[R-sig-phylo] which.node function

("numeric",length(tips)) for (i in 1:length(tips)) rows[i] = which(phy$edge[,2] == tips[i]) nodes = sort(phy$edge[rows,1]) return(nodes[1]) } else if (is.null(tips) == TRUE){ stop('tips vector is empty') } } All the best, Santiago -- Santiago Sánchez-Ramírez Department of E

[R-sig-phylo] Fwd: which.node function

-- Forwarded message -- From: *Santiago Sánchez* Date: Monday, November 25, 2013 Subject: which.node function To: "Liam J. Revell" Hi Liam, Great! What a waste of time! Anyway thank you pointing this out. I also notice the error, and just in case, I'm post

Re: [R-sig-phylo] Error in read.beast()

will solve the issue. > read.beast("tree", digits=2) Or > read.beast("tree", digits=10) Cheers, Santiago -- Santiago Sánchez-Ramírez Department of Ecology and Evolutionary Biology, University of Toronto Department of Natural History (Mycology), Royal Ontario Museum 1

Re: [R-sig-phylo] Error in read.beast()

avior > Integrative Biology > The University of Texas at Austin > > > > > On Jan 21, 2014, at 7:22 AM, Santiago Sánchez > 'santiago.snc...@gmail.com');>> > wrote: > > Hello Mariana, > > When I use read.beast() I usually specify a digit numbe

[R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the same function

is no "compar.bm" in ape. Any help is greatly appreciated. Cheers, Santiago -- Santiago Sánchez-Ramírez Department of Ecology and Evolutionary Biology, University of Toronto Department of Natural History (Mycology), Royal Ontario Museum 100 Queen's Park Toronto, ON M5S 2C

Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the same function

> Dept. of Ecology & Evolutionary Biology > U. of Tennessee, Knoxville > http://www.brianomeara.info > > Students wanted: Applications due Jan. 1, annually > Postdoc collaborators wanted: Check NIMBioS' website > Calendar: http://www.brianomeara.info/calendars/omeara > > >

Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the same function

t; > > > Christofer > > > > > > > > -- > > > > Message: 2 > > Date: Mon, 17 Feb 2014 08:55:00 + (UTC) > > From: Christofer Clemente > > To: r-sig-phylo@r-project.org > > Subject: Re: [R-sig-phylo] F

Re: [R-sig-phylo] profiles.plot legends

://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > -- > Nicholas Crouch > Graduate Student > Department of Biological Sciences > University of Illinois at Chicago > > > > -- > Nicholas Crouch > Graduate Student > Department of Biological Sciences

Re: [R-sig-phylo] Help interpreting diversitree:MuSSe results

to me or one in > general? > > I hope this makes sense! > > Cheers > > *Tim Astrop PhD <http://timastrop.wordpress.com/>* > Ammonoid Palaeobiology Lab <http://aplbath.wordpress.com/> > Department of Biology & Biochemistry > University of Bath > > *

[R-sig-phylo] Add a random outgroup lineage to a phylo object

gth)/2) > plot(ladderize(phynbl.w.out,FALSE), main="no branch lengths") > # for an ultrametric tree > phy <- pbtree(n=20) > nodes <- (length(phy$tip.label)+1):(length(phy$tip.label)+phy$Nnode) > root.node <- sample(nodes, 1) > phy.w.out <- add.outgroup(phy=ph

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

Hi Jacob, You might want to check Joseph Heled's python package biopy (https://code.google.com/p/biopy), I know it has some simulation capabilities. Also check Z. Yang's program MCMCcoal, I know some people have used it for simulation analyses in BPP. Cheers, Santiago Sent from my iPhone

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

u can also import "raw" posterior trees with their metadata. I've tried it on species trees from *BEAST and it works well. In contrast to "read.beast" from phyloch, "read.annotated.nexus" will associate metadata to edges (e.g. edge number), rather than nodes. Cheers

Re: [R-sig-phylo] getBtimes vs. branching.times

l structure of both trees is identical > identical(treeNN$edge,treeBL$edge) [1] TRUE > if (identical(treeNN$edge,treeBL$edge)){ + newtree <- treeBL + newtree$node.label <- treeNN$node.label } > newtree Phylogenetic tree with 10 tips and 9 internal nodes. Tip labels: t1, t9, t4,

[R-sig-phylo] need finite 'xlim' values error with plot.phylo

Hello, I was wondering if there could be a bug in the plot.phylo code. I'm trying to plot a tree which is scaled in yr units (less than 1 million years). However I'm getting this error: Error in plot.window(...) : need finite 'xlim' values I tried rescaling to kyr and it plots well. Here is a sa

Re: [R-sig-phylo] need finite 'xlim' values error with plot.phylo

liam.rev...@umb.edu > > Sent from my Windows 10 phone > > > > *From: *Santiago Sánchez > *Sent: *Tuesday, June 13, 2017 11:35 AM > *To: *r-sig-phylo@r-project.org > *Subject: *[R-sig-phylo] need finite 'xlim' values error with plot.phylo > > > Hello, &

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, As Eduardo says, if in fact you want to see how different trees are from a "consensus", something that you could try is find the maximum-clade-credibility (MCC) tree (you can do this with treeAnnotator from BEAST). This will be a fully bifurcating tree and is essentially the tree in the