Re: [R-sig-phylo] bind.tree() error

reorder from ape or phangorn:::reorderPruning (a bit faster) are generally a much faster alternative for read.tree(write.tree(...)), even this got also faster recently. Cheers, Klaus On 3/8/11, David Bapst dwba...@uchicago.edu wrote: Hello all, Apologies for sending another post this week

[R-sig-phylo] bind.tree() error

; no branch lengths. Anyone have any idea what's going on? For now, I'll solve it by using the read.tree(write.tree()) kludge. -Dave -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

Re: [R-sig-phylo] The Speed of Different Methods For Obtaining the Descendant Tip Taxa per Node

it): library(multicore) job - parallel(prop.part(res_tree)) system.time(out - collect(job))   user  system elapsed  0.080   0.010   0.002 out - out[[1]] identical(out, desc2) [1] TRUE This might be even more interesting with lists of trees. David Bapst wrote on 07/03/2011 04:32: Klaus

[R-sig-phylo] The Speed of Different Methods For Obtaining the Descendant Tip Taxa per Node

) nodeDescendents(res_tree_ou,x))) user system elapsed 65.910.23 68.47 -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ ___ R-sig-phylo mailing list R-sig-phylo@r

Re: [R-sig-phylo] Dealing with Bounded Trait Measures

                        El 4/3/11 9:14 p.m., David Bapst escribió:      All-      As far as I understand it, the vast majority of continuous     character      analyses assume that the trait is distributed normally and     without      bounds. Is there an appropriate transformation

Re: [R-sig-phylo] The Speed of Different Methods For Obtaining the Descendant Tip Taxa per Node

(edge_end,function(x) node.tips(res_tree,x)))   user  system elapsed   4.07    0.00    4.07 Cheers, Klaus On 3/6/11, David Bapst dwba...@uchicago.edu wrote: Hello all, I'm currently trying to measure a parameter over a large number of large trees (1700 tips), and part of this calculation

[R-sig-phylo] Dealing with Bounded Trait Measures

' for that trait? Must we convert these traits to discrete categories to deal with them at all? As always, I appreciate your advice. -Dave Bapst, UChicago -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

[R-sig-phylo] Problems with transferring trees back into ape from Mesquite

) and the write.nexus() and write.tree() errors (trash_b). These are small, partially collapsed portions of my supertree with the species names deleted. They can be found at: http://home.uchicago.edu/~dwbapst/trash_a.nex http://home.uchicago.edu/~dwbapst/trash_b.nex -Dave -- David Bapst Dept

Re: [R-sig-phylo] K for discrete unordered traits

and to be pointed to any releveant literature. Thanks! Stacey ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago

Re: [R-sig-phylo] Model-Selection vs. Finding Models that Fit Well

(Alroy, 1998). Thus, it is of interest to me to know if none of the models I have considered are adequate descriptions of the real processes. Interesting responses, all! Thank you very much for this discussion! -Dave -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis

Re: [R-sig-phylo] fitContinuous on a distance matrix

the evolution of that property (Brownian or otherwise) in each species relative to other species? On 19/1/11 12:41 AM, David Bapst dwba...@uchicago.edu wrote: fitContinuous is for analyzing lineage-level trait evolution on a phylogeny, and a distance-matrix does not describe lineage-level

Re: [R-sig-phylo] Error in if (tp[3] != ) obj$node.label - tp[3] :

You mention read.tree(), but have you tried read.nexus()? I just tried it now on your file and it was read into R by read.nexus() fine and plotted with plot.phylo() without error. -Dave On Mon, Oct 25, 2010 at 4:13 PM, Joey Pakes joey.pa...@gmail.com wrote: Hello, I have made a tree with

[R-sig-phylo] Errors with ace and Confidence Intervals for Ancestral Traits

Hello all, I have been using ace() to reconstruct ancestral states for a number of continuous morphological traits. I need confidence intervals for my analysis. However, for some sets of traits, I get the following error: Warning message: In sqrt(diag(solve(out$hessian))) : NaNs produced The

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