org -- Sent from Windows Phone -Original Message- From: Ferguson-Gow, Henry Sent: 2/25/2014 10:23 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] utilise more data by making polytomies Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add those tips in as a polytomy with their congenerics present on the tree. Is there a method in R that would help me to do this? Many thanks Henry [[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/ [[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/
Re: [R-sig-phylo] utilise more data by making polytomies
Hi, There is also the stickTip function: http://rleca.pbworks.com/w/file/fetch/40813743/stickTips_1.2.html it is possible to tweak the code for more specific things... Best, Julien From: liam.rev...@umb.edu Date: Tue, 25 Feb 2014 10:32:36 -0500 To: h.ferguson-...@ucl.ac.uk; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] utilise more data by making polytomies Something similar to this is in phytools (http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html), though not yet on CRAN. Let me know if this is what you're thinking of. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org -- Sent from Windows Phone -Original Message- From: Ferguson-Gow, Henry Sent: 2/25/2014 10:23 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] utilise more data by making polytomies Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add those tips in as a polytomy with their congenerics present on the tree. Is there a method in R that would help me to do this? Many thanks Henry [[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/ [[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/ [[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/
Re: [R-sig-phylo] utilise more data by making polytomies
At the risk of inundating you with options, Henry, there is also expandTaxonTree in the package paleotree (on CRAN) which is similar to the above, but also lets you collapse higher taxa you list as paraphyletic, which can be useful if the taxonomic work of your group has never been concerned with monophyly. Cheers, -Dave On Tue, Feb 25, 2014 at 3:33 PM, Julien Clavel julien.cla...@hotmail.frwrote: Hi, There is also the stickTip function: http://rleca.pbworks.com/w/file/fetch/40813743/stickTips_1.2.html it is possible to tweak the code for more specific things... Best, Julien From: liam.rev...@umb.edu Date: Tue, 25 Feb 2014 10:32:36 -0500 To: h.ferguson-...@ucl.ac.uk; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] utilise more data by making polytomies Something similar to this is in phytools ( http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html), though not yet on CRAN. Let me know if this is what you're thinking of. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org -- Sent from Windows Phone -Original Message- From: Ferguson-Gow, Henry Sent: 2/25/2014 10:23 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] utilise more data by making polytomies Hi All I have a large dataset and a large tree, however the intersection between them both is quite low. As a supplement to analyses solely on the species that appear in both the dataset and the tree I thought I could take the species that are present in the dataset and not the tree, and add those tips in as a polytomy with their congenerics present on the tree. Is there a method in R that would help me to do this? Many thanks Henry [[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/ [[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/ [[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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html [[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] dropping taxa from list of trees
Hi all, I have an issue with using the drop.random to drop taxa from a set of simulated trees. When I try to give the list as input it shows an error: Error in drop.random(simtrees, 937) : object phy is not of class phylo I also tried using lapply and it keeps showing the same message. Thanks in advance for your help! Juanita _ Here is the code I have used: treesim-sim.bd.taxa.age(n=1008, numbsim=1000, lambda=9.111433e-02, mu=3.242355e-07, frac = 1, age=31, mrca = FALSE) drop.random(treesim,937) Error in drop.random(treesim, 937) : object phy is not of class phylo lapply(simtrees, drop.random (simtrees,937)) Error in drop.random(simtrees, 937) : object phy is not of class phylo -- Utah State University Department of Biology 5305 Old Main Hill Logan, UT/ USA 84322 (435) 797-0358 [[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/
Re: [R-sig-phylo] dropping taxa from list of trees
Hi Juanita try: lapply(simtrees, drop.random, n = 937) when using lapply (or any of the apply family) you need to specify additional arguments taken by the function youre applying by name, along with their values. graham Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edumailto:slat...@si.edu www.fourdimensionalbiology.comhttp://www.fourdimensionalbiology.com On Feb 25, 2014, at 9:49 PM, Juanita Rodriguez juanitarodrigu...@gmail.commailto:juanitarodrigu...@gmail.com wrote: Hi all, I have an issue with using the drop.random to drop taxa from a set of simulated trees. When I try to give the list as input it shows an error: Error in drop.random(simtrees, 937) : object phy is not of class phylo I also tried using lapply and it keeps showing the same message. Thanks in advance for your help! Juanita _ Here is the code I have used: treesim-sim.bd.taxa.age(n=1008, numbsim=1000, lambda=9.111433e-02, mu=3.242355e-07, frac = 1, age=31, mrca = FALSE) drop.random(treesim,937) Error in drop.random(treesim, 937) : object phy is not of class phylo lapply(simtrees, drop.random (simtrees,937)) Error in drop.random(simtrees, 937) : object phy is not of class phylo -- Utah State University Department of Biology 5305 Old Main Hill Logan, UT/ USA 84322 (435) 797-0358 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto:R-sig-phylo@r-project.org https://urldefense.proofpoint.com/v1/url?u=https://stat.ethz.ch/mailman/listinfo/r-sig-phylok=diZKtJPqj4jWksRIF4bjkw%3D%3D%0Ar=9yz%2F9T5DbvC96h83J%2BUFBQ%3D%3D%0Am=nBHH4FozRe%2BJBfaYNGYL8YxZ3Qs5Kk4u7XWcLurz4LU%3D%0As=629a8efb96259d10466e94079ab3b36b6d07e293356889f6fedc23b6c771f259 Searchable archive at https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/r-sig-phylo%40r-project.org/k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0Ar=9yz%2F9T5DbvC96h83J%2BUFBQ%3D%3D%0Am=nBHH4FozRe%2BJBfaYNGYL8YxZ3Qs5Kk4u7XWcLurz4LU%3D%0As=5524830b2278d27fff1850cbc75e4875d7e182861b1b072624cd43cb509afad6 [[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/
