[R-sig-phylo] Simulated phylogenies with character divergence
Hi all, There seem to be an ever growing number of functions for simulating phylogenies along with traits and associated models of evolution. I'm wondering different users suggestions for the simplest way to do the following two cases. This is not for a full paper, but just a side supporting analysis, so it doesn't have to be exhaustive. 1. Simulate a conserved trait (environmental tolerance) along a specified sized phylogeny. 2. Simulate the same conserved trait along the same phylogeny but with the additional of repulsion (character divergence) among closely related species. Extra bonus would be if i could control the strength of phylogenetic conservatism and character divergence in a nice array. If anyone has some general 'psudeo code' or package::function steps in this direction i'd appreciate all feedback. Thanks, Ben Weinstein -- Ben Weinstein PhD Candidate Ecology and Evolution Stony Brook University http://benweinstein.weebly.com/ [[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] Simulated phylogenies with character divergence
Hi all, There seem to be an ever growing number of functions for simulating phylogenies along with traits and associated models of evolution. I'm wondering different users suggestions for the simplest way to do the following two cases. This is not for a full paper, but just a side supporting analysis, so it doesn't have to be exhaustive. 1. Simulate a conserved trait (environmental tolerance) along a specified sized phylogeny. 2. Simulate the same conserved trait along the same phylogeny but with the additional of repulsion (character divergence) among closely related species. Extra bonus would be if i could control the strength of phylogenetic conservatism and character divergence in a nice array. If anyone has some general 'pseudo code' or package::function steps in this direction i'd appreciate all feedback. I'm currently trying to use the growTree inheritance rules in caper, but i haven't had much success. I've also tried tweaking the plgmm.sim function in picante but i can't figure out what parameters would control the repulsion and signal in the trait. Thanks, Ben Weinstein PS: Sorry if i double posted, wasn't sure which email address was signed into the list. -- Ben Weinstein PhD Candidate Ecology and Evolution Stony Brook University http://benweinstein.weebly.com/ [[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] breaking up phylogeny figure
Hi all, I'm wondering if there is a way to plot a phylogeny in R that is broken up and displayed side by side to condense space. I've made a backbone in R that i'd like to make into a figure, but it is too tall. If this isn't the write setup, could someone suggest what program (and format for me to write.tree) from R. I am using windows, in terms of potential third part programs. Thanks, ben -- Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/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
[R-sig-phylo] find mrca of multiple taxa.
Hello all, I'm trying to replace a clade of tips with a single tip, placed at the mrca of all taxa clade (similar Q to here https://stat.ethz.ch/pipermail/r-sig-phylo/2012-March/001895.html). Before i bind tree, I just need to a nice way to identify which node encompasses all descendants. I see many packages and functions, but i can't quite get the result i want. Forgive me if i've just missed this function somewhere, it seems hard to believe it hasn't been written explicitly. Clearly the package phylobase knows which node i want, when i subset by the tips.include library(phylobase) data(geospiza) nodeLabels(geospiza) - paste(N, nodeId(geospiza, internal), sep=) geotree - extractTree(geospiza) ## subset examples tips - c(difficilis, fortis, fuliginosa, fusca, olivacea, pallida, parvulus, scandens) subset(geotree, tips.include=tips) How can i get it to return which node it used, numbered from the original tree? My other attempt was to use expand.grid and mrca through an sapply command to brute force walk through every pair of taxa, and then take the maximum node number (since its farthest up the tree). This seems inelegant, and i'm not convinced it works 100% of the time. Thanks for your input. Ben Weinstein -- Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/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
[R-sig-phylo] retraction
Hi all, Just to be complete for any future readers, the function findMRCA from phytools meets this need. Took me awhile to go through all eight phylogeny related packages i have. Thanks Ben -- Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/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
[R-sig-phylo] Cophenetic repeats
Hi all, I'm trying to decide if this an R error, or an error in how I've implemented branch lengths. When i create the cophenetic matrix for my tree, and look at the relatedness of all tips to a single tip (i.e just looking at one column in the matrix). I find that a large portion of them have identical cophenetic distances. I thought the cophenetic would be the sum of the branch length between tips (patristic distance), therefore there should only be pairs (sister species have equal terminal branch length) with *exactly * the same value. Comparisons from distantly related taxa should be similar, since most of the distance is dictated by the internal branches, but the terminal branch should atleast create some difference. Sorry that i can't really create a reproducible example for the question. Here is some documentation: trx-read.nexus(ColombiaPhylogenyUM.tre) seeds-sample(trx$tip.label,1) sp.weight.alpha-cophenetic(trx)[,seeds] table(sp.weight.alpha)sp.weight.alpha 0 0.00775074 0.1179723 0.2187406 0.2379734 0.23797341 0.2525792 1 1 2 4 3 2 6 0.36612256 0.36612257 0.52326843 0.59034104 0.59034105 0.59034106 0.607038 2 2 2 31 82 29 3 82 of the species have the exact same distance to my selected tip .59034105 Am i using this function correctly? I appreciate the help, Ben Weinstein -- Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/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
[R-sig-phylo] collapse nodes based on node labels
Hello all, Is there an analogous function to ape's di2multi which collapses descendant branches based on an input node? Instead of minimum branch tolerance to create polytomies, what would the best strategy to collapse all descendant branches of node X. I've played around with node.leaves, but haven't had great luck. I'm considering pruning the tree, collapsing the entire subtree and regrafting it on. Similarly to this, is there a way to maintain the original node numbering, even after setting nodelabels? For example if i set my nodelabels to my support values, but still want to highlight the first node in the tree. The support values are non unique (multiple 99s), so it becomes harder to specify commands to specific nodes. I appreciate the help, Ben Weinstein -- Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/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
