[R-sig-phylo] Is my subset of species random?
Dear list, I am now browsing through a large phylogeny trying to select species for multilocus analysis. I am, of course, constrained at least by availability of material and thus I cannot pick a purely random subset of species. Therefore, I would like to know how much is any particular selection non-random (with implications for subsequent analyses). In an ideal random sampling the picks are completely independent - if you know that some species was sampled it tells you nothing about sampling of any other species. In fact I need to know whether branches retained after sampling are on the original phylogeny predictably separated by the dropped branches. If sampling is random (or close to complete), there is no regularity in distribution of dropped branches. Otherwise, some pattern is (at least theoretically) recognizable - e.g. in diversified sampling they tend to be closer to tips, in other cases they may be preferably in some clades. Does any measure of this kind exist (ideally implemented in R)? Best wishes, Ondrej Mikula -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[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] mulRF distance
Dear colleagues, is anybody aware of any R implementation of mulRF distance introduced by Chaudhary et al. 2013 & 2014? Best regards, Ondrej -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[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] how to add phylogenetic tree to an existing plot
Dear list, does any simple trick exist to add phylogenetic tree to an existing plot? And if not, would it be complicated to build in an argument 'add' to 'plot.phylo' function (with the same effect as in many other plotting functions)? I want to underlay my phylogeny with some metadata and with such argument it would become as easy as to overlay it. Best wishes, Ondřej -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[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] R-sig-phylo Digest, Vol 80, Issue 4
Dear Roi, perhaps you could consider paper Zapata, F. and I. Jimenez. 2012. Species Delimitation: Inferring Gaps in Morphology across Geography. Systematic Biology 61:179-194. ( http://sysbio.oxfordjournals.org/content/61/2/179) where the authors introduce tolerance regions of multivariate normal distributions. Associated are also some R scripts which I have modified to be applicable for 2 dimensional case. I could provide you with them if you were interested. Best wishes, Ondřej On 16 September 2014 12:00, r-sig-phylo-requ...@r-project.org wrote: Send R-sig-phylo mailing list submissions to r-sig-phylo@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-phylo or, via email, send a message with subject or body 'help' to r-sig-phylo-requ...@r-project.org You can reach the person managing the list at r-sig-phylo-ow...@r-project.org When replying, please edit your Subject line so it is more specific than Re: Contents of R-sig-phylo digest... Today's Topics: 1. points overlap in multidimensional space (Roi Holzman) -- Message: 1 Date: Tue, 16 Sep 2014 12:28:05 +0300 From: Roi Holzman roi.holz...@gmail.com To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] points overlap in multidimensional space Message-ID: a52d461b-9eb8-4c4f-8072-f084e1f23...@gmail.com Content-Type: text/plain; charset=UTF-8 fellow R-sig-phylo users- I know this is not strictly a phylogenetic question, but I was hoping someone can help I have a 6 diminutional morphospace of observed traits (6 traits, 110 observations) and another morphospace of simulated traits (same dimensions). I want to quantify the overlap between the two morphospaces. my original idea was to produce a kernel density estimation using one matrix, and ask how many points from the other matrix fall within a a certain contour (say the 50% contour). I used package ?ks? to produce a kernel, as following: library(ks) set.seed(8192) x1 - rmvnorm.mixt(110, mus=rep(0,6), diag(6)) set.seed(4192) x2 - rmvnorm.mixt(110, mus=rep(0,6), diag(6)) fhat - kde(x1, eval.points=x1) ct - contourLevels(fhat, cont=50) but I could not figure out the second part, e.g. how many points from x2 fall within the kde that was calculated based on x1 . any ideas? maybe I should approach this differently? I already tried reducing dimensionality using PCA, and I could reduce the data to 3x110, but not less many thanks! Roi Roi Holzman, Ph.D. Department of Zoology, Tel Aviv University and the Inter-University Institute for Marine Sciences in Eilat Tel. (972)-8-6360-134 holz...@post.tau.ac.il http://iui-eilat.ac.il/People/AcademicStaffProfile.aspx?sid=106 [[alternative HTML version deleted]] -- ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo End of R-sig-phylo Digest, Vol 80, Issue 4 ** -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[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] phyloxml
Dear all, are you aware of any routine importing phylogenetic trees in .phyloxml format into R? Best wishes, OndÅej -- OndÅej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[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] basal dichotomy in phylo object
Hello, I have an unrooted tree, but I know that basal dichotomy is between nodes labeled 174 and 500. I am wandering how to indicate it in the object of class 'phylo'. I tried 'root' function of 'ape' but with no success. I will be grateful for any advice. Best wishes Ondrej Mikula -- Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] basal dichotomy in phylo object
Dear Liam and Klaus, thanks a lot for your suggestions. 174 and 500 are actually labels of the nodes, but I used their numbers instead and it works well. All the best Ondrej On 25 October 2011 17:28, Liam J. Revell liam.rev...@umb.edu wrote: On seeing this email, I also realized that to have node numbers up to 500, that you must have 174 tips (i.e., node number 174 is actually a tip), meaning the code I gave before should be: rooted.tree-reroot(tree,node.**number=174,position=tree$edge.** length[tree$edge[,2]==174]/2) I hope this helps. Also, thanks Klaus. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 10/25/2011 11:19 AM, Klaus Schliep wrote: Dear Ondrej, there is also a function midpoint in phangorn, which roots the trees in the middle of the longest path. Maybe you are lucky and your edge (500, 174) is one in the middle. Regards, Klaus On 10/25/11, Liam J. Revellliam.rev...@umb.edu wrote: In my phytools package (http://cran.r-project.org/**web/packages/phytools/index.**htmlhttp://cran.r-project.org/web/packages/phytools/index.html) there is a function reroot() that is really just a simple wrapper around root() that allows you to root along internal or terminal edges (rather than only at nodes). In your example, assuming that the node 500 is tipward of 174 in the tree, to re-root the tree halfway along the edge leading to node number 500 (in tree$edge), you would just do: rooted.tree-reroot(tree,node.**number=500,position=tree$edge.** length[tree$edge[,2]==500]/2) I think. All the best, Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 10/25/2011 10:44 AM, OndÅej Mikula wrote: Hello, I have an unrooted tree, but I know that basal dichotomy is between nodes labeled 174 and 500. I am wandering how to indicate it in the object of class 'phylo'. I tried 'root' function of 'ape' but with no success. I will be grateful for any advice. Best wishes Ondrej Mikula __**_ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/**listinfo/r-sig-phylohttps://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] squared-change parsimony reconstruction
Dear all, I would like to make squared-change parsimony reconstruction of ancestral states for continuous multivariate data as recommended by: Rohlf, F. J. 2002. Geometric morphometrics in phylogeny. Pp. 175-193 in Forey, P. and N. Macleod (eds.) Morphology, shape and phylogenetics. Francis Taylor: London. Is it currently possible in R? Best regards Ondrej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
