Re: [R-sig-phylo] pruning tree of 10000 species

the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/10/2013 7:04 PM, Elaine Kuo wrote: Hello

Re: [R-sig-phylo] pruning tree of 10000 species

On Fri, Apr 12, 2013 at 7:03 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello, Thanks to both Jose and Liam. Let me explain more about my question. 1. The file is from Jetz et al. (2012) bird phylogeny. (Jose got a right guess) The file is composed of a backbone tree and 9 other

[R-sig-phylo] pruning tree of 10000 species

Hello This is Elaine. I downloaded a bid phylogeny tree of 1 species. The file of the whole tree (1 species) is about 3.9 GB. I want like to extract to 3000 species of them for my research. Here comes two questions: 1. Please kindly advise if R is able to input a phylogeny tree of 1

[R-sig-phylo] error running fitContinuous in geiger

Hello, This is Elaine. I want to calculate lambda based on a bird data and a polygeny tree, using geiger. However, an error message below jumped out. I do not understand it quite well. Please kindly help explain its meaning and advise any code modification to calculate lambda. (BTW, I found

[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

[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

[R-sig-phylo] error in pruning tree

Hello, I am using the following code to prune a phylogeny tree of bird family. However, an error appeared when running the last line of the code, saying: error in data[tree.pruned$tip.label, ] : 'closure' type objects cannot have subsets. I do not understand the error message. Please kindly

[R-sig-phylo] Fwd: error in pruning tree

Hello, I am using the following code to prune a phylogeny tree of bird family. However, an error appeared when running the last line of the code, saying: Error in data[tree.pruned$tip.label, ] : object of type 'closure' is not subsettable I do not understand the error message. Please kindly

[R-sig-phylo] how to modify tip label of a phylogenetic tree

Hello I have downloaded a phylogenetic tree of global birds. (.nex file) Some of its tips are labelled as codes, such as BB3 and BB4. I want to rename the codes with normal family names. Please kindly advise the package and command to do it. Thank you. Elaine [[alternative HTML version

[R-sig-phylo] PGLS in caper for only bifurcating tress

Dear all, I am a beginner to PGLS with R. (phylogenetic generalized least squares) I read the package pdf of caper. In the section of fusco.test, it mentioned that bifurcating node is in need for this test. I am going to use caper for PGLS of about 3000 bird species to tell if any phylegenetic