[R-sig-phylo] Count Deep Coal in R?

Greetings all, I am building some R simulations to assess patterns of different demographic histories in simulated phylogenies which has me keeping track of a large number of summary statistics for simulated gene trees and species trees. Over all I have been very happy with the programs availab

Re: [R-sig-phylo] Posterior probabilities from MrBayes in R

you might want to check out the Phybase package, it reads trees in a slightly different way but I've had no problems reading in posterior trees from MrBayes output. Like I said it's just a quick couple of command to convert from phybase objects to ape objects Cheers, -Dan __

Re: [R-sig-phylo] Count Deep Coal in R?

Hi Melisa, I agree with Brian, so far I have used phybase to do this. I haven't tested it completely but I believe you can use the getcoaltime() command from phybase to get at this information. You can try this code (most of which is from the phybase manual): install.packages('/home/dan/Downlo

Re: [R-sig-phylo] coalescent trees

Hi Marcelo, I'm not familiar with that specific function in Mesquite but from the explanation I saw on the Mesquite website you may want to check out the package phybase by Liang Liu (http://code.google.com/p/phybase/). It has functions to simulate coalescent trees or DNA sequences from a speci

[R-sig-phylo] FW: Reading sets of multiple DNA sequence alignments

Apologies for not replying to the list correctly the first time! Hi Fabricia, This may look a little complicated but it's pretty easy to get any string of characters into a matrix using the s2c function in seqinr and from there it's simple to get them into ape's DNAbin by running the matrix th

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

Hi Imran, I'm by no means an expert on phylogenetic signal with incomplete phylogenies but I would check out the GEIGER package, specifically the "mecca" function. I think mecca is set up to do estimates based on incomplete tip sampling. Cheers, -Dan Gates PhD candidate Smith/Pilson Lab Univers

Re: [R-sig-phylo] midpoint rooting? how to get the outgroup?

Hi Romain, I think I've done something similar to this by searching the subtrees for the name of the taxa in question. The code is probably pretty slow on really big trees (since the subtrees function takes a while). library(phybase) library(phytools) set.seed(5) #make 100 20 tip trees rand

Re: [R-sig-phylo] suset DNAbin

Hi Kirston, I generally convert DNAbin into general R objects like matrices, lists, and vectors for my subsetting so I don't have to make DNAbin specific functions. I typically use as.character() which converts DNAbin to matrix, then as.DNAbin() which converts matrix back to DNAbin example:

Re: [R-sig-phylo] simulating gene trees on a given species tree and theta

Hi Carlos, I would check out phybase at http://faculty.franklin.uga.edu/lliu/content/phybase . I have used it to simulate gene trees from species trees. It works quite well and is very fast. -Dan From: R-sig-phylo on behalf of john d Sent: Sunday, December