Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Hi Daniel, There’s a difference between a method being able to handle fossil data, that is a dataset consisting of a non-ultrametric tree an data for all tips including non contemporaneous ones, and a method allowing you to directly specify trait values at nodes. Most trait evolution methods

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Oops - sorry Daniel, yes that should have been addressed to Nathan... Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Thanks, Graham ...but I'm not the OP. I was just shooting off a quick lead without actually checking the specifics in case it was useful. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

Re: [R-sig-phylo] Problem with traitDependentBAMM function

Hi Diego, This error occurs when traitDependentBAMM gets a posterior sample with no rate shift, so that is why �the standard deviation is zero�. Now we fixed this issue in the github version of BAMMtools, https://github.com/macroevolution/bammtools By the way, the manuscript describing this is

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Hi Nathan, Although it is still possible to impute the missing data prior to the analysis, you can fit multivariate models with missing cases (NA values), using the mvMORPH (development version) from my gitHubhttps://github.com/JClavel/mvMORPH/ Non-ultrametric trees (trees with fossil species)

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Couldn't remember, so went and looked. Turns out that NAs are a problem in the tips. This isn't necessitated by the structure of the problem, only by the structure of the package, i.e., because ouchtrees are constructed in ignorance of where the data are. Unfortunately, it will require

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Aaron, While contemplating Nate's question, I wondered, doesn't hansen currently support NA codings for missing variables for tip taxa? Unfortunately the donotrun{} example for hansen() using geiger data isn't currently functioning, so I couldn't test this. -Dave Bapst On Thu, Jun 4, 2015 at

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Interesting question, Nate. Do I understand you to say that you have data on some variables (and not others) at internal nodes? If so, what happens when you just add those to the data, with NA to indicate missing values? Have you tried this? A. On Thu, Jun 4, 2015 at 11:10 AM, Nathan Thompson

[R-sig-phylo] Constraining node values in an OUCH analysis

Hi all, I am performing an multivariate analysis in ouch on a group of extant species. I would ideally like to include information for fossil taxa in the analysis, however, no single fossil taxon preserves all of the variables of interest. However, I have performed univariate ancestral state

Re: [R-sig-phylo] A perfect storm: phylogenetic trees, random effects and zero-inflated binomial data

Hi all, thank you for your suggestions! I will delve into the suggested packages and may come back to you when the learning curve becomes too steep :-). thanks again, Diederik On 6/3/2015 5:44 PM, Peter Smits wrote: The alternative to MCMCglmm would be to use stan or bugs for writing your

[R-sig-phylo] Phylogenetic PCA

Dear all, I'm wondering if there is a package in R with which I can run a phylogenetic PCA. Please, if you know something or if you you know another software useful to use this technique, let me know. Thanks in advance. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira

Re: [R-sig-phylo] Phylogenetic PCA

Hello Dne Čt 4. června 2015 11:26:10, Sergio Ferreira Cardoso napsal(a): Dear all, I'm wondering if there is a package in R with which I can run a phylogenetic PCA. Please, if you know something or if you you know another software useful to use this technique, let me know. Function ppca

Re: [R-sig-phylo] Phylogenetic PCA

Hi Sergio, there you go http://blog.phytools.org/2011/04/new-function-phylpca.html http://cran.r-project.org/web/packages/phytools/index.html best wishes 2015-06-04 11:26 GMT+01:00 Sergio Ferreira Cardoso sff.card...@campus.fct.unl.pt: Dear all, I'm wondering if there is a package in R

Re: [R-sig-phylo] Converting species cladogram to dendrogram for heatmap with R

Hi Anand. Have you tried eliminating spaces line breaks from your Newick string. When I do that I am able to read the tree with read.newick with no problem. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web:

[R-sig-phylo] Problem with traitDependentBAMM function

Hi all, I am using BAMM and BAMMtools for analyse effect of a continuous trait on evolutionary rates. But I have a problem with traitDependentBAMM function, there is a warning which is repeated a lot of times: 1: In cor(rank(x), rank(y)) : the standard deviation is zero On the other hand in

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Isn't at least some of this functionality in mvSLOUCH and/or geiger? ...it's definitely the case that mvSLOUCH can handle missing data at the tips, and I think fossil data can be incorporated in it and geiger as well. At least Slater 2013 has code for incorporating fossils in geiger or