[R-sig-phylo] Plotting ancestral reconstructions on subtrees

Dear all, I am attempting to plot ancestral reconstructions (using asr.marginal in Diversitree) of a discrete trait on a number of subtrees (subtree=T in ape), but I'm having trouble assigning node probabilites and tip states to the correct nodes and tips. I have been using the following

[R-sig-phylo] atomic vector for write.nexus

Hello, This is Elaine. I am using the command write.nexusin package (ape) to generate a nexus file after pruning a phylogeny tree. However, an error appeared, saying Error in obj[[i]]$tip.label : $ operator is invalid for atomic vectors I searched the archive but found no similar experience in

[R-sig-phylo] Fwd: atomic vector for write.nexus

I changed pruned.tree to tree.pruned. The error still existed. Elaine -- Forwarded message -- From: Elaine Kuo elaine.kuo...@gmail.com Date: Fri, Apr 5, 2013 at 6:12 PM Subject: atomic vector for write.nexus To: r-sig-phylo@r-project.org Hello, This is Elaine. I am using the

[R-sig-phylo] pruning a tree

Hello This Elaine. I tried to prune a phylogeny tree using two methods based on the code attached. Method 1 returned the tip.label sharing between birddata and birdtree. Method 2 returned nothing. Please kindly indicate why Method 2 failed to prune the tree. Also, please kindly

Re: [R-sig-phylo] ML ancestral state reconstruction using different softwares

Jingchun, Thanks to Daniel for giving a detailed answer to your first question. You can use ace() to fit a model with irreversible change. You need to build a custom model like this: Q - matrix(0, 2, 2) Q[2, 1] - 1 Q [,1] [,2] [1,]00 [2,]10 In this case there's one

Re: [R-sig-phylo] ML ancestral state reconstruction using different softwares

Thank you very much Daniel and Emmanuel! Now things start to make sense. I guess my last question is, if there is biological evidence that the transition rates between the two traits are different, is it even meaningful to compare the two models? Should I simply avoid using the equal rates model?

Re: [R-sig-phylo] pruning a tree

Hi Elaine. A simpler way to do method 1 that doesn't require na.omit or match is: # if there are species in the tree that are missing from the data: ss-species.to.keep[,1] # species in the data tree-birdtree tree.pruned-drop.tip(tree,setdiff(tree$tip.label,ss)) I would guess that method 2

[R-sig-phylo] Seeking list of nucleotide substitution models

Hello, Is there a review or list of ~every specific nucleotide substitution model that has been proposed or used in the literature (with references)? I'm interested in reversible models. The most exhaustive list I have is from the jModeltest documentation,

[R-sig-phylo] read.nexus.data parser

Hi All, I am wondering if there is anyway to increase the speed of the read.nexus.data parser. Or if there is an alternative that is a faster nexus file data parser. THanks, Jess -- Jessica L. Sabo js...@ufl.edu sabo.j...@gmail.com PhD Student, The Edward

[R-sig-phylo] Exporting Ancestor Reconstruction from Mesquite to R for ouch

Dear forum, I am trying to conduct an ouch analysis and for it I must determine the ancestral selective regime at each node in my tree. To do so I need to conduct ancestral reconstruction on discrete unordered data. To my knowledge no package can do this in R (I hope I am wrong) and

Re: [R-sig-phylo] Exporting Ancestor Reconstruction from Mesquite to R for ouch

Hi Martin. Without more information or your input file, it's hard for me to evaluate why read.simmap is hanging. Did you run: tree-read.simmap(filename,format=nexus,version=1.5) If you have your discrete character data in R, you can also use the phytools function make.simmap to generate

[R-sig-phylo] R-Heatmap--- node stack overflow

Dear All R-sig-phylo users, I was using R ploting a heatmap recently. The datatable consisting 2400 rows and 6 columns, which I do not think is too big for R to handle, however I keep receiving the error message node stack overflow. Does anyone have similar problem? Any help will be