Re: [R-sig-phylo] data anlysis

of evidence. The American Naturalist 160, 712–726. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu

Re: [R-sig-phylo] simulating continuous data

.com] Sent: Tuesday, May 10, 2016 3:32 PM To: Theodore Garland Jr Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] simulating continuous data Thanks Joe and Ted, By similar scaling, I just meant (as Ted guessed) that the root value depends on the empirical trait data, and does not start at 0

Re: [R-sig-phylo] simulating continuous data

Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com

Re: [R-sig-phylo] Normal distribution in trait values before testing for phylogenetic signals?

o see what they did for the various traits studied. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.

Re: [R-sig-phylo] Testing for relationship between one categorical and one continuous variable in a phylogenetic framework.

. Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265–292. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone

Re: [R-sig-phylo] How to use categorical vectors in package ape for phylogenetic independent contrasts

. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com

Re: [R-sig-phylo] multiple regression with binomial distribution

. Phylogenetic regression for binary dependent variables. Pages 231-261 in Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice, L. Z. Garamszegi, ed. Springer: Heidelberg. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology

Re: [R-sig-phylo] PGLS multiple regression with dummy variables and interaction terms

are equivalent. Systematic Biology 61:382–391. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu

Re: [R-sig-phylo] simulating rate shifts

called for. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http

Re: [R-sig-phylo] R-squared alternative for gls

It's not that r squared isn't meaningful for generalized least squares but rather that it cannot be compared directly with values from OLS models. Cheers, Ted From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent:

Re: [R-sig-phylo] PGLS with non-ultrametric tree

as for phylogenetically independent contrasts. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Yep, we've all been down this road before, but I'm too old to remember! Thanks and cheers, Ted From: Paolo Piras [paolo.pi...@uniroma3.it] Sent: Thursday, July 16, 2015 2:38 PM To: Solomon Chak; Theodore Garland Jr Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] PGLS with non

Re: [R-sig-phylo] testing for variation in rates of evolution among traits

traits, but I am sure you could do this with simulations. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http

Re: [R-sig-phylo] phyres function R package caper

(through the origin, of course) of one trait on the other. Save the residuals. Compare them with the phylogenetic residuals you get from some other program that does a PGLS regression (not with any transformation of the branch lengths). Let us know what you find! Cheers, Ted Theodore Garland, Jr

Re: [R-sig-phylo] phyres function R package caper

Thank you, Liam! Cheers, Ted From: Liam J. Revell [liam.rev...@umb.edu] Sent: Wednesday, June 24, 2015 10:24 AM To: Theodore Garland Jr; Sergio Ferreira Cardoso; R phylo mailing list mailing list Subject: Re: [R-sig-phylo] phyres function R package caper Hi all. To the original question, you

Re: [R-sig-phylo] Non-ultrametric tree PGLS

of the transform models (Pagel's lambda, Grafen's rho, OU in various implementations, ACDC) can sometimes yield really bizarre results when you start with a non-ultrametric tree. You need to be careful and check the REML likelihood surface for multiple peaks, etc. Cheers, Ted Theodore Garland, Jr

Re: [R-sig-phylo] Non-ultrametric tree PGLS

, May 14, 2015 8:47 AM To: Theodore Garland Jr Cc: Sergio Ferreira Cardoso; R phylo mailing list mailing list Subject: Re: [R-sig-phylo] Non-ultrametric tree PGLS Hi Sergio, I would add to Ted’s reply that you are not only considering alternative statistical models but that the evolutionary

Re: [R-sig-phylo] Weird estimated Lambda values (PGLS)

Do you have a plot of the likelihoods versus the parameter value? Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http

Re: [R-sig-phylo] PGLS vs OUwie?

