Re: [R-sig-phylo] simulating rate shifts
Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? 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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/301iAWLdbwV ___ 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] Plotting error edgelabels in phylogeny type=fan
Hi Klaus.
Thanks for the fix. In ape now.
Cheers,
Emmanuel
Le 30/07/2015 22:45, Klaus Schliep a écrit :
Dear Julia,
this function should fix your problem and Emmanuel may can include it
into edgelables function:
edgeLabelsFan - function (text, edge, adj = c(0.5, 0.5), frame =
rect, pch = NULL,
thermo = NULL, pie = NULL, piecol = NULL, col = black,
bg = lightgreen, horiz = FALSE, width = NULL, height = NULL,
date = NULL, ...)
{
lastPP - get(last_plot.phylo, envir = .PlotPhyloEnv)
if (missing(edge)) {
sel - 1:dim(lastPP$edge)[1]
subedge - lastPP$edge
}
else {
sel - edge
subedge - lastPP$edge[sel, , drop = FALSE]
}
r - sqrt(lastPP$xx^2 + lastPP$yy^2)
XX - lastPP$xx[subedge[,2]] * (r[subedge[,2]] + r[subedge[,1]]) /
(r[subedge[,2]] * 2)
YY - lastPP$yy[subedge[,2]] * (r[subedge[,2]] + r[subedge[,1]]) /
(r[subedge[,2]] * 2)
if (!is.null(date))
XX[] - max(lastPP$xx) - date
BOTHlabels(text, sel, XX, YY, adj, frame, pch, thermo, pie,
piecol, col, bg, horiz, width, height, ...)
}
Kind regards,
Klaus
On Thu, Jul 30, 2015 at 1:10 PM, Julia Dupin julia.du...@gmail.com
mailto:julia.du...@gmail.com wrote:
Dear all,
I'm trying to plot a tree with some branches marked using
edgelabels() but
the function is misplacing the labels (it misses the actual
branches) when
I use it in a fan type tree.
Here is an example
tree-pbtree(n=10,scale=10)
plot(tree,type=fan)
edgelabels()
The phylogeny I am working on is pretty big so fan is the best
option for
me to visualize it.
Has anyone had this issue before? Is there a way to fix it? Or maybe an
alternative to edgelabels?
Thanks in advance!!
Julia
--
Julia Dupin
PhD candidate
Smith lab
Dept. Ecology and Evolutionary Biology, Ramaley Hall C127A
University of Colorado - Boulder
email: julia.du...@colorado.edu mailto:julia.du...@colorado.edu
website: http://www.colorado.edu/smithlab/
[[alternative HTML version deleted]]
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Klaus Schliep
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Revell Lab, University of Massachusetts Boston
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Re: [R-sig-phylo] simulating rate shifts
Hi Emmanuel Eric. I think it's possible that Eric is interested in simulating shifts in the lineage diversification (speciation and/or extinction) rate, rather than the rate of phenotypic trait evolution. It is possible to simulate various scenarios of trait-based diversification in the package diversitree, I believe; however if you are merely interested in taking (or simulating some tree) and then imagining (and simulating) a different diversification process for part of that tree, then this is exactly the same as simulating first one tree under process 1 - then pruning a subtree, simulating a replacement subtree under process 2, and attaching the new subtree from whence the previous subtree was removed. Since this is easier said then done, I posted a more detailed worked example on my blog here: http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? 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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/301iAWLdbwV ___ 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 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/
