,
Ted
Theodore Garland, Jr., Distinguished 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
G_HTML.php
>
> Gemeinsam einen Unterschied machen!
> www.synagieren.de
>
> 'For every complex problem there is an answer that is clear, simple, and
> wrong.' (Henry Louis Mencken)
>
>
> --
> *Von:* Theodore Garland
> *Gese
And don't forget that measurement error in the tip data will also cause
underestimation of phylogenetic signal, unless you use methods specifically
designed to allow for that!
Ives, A. R., P. E. Midford, and T. Garland. 2007. Within-species variation
and measurement error in phylogenetic comparati
Dear Ting-Wen,
This is a question about statistical philosophy in general, not specific to
tests for phylogenetic signal. How best to correct for making multiple
tests with related data is a huge and complicated topic. Another issue is
whether your traits are correlated with each other, which wo
I don't think you can compare models like this for different transforms of
the dependent variable. The likelihood, etc., values are not comparable,
as your results suggest. But I am sure someone will correct me if I am
wrong!
Assuming this is some sort of regression model (i.e., you have one or
American Naturalist 140:509–519.
Cheers,
Ted
Theodore Garland, Jr., Distinguished 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
The original paper is here, with Matlab code. Others can tell you where
this is in R.
Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species
variation and measurement error in phylogenetic comparative methods.
Systematic Biology 56:252–270.
Cheers,
Ted
On Wed, Aug 2, 2017 at 7:50
c bootstrapping is also useful.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal Biology (EEOB)
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confidential)
es force a tree to become ultrametric, then make sure you provide
that tree and the original in the Online Supplemental Material or whatever,
and clearly say what you did.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal Biology (EEOB)
.
Evolution 57:717–745.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal Biology (EEOB)
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confidential)
Email: tgarl
.1/BayesTraitsV3.0.1.html)
> and I think the pgls function in the caper R package should be also able to
> do this if I recall correctly.
>
> thanks,
> Manabu
>
> On Fri, 13 Jul 2018 at 20:43, Theodore Garland
> wrote:
>
> > I agree with everything that Liam w
: contrasts revisited and revised. The American
Naturalist 171:713–725.
We have Matlab code for the first one; Joe has code for the second one.
Other can tell you about options in R.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal
Have you thought about also trying models that just treat this as a
quantitative trait (for which you have crude data), under the presumption
that evolution occurs along the scale of 0 -> 1 > 2 or backwards?
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evo
ext of the set of species under analysis. So, your expected
variance-covariance matrix for the trait (or for residuals from a
regression model) will have some blocks of zeros on the off-diagonals.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and
As the lead author of the paper in question, I'll be curious to find out
what you uncover.
Thanks and cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal Biology (EEOB)
University of California, Riverside
Riverside, CA 92521
O
A slope from RMA will always be > than the corresponding OLS slope because
RMA = OLS/r, where r is the correlation coefficient.
And note that the RMA slope calculated this way is undefined if r = 0.
This is why you want to use measurement-error models.
Cheers,
Ted
On Tue, Jun 9, 2020 at 1:34
Carla, I can also suggest looking at some of the papers on this, such as:
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.
Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Wi
et al. (2003) on those calculated nodal values.
Cheers,
Ted
Theodore Garland, Jr., Distinguished Professor
Department of Evolution, Ecology, and Organismal Biology (EEOB)
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confide
OK, Joe, that's for one trait at a time.
Would you please continue your discourse, but extend to multiple traits and
their covariances?
Many thanks,
Ted
P.S - What's the emoji for tongue in cheek? I don't see a great one, but
here's an emoticon:
:-J
On Fri, Mar 19, 2021 at 1:08 PM Joe Felsenstein
No, they are the same.
The difference between GLS and OLS is only in the specified (assumed)
variance-covariance matrix of the residuals.
Cheers
Ted
P.S. "PGLS" can be viewed as costing 1 df if you estimate a branch length
transformation parameter.
On Fri, Jun 11, 2021, 9:54 PM Russell Engelman
w
I'll just add one note of caution. If you do the independent contrasts
calculations, make sure the package you use to compute correlations is
actually doing them through the origin. In years past, I ran into stats
programs that would give you a regression through the origin (slope) as
requested,
The other possible null model would be a "star" phylogeny with no
hierarchical structure, equal-length branches, and also Brownian motion.
But that's generally viewed as outside of the range of reasonable
possibilities.
Cheers,
Ted
On Tue, Jun 29, 2021 at 12:05 PM Nathan Upham wrote:
> Hi Russel
All true. I would just add two things. First, always graph your data and
do ordinary OLS analyses as a reality check.
