Re: [R-sig-phylo] VCV based on admixture?

Hi Jon, There are now comparative methods that can use admixture graphs (or phylogenetic networks), beyond trees. See this tutorial: https://cecileane.github.io/networkPCM-workshop/topic-overview.html or the software documentation section on comparative methods:

Re: [R-sig-phylo] VCV based on admixture?

Hi Jon, There are now comparative methods that can use admixture graphs (or phylogenetic networks), beyond trees. See this tutorial: https://cecileane.github.io/networkPCM-workshop/topic-overview.html or the software documentation section on comparative methods:

Re: [R-sig-phylo] VCV based on admixture?

Hi Jon, There are now comparative methods that can use admixture graphs (or phylogenetic networks), beyond trees. See this tutorial: https://cecileane.github.io/networkPCM-workshop/topic-overview.html or the software documentation section on comparative methods:

Re: [R-sig-phylo] Model Selection and PGLS

Alternatively, you could use Rphylopars (https://github.com/ericgoolsby/Rphylopars), so you don’t need to code predictions by hand. I included a reproducible example below, using a single variable. You could use multiple variables to take advantage of the correlation between variables for

Re: [R-sig-phylo] Model Selection and PGLS

On Jun 30, 2021, at 11:20 PM, neovenatori...@gmail.com wrote: This is something that seems really, really concerning because if there is a method of using phylogenetic covariance to adjust the position of new data points it seems like a lot of workers don’t

Re: [R-sig-phylo] Model Selection and PGLS

Hi Russel, What you see is the large uncertainty in “ancestral” states, which is part of the intercept here. The linear relationship that you overlaid on top of your data is the relationship predicted at the root of the tree (as if such a thing existed!). There is a lot of uncertainty about

Re: [R-sig-phylo] phylogenetic correlation analysis

Rphylopars is an option too (https://github.com/ericgoolsby/Rphylopars) [[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

Re: [R-sig-phylo] Odd behavior of phylogenetic regressions

given predictor in the resulting best model if I cannot rely on the Walds test or the estimated effect sizes from the summary call in this case? Cheers, Søren - Søren Faurby http://antonelli-lab.net<http://antonelli-lab.net/> ________ Fra: Cecile Ane mailto:cecil

Re: [R-sig-phylo] model averaging using brownie.lite

Thanks Brian, great review, as always! To add one bit: this paper looks at the effective sample size that should be used for BIC, in the standard BM model (univariate). https://projecteuclid.org/download/pdfview_1/euclid.aoas/1223908053 It gives a formula that depends on the tree shape and

Re: [R-sig-phylo] Odd behavior of phylogenetic regressions

I suspect that “Climbing” and “Rainforest” are correlated with each other, so one of both lose significance when both are included in the model. Also, the Wald-type tests in logistic regression are not exact, and they typically give a different p-value than a likelihood ratio test. Both Wald

Re: [R-sig-phylo] using color function in phylomorphospace

colors can be numeric. for example: plot(1:36, 1:36, col=1:36) Cécile On Mar 8, 2019, at 8:42 PM, Liam Revell mailto:liam.rev...@umb.edu>> wrote: Dear Amanda. I'm a little confused by your code. If you want to use control=list(col.edge) you need to set col.edge to a vector of colors, but in

Re: [R-sig-phylo] estimate ancestral state with OUwie models

It is possible to transform the branch lengths of a non-ultrametric tree to make the OU process equivalent to a BM process (on the transformed branch lengths), but there’s an extra correction needed at the tips (i.e. need to transform the data too via a diagonal matrix). It makes likelihood

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

herwise I'm stuck using cophenetic again... Max Max On Fri, Dec 15, 2017 at 4:36 PM, Cecile Ane <cecile@wisc.edu<mailto:cecile@wisc.edu>> wrote: In the package phylolm, the function "transf.branch.lengths” might do what you need. It has an option model=“EB” for early bur

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

In the package phylolm, the function "transf.branch.lengths” might do what you need. It has an option model=“EB” for early burst. Cécile > On Dec 15, 2017, at 3:27 PM, Max Farrell wrote: > > I have been using the rescale function from geiger for a link prediction >