Dear Will, I suggest that you read the Appendix in this paper Lavin et al. (2008) (available on my website) and then the original papers by Butler and King on OUCH, etc. http://www.jstor.org/stable/10.1086/590395 Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University

Re: [R-sig-phylo] Non normal PGLS results

If you get such a large difference between ML and REML estimation in this sort of situation then probably either (1) something is wrong with the code (bad search algorithm?) or (2) you have something pathological in your tip data set and/or the tree (e.g., some really long singleton branches or

Re: [R-sig-phylo] PGLS transformations

In Mesquite, make sure you have the Branches proportional to lengths option checked so that the tree you are looking at shows the real branch lengths it has! this is NOT the default option in Mesquite! Cheers, Ted From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio

Re: [R-sig-phylo] PGLS transformations

, you have a different beast. See the appendix noted above and, for the original source of this sort of model, Grafen (1989). Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827

Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives

Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl

Re: [R-sig-phylo] How to test if the slope is different from 1 in PGLS?

have soft polytomies then you may want to subtract some d.f.: Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42:569–575. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside

Re: [R-sig-phylo] Concentrated changes test

Isn't it in Mesquite? Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people

Re: [R-sig-phylo] fitting cuadratic model using gnls

that value and use it for the quadratic This is referred to as an orthogonol polynomial. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026

Re: [R-sig-phylo] best fit vs normality of residuals

Good advice! Cheers, Ted From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Luke Matthews [lmatth...@activatenetworks.net] Sent: Tuesday, December 03, 2013 8:29 AM To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] best fit vs normality of residuals

Re: [R-sig-phylo] Transforming data for OU model

somewhere, maybe phytools? Liam Revell, want to jump in here? Happy thanksgiving, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone

Re: [R-sig-phylo] Transforming data for OU model

Good point, Joe. However, if they have graphics screens (as in our PDTREE.EXE and PDSIMUL.EXE) programs, then you sometimes have trouble with the display of those particular screens. Plain text screens (ASCII characters only) aren't a problem. Also, you can get idiosyncratic problem, such as

Re: [R-sig-phylo] Transforming data for OU model

. As Liam wrote, we all need more info about what you are doing. And we need to get the hell off the computer on a holiday! Cheers, Ted From: Liam J. Revell [liam.rev...@umb.edu] Sent: Thursday, November 28, 2013 12:16 PM To: Theodore Garland Jr; Anna Rice; r-sig-phylo@r-project.org Subject

Re: [R-sig-phylo] PGLS vs lm

analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534-557. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab

Re: [R-sig-phylo] PGLS vs lm

Maybe what we need here is an approach based on  simultaneous equations (aka structural equation models), but I'm not  aware whether this exists in a phylogenetic framework. Exactly! And it will need to incorporate measurement error in all variables as well as, eventually, uncertainly in the

Re: [R-sig-phylo] PGLS vs lm

. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026

Re: [R-sig-phylo] Phylosignal with phylo.d

. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827

Re: [R-sig-phylo] pagel's lambda vs. abouheif's Cmean

, is not large for any trait (compare with values in Blomberg et al. 2003). Finally, other ways to test for signal besides lambda might perform better, such as an OU model. Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office

Re: [R-sig-phylo] trait correlations with PICs

, and probably others! Enough rambling! Hope that helps!!! Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Skype: theodoregarland Facsimile: (951) 827-4286 = Dept. office (not confidential

Re: [R-sig-phylo] trait correlations with PICs

al., 2004). Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Skype: theodoregarland Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http

Re: [R-sig-phylo] trait correlations with PICs

). Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 17, 2013 9:38 AM To: Theodore Garland Jr Cc: Anne Kempel; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] trait correlations with PICs Can I risk a question here, maybe a result of ignorance

Re: [R-sig-phylo] Ancestral state estimates of continuous traits

Yes, we have always used REML for this! Cheers, Ted From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Emmanuel Paradis [emmanuel.para...@ird.fr] Sent: Friday, March 15, 2013 11:21 PM To: Liam J. Revell; r-sig-phylo-boun...@r-project.org; Alejandro Gonzalez

Re: [R-sig-phylo] Some questions about pPCA - phylogenetic anti-signal

You can test for anti-signal using the randomization procedures of: Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. See page 719. Cheers, Ted Theodore Garland, Jr., Professor