Second, I think this is the original paper for phylogenetic prediction:
Garland, Jr., T., and A. R. Ives. 2000. Using the past to predict the
present: confidence intervals for re
gt;> For multivariate linear model you can also do it by specifying a tree
>> including both the species used to build the model and the ones you want to
>> predict using the “predict” function in mvMORPH (I think that Rphylopars
>> can deal with multivariate phylogenetic reg
>
> preds
> ## [1] -2.440567 -2.370682 -1.035975 -2.583952
>
> mu
> ## (Intercept) x
> ## t26 0 -0.2208723
> ## t27 0 0.5918446
> ## t43 0 -1.1822058
> ## t39 0 -0.8706877
>
> preds+mu[,2] ## "correct"
alyses 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
Uni
nches connecting 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: (9
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 of
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
.r...@libero.it]
Sent: Friday, August 05, 2011 9:41 AM
To: Theodore Garland Jr; Hunt, Gene; r-sig-phylo@r-project.org
Subject: R: Re: [R-sig-phylo] R: ancestral state reconstruction for tips
Of course Ted is right, but my problem with this computation, or with the
simple exercise I was proposing
eages (by comparison with real branch lengths).
Yes, I think that is an excellent way to proceed.
Cheers,
Ted
From: pasquale.r...@libero.it [pasquale.r...@libero.it]
Sent: Friday, August 05, 2011 12:00 PM
To: dwba...@uchicago.edu; j...@gs.washington.edu; hu...@si.edu; Theodore
Garland Jr
Cc: r-sig-
g something?
Cheers,
Ted
From: pasquale.r...@libero.it [pasquale.r...@libero.it]
Sent: 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 reconstru
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
T. Garland, Jr. 2007. Within-species variation
and measurement error in phylogenetic comparative methods. Systematic Biology
56:252-270.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Wet
han a conventional analysis, assuming a star phylgony, so present
both.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office
., one), the you don't need AIC. Just look
at the likelihoods. Bigger is better.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 =
ating 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:
Why not just include an interaction term between your main effect coding
variable (presumably coded as 0, 1 to indicate your two ecomorphs) and one or
more of your continuous independent variables?
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California
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
alysis
Activate Networks, Inc.
Message: 3
Date: Wed, 18 Jan 2012 17:34:14 +0100 (CET)
From: ppi...@uniroma3.it
To: "Theodore Garland Jr"
Cc: "r-sig-phylo@r-project.org" ,Ana Longo
Subject: Re: [R-sig-phylo] Comparing slopes from regressions and
(see
Blomberg et al., 2003).
All this said, I'd like to see your tree and some tip data -- can you send it
as a Nexus file I can read into Mesquite?
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951
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
can send our
Matlab code.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office (not confidential)
Email: tgarl...@ucr.edu
http
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
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
ely affect 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
f 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 =
art 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.
Profes
-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
ented 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.biolo
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
id this for non-phylogenetic nuisance variables (such as
calculation method for home range size), but you could also do it for a "real"
trait that was clearly non-phylgenetic (if there is such a thing -- see Joe's
comment).
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Bi
anation 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
Uni
well have underestimated how many species you
need in the real world! As they say, your mileage may vary ...
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
statistically from 1.00.
However, K is for continuous-valued traits. It does not make sense for many
categorical traits!
What, exactly, is you trait?
cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827
to compare 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
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
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
odel implemented in various programs may
differ a bit!
See also Butler and King work, O'Meara, 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:
g studies (e.g. Wolf et al.,
1998; Perry and Garland, 2002; Rezende et 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
and Ives (2000).
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 resu
c, 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 92
nd A. R. Ives. 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 Phon
ones. 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: (951) 827-3524
Wet Lab Phone: (951) 827-5724
Dry Lab Phone:
"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
in the trait in that bifurcation of your tree.
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
Skype:
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
nd dorsal scale rows in
Sceloporus lizards: a phylogenetic perspective. Evolution 65:3590-3607.
Nobody knows how well a "model selection" approach that really works in this
specific context, but we are going with it for now until somebody does massive
simulations!
Cheers,
Ted
Th
this in R 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
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 a
hough. 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
Su
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
H
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:
Couldn't you also just do this back at the level of the original tree and tip
data, creating subsets by pruning the tree before you compute contrasts?
Cheers,
Ted
Theodore Garland, Jr., Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone:
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/p
Dear Jorge,
For simplicity, I'd start with these two papers, both available on my webpage:
Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of
continuous characters. Systematic Biology 42:569–575.
Theodore Garland, Jr., Paul H. Harvey, and Anthony R. Ives.
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
Andrea, remember that you can and should also do the "OLS" models (i.e.,
assuming a star phylogeny) with measurement error considered. That's in the
programs that accompany Ives, Midford, and Garland (2007, Syst. Biol.
56:252–270), and were in the batch I just sent you.
Cheers
eters, 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
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
Fer
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
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
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
e is that any 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.
Che
: Thursday, 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 ev
rm a regression (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!
Chee
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
of the bounded degrees of freedom approach. Systematic
Biology 48:547-558.
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
he same 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.biolo
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] PGL
among 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
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: Monday,
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
GLS regression estimators 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
h
. 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
.
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
.
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
and to 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
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
.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
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