Re: [R-sig-phylo] predict using the PGLS model output

Rphylopars can make phylogenetic predictions: it’s on CRAN and on github https://github.com/ericgoolsby/Rphylopars Cécile On Oct 9, 2017, at 9:59 AM, Clara Grilo > wrote: Hi everyone, I run a phylogenetic generalised least squares

Re: [R-sig-phylo] Fwd: Fw: Help with tree manipulation

Hi Monica, Perhaps it's because your bootstrap values are stored as node labels, instead of edge labels. This problem is well documented here: https://doi.org/10.1093/molbev/msx055 But perhaps it's a different issue in your case. Cécile On Jun 24, 2017, at 9:18 AM, Monica Carlsen

Re: [R-sig-phylo] How to set up the minimum limit of the imputated value in phylopars(), (RPhylopars package), in R

Hi Judit, Negative predictions are surprising indeed if your observed data are all positive values, and if you have a single trait. Do you have multiple traits? If they are correlated, information on one trait can push imputation of another in the negative range. In any case, one option would

Re: [R-sig-phylo] simulating gene trees on a given species tree and theta

to install phybase from the CRAN archive: install.packages("https://cran.r-project.org/src/contrib/Archive/phybase/phybase_1.1.tar.gz;, repos = NULL, type="source") Cécile On Dec 18, 2016, at 4:26 AM, Liam J. Revell > wrote: Hi John. I believe

Re: [R-sig-phylo] get branch lengths from distances to root

One way would be to label the root to make it a leaf, and apply NJ. Neighbor-joining reconstructs the original branch lengths (and topology) given tree-distances between the leaves. Cécile On Nov 30, 2016, at 10:30 AM, Juan Antonio Balbuena > wrote:

Re: [R-sig-phylo] Standard errors of theta estimates in OU models

I would say no: standard errors of theta values do not have a biological interpretation, in my opinion. Going back to a sample from a single population and its mean: the standard deviation of the sample has a biological interpretation (e.g within-population variation), but the standard error

Re: [R-sig-phylo] hierarchical model with phylogenetic dependence term

, the elements of the matrix are just the sum of the shared branch lengths. Is this appropriate? Why or why not? Any input would be much appreciated. Cheers, Peter Smits -- Cecile Ane Departments of Statistics and of Botany University of Wisconsin - Madison www.stat.wisc.edu/~ane/ CALS statistical

Re: [R-sig-phylo] hierarchical model with phylogenetic dependence term

. Now my posterior sampling at least gets off the ground and finishes. The stan list discussion possibly provides a useful starting template for other people on this list trying to do similar things. Cheers, Peter On Mon, Dec 22, 2014 at 11:32 AM, Cecile Ane a...@stat.wisc.edu wrote: Hi Peter

[R-sig-phylo] How to speed up pblm in picante

archive athttp://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Cecile Ane Departments of Statistics and of Botany University of Wisconsin - Madison www.stat.wisc.edu/~ane/ CALS statistical consulting lab: www.cals.wisc.edu/calslab/stat_consulting.php

Re: [R-sig-phylo] compar.ou

, Edmondson Hall 216 Honolulu HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-9812 http://www.hawaii.edu/zoology/faculty/butler.html http://www2.hawaii.edu/~mbutler http://www.hawaii.edu/zoology/ -- Cecile Ane Departments of Statistics and of Botany University

Re: [R-sig-phylo] Convert instantaneous transition rate to time.

Hi Simon, One option could be to look at the expected number of substitutions over time t, and find the smallest time t for which you expect at least 1 substitution. The idea here is that the first substitution is the one that most disrupts the signal. Technically, if Q is your rate matrix

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

with infinite alpha. lh On Jan 30, 2011, at 3:18 PM, David Bapst wrote: ... -- Cecile Ane Assistant Professor, University of Wisconsin - Madison www.stat.wisc.edu/~ane/ CALS statistical consulting lab: www.cals.wisc.edu/calslab/stat.html ___ R-sig-phylo mailing