Re: [R-sig-phylo] R: Re: From ClustalW2 Tree to Heat Map in R

your K value with other studies that did not use lambda and/or OU transforms. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home

Re: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances

of method used by Collar et al., 2005] Rezende, E. L., and J. A. F. Diniz-Filho. 2012. Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms. Comprehensive Physiology 2:639-674. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University

Re: [R-sig-phylo] testing binomial characters

Check this: Ives, A. R., and T. Garland, Jr. 2010. Phylogenetic logistic regression for binary dependent variables. Systematic Biology 59:9-26. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827

Re: [R-sig-phylo] pPCA - global and local components

by a bunch of mini-star phylogenies. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu

Re: [R-sig-phylo] Can PGLS cope with collinearity between explanatory variables?

-0.8 in magnitude to cause serious problems. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http

Re: [R-sig-phylo] PIC or PGLS for genome-wide SNP screening

of the PHYSIG package] Gartner, G. E. A., J. W. Hicks, P. R. Manzani, D. V. Andrade, A. S. Abe, T. Wang, S. M. Secor, and T. Garland, Jr. 2010. Phylogeny, ecology, and heart position in snakes. Physiological and Biochemical Zoology 83:43-54. Cheers, Ted Theodore Garland, Jr. Professor

Re: [R-sig-phylo] Best way to test correlation between discrete and continuous variables ?

of the PHYSIG package] Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept

Re: [R-sig-phylo] nonparametric PGLS

the likelihood of a model, so particularly check for big outliers. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951

Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)

To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's

Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)

Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 9:19 AM To: Theodore Garland Jr Cc: Alejandro Gonzalez; Hunt, Gene; Enrico Rezende; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger

Re: [R-sig-phylo] Testing for phylogenetic signal in proportions

It is really too few species to have a sufficiently powerful test for phylogenetic signal. See Blomberg et al. (2003), available on my website. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 48, Issue 12

Networks, Inc. Message: 3 Date: Wed, 18 Jan 2012 17:34:14 +0100 (CET) From: ppi...@uniroma3.it To: Theodore Garland Jr theodore.garl...@ucr.edu Cc: r-sig-phylo@r-project.org r-sig-phylo@r-project.org,Ana Longo ana.lo...@gmail.com Subject: Re: [R-sig-phylo] Comparing slopes from regressions

Re: [R-sig-phylo] Comparing slopes from regressions and PIC regressions

Long story short, you don't want to think about it in those terms. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone

Re: [R-sig-phylo] Comparative Methods and Pseudo-Traits

phenotypes withenvironmental characteristics require furtherstudy. Cheers,Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951

Re: [R-sig-phylo] squared-change parsimony reconstruction

this is just a limitation in ACE? Also, how does ACE handle polytomies? I know that some algorithms have trouble with polytomies, which may be indicated as zero-length branches. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521

Re: [R-sig-phylo] R: ancestral state reconstruction for tips

The methods in the Garland and Ives (2000) paper are in our package of DOS PDAP programs, and should also be functional in the PDAP module of Mesquite. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951

Re: [R-sig-phylo] R: Re: R: Re: R: ancestral state reconstruction for tips

: Friday, August 05, 2011 12:38 PM To: j...@gs.washington.edu Cc: dwba...@uchicago.edu; hu...@si.edu; Theodore Garland Jr; r-sig-phylo@r-project.org Subject: R: Re: R: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips Folks, I was intending my most recent message to be off-list

Re: [R-sig-phylo] pic() vs gls()

39:374-388. Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346-364. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University

Re: [R-sig-phylo] small sample size and detecting phylogenetic signal with Blombergs K statistic

and phylogenetically independent contrasts (which is equivalent to PGLS models without any sort of branch length transform). Hopefully, results will be similar. If not, then you probably cannot conclude much from your data. Sincerely, Ted Theodore Garland, Jr. Professor Department of Biology University

Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)

the nodes) should be reduced, and sometimes substantially, if the constrained node is close by. Right? Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone