Re: [R-sig-phylo] Dollo character using ace/make.simmap
Graeme, You can simulate characters (and associated tree) in the package diversitree. For a binary character, the parameters specified are the speciation rates, extinction rates, and transition rates between the two states. If you want to simulate unidirectional evolution, you can just specify the respective transition rate to 0, e.g.: # No transitions from state 1 to state 0 pars <- c(0.1,0.08, 0.03,0.03,0.01, 0) phy <- tree.bisse(pars, max.taxa=50, x0=0) Nick On Mon, Sep 14, 2015 at 7:00 PM, Graeme Lloyd <graemetll...@gmail.com> wrote: > Hi Everyone, > > I was wondering if anyone knows if it is possible to set up a custom rate > model to represent a binary discrete Dollo character with ace or > make.simmap? > > Thanks, > > > Graeme > ___ > 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/ > -- Nicholas Crouch Graduate Student, Igić Lab Department of Biological Sciences University of Illinois at Chicago [[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] problem with write.nexus.data
This solved the problem exactly, thank you very much. Nick On Thu, Sep 18, 2014 at 12:22 AM, Liam J. Revell liam.rev...@umb.edu wrote: Hi Nicholas. I think this is a bug. Try the following to circumvent: write.nexus.data(as.list(data), file=test.nex, interleaved=TRUE, charsperline=100) Since I don't have your dataset, I can't check it; but it fixed the problem in another dataset with which I was able to reproduce the error. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 9/17/2014 10:46 PM, Nicholas Crouch wrote: Hi, I am having a problem with write.nexus.data, such that the file generated is nonsense. I have a very, very large data set, but have been working with a subset trying to solve this problem. My data is in .fasta format, and I am looking to convert it into nexus format. I load the data: library(ape) data - read.dna(concat.fasta, format=fasta, as.matrix=TRUE) This gives the following: data 5 DNA sequences in binary format stored in a matrix All sequences of same length: 5023 Labels: Species etc. Base composition: a c g t Also: class(data) DNAbin This is exactly the same as the woodmouse example data provided in the package ape, which I have been following when trying to solve this issue (see ?write.nexus.data). When I export the data: write.nexus.data(data, file=test.nex, interleaved=TRUE, charsperline=100) a file is produced which begins: BEGIN DATA; DIMENSIONS NTAX=135165 NCHAR=1; FORMAT DATATYPE=DNA MISSING=? GAP=- INTERLEAVE=YES; MATRIX 1 040 etc. I haven't been able to find other posts on this, any help is greatly appreciated. Sincerely, Nick -- Nicholas Crouch Graduate Student, Igić Lab Department of Biological Sciences University of Illinois at Chicago [[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] problem with write.nexus.data
Hi, I am having a problem with write.nexus.data, such that the file generated is nonsense. I have a very, very large data set, but have been working with a subset trying to solve this problem. My data is in .fasta format, and I am looking to convert it into nexus format. I load the data: library(ape) data - read.dna(concat.fasta, format=fasta, as.matrix=TRUE) This gives the following: data 5 DNA sequences in binary format stored in a matrix All sequences of same length: 5023 Labels: Species etc. Base composition: a c g t Also: class(data) DNAbin This is exactly the same as the woodmouse example data provided in the package ape, which I have been following when trying to solve this issue (see ?write.nexus.data). When I export the data: write.nexus.data(data, file=test.nex, interleaved=TRUE, charsperline=100) a file is produced which begins: BEGIN DATA; DIMENSIONS NTAX=135165 NCHAR=1; FORMAT DATATYPE=DNA MISSING=? GAP=- INTERLEAVE=YES; MATRIX 1 040 etc. I haven't been able to find other posts on this, any help is greatly appreciated. Sincerely, Nick -- Nicholas Crouch Graduate Student, Igić Lab Department of Biological Sciences University of Illinois at Chicago [[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] Drop terminal branches
Liam, That works fantastically, thanks very much! Nick On Tue, Aug 13, 2013 at 10:39 AM, Liam J. Revell liam.rev...@umb.eduwrote: Hi Nick. drop.tip(...,trim.internal=**FALSE) almost does this, but it will not allow you to trim all the leaves in the tree. Why don't you try the attached function, which I'm calling drop.leaves. It does what you want, I think, and should be straightforward to figure out. The tip labels on the pruned tree are either the node labels (if they exist) or the node numbers in the original tree; or (if keep.tip.labels=TRUE) they are a comma separated list of the tips descended from that node in the input tree. Note that not all tips will be in these lists because some edges from internal nodes lead to only one tip. Feedback welcome. All 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 8/13/2013 10:43 AM, Nicholas Crouch wrote: Hi All, For an analysis I am performing I am looking to drop all terminal branches from a phylogeny (class phylo). The idea is to end up with only branches that lead to nodes. Does anyone know how to drop these lengths to leave me everything else? Thanks, Nick [[alternative HTML version deleted]] __**_ 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 Searchable archive at http://www.mail-archive.com/r-** sig-ph...@r-project.org/http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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] Find common ancestor of multiple taxa
Hi All, The 'mrca' function in Ape provides a method for finding the common ancestor of a pair of taxa. What I would like have not found is a function where you can pass a (long) list of tips from a phylogeny and find the node which represents the common ancestor to all these tips. Does such a function exist? Or could the 'mrca' function be expanded to loop over all the taxa within a list a somehow boil down to what is the common ancestor that way? Thanks, Nick [[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] PGLS with class multiphylo
Sam,
In order to run on one tree try phy=trees[[1]], otherwise you will need
to run a loop of the function over all the trees.
e.g.
for(i in 1:length(trees)){
phy - trees[[i]]
then code as normal
Nick
On Tue, Apr 30, 2013 at 7:33 AM, Samantha DelSerra s.delse...@gmail.comwrote:
Hello,
I am trying to analyse 100 trees against morphological continuous data
using a phylogenetic GLS. I'm using the comparative.data function in order
to do this, but I keep getting an error saying that the class must be
phylo. I understand that my data is multiphylo, but is there a way to
convert this data into the phylo class? Below is my code and the error
message.
trees - read.nexus(testrees1.tree)
bats - comparative.data(phy = trees, data = corr.data, names.col =
Phyloname, vcv = TRUE, na.omit = FALSE, warn.dropped = TRUE)
Error in comparative.data(phy = trees, data = corr.data, names.col =
Phyloname, :
'trees' not of class 'phylo'
Thanks very much!
Sam
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[R-sig-phylo] Information on {ape] function nodelabels
Hi, Hoe does the function nodelabels match data to the phylogeny? Ancestral reconstruction produces a vector with a sample output: st [,1] [,2][,3] [,4][,5] [1,] 0.0001381085 0.007642601 0.01638118 0.001591162 0.001268793 [2,] 0.9998618915 0.992357399 0.98361882 0.998408838 0.998731207 The numbers across the top do no correlate with the node numbers on the phylogeny: compare nodelabels(pie=t(st)) with nodelabels() Would it be possible to create a list vector of the nodes in a phylogeny with the corresponding values from an ancestral reconstruction? An example could be something like: vector Node 1 [1] 0.05 [2] 0.95 Node 2 [1] 0.3 [2] 0.7 Thanks [[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/
