[R-sig-phylo] PGLS with non-ultrametric tree
Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] PGLS with non-ultrametric tree
Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the 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.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Solomon Chak [tc...@vims.edu] Sent: Thursday, July 16, 2015 3:31 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS with non-ultrametric tree Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] PGLS with non-ultrametric tree
Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book http://www.springer.com/us/book/9783662435496ch. 2 pg. 38: most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic traits of extant species with the underlying assumption is that the time available for phenotypic evolution is the same for all taxa. I understand that the methodology of PGLS can use any tree form, I suppose there're different assumptions if I used an additive tree or an ultrametric tree. Could you guide me to some references that explicitly discuss about this? Is it necessary to use an ultrametric tree If I want to estimate lambda in the residual error of the gls and do a branch length transformation as Revell 2010 http://onlinelibrary.wiley.com/doi/10./j.2041-210X.2010.00044.x/pdf suggested? Many thanks! Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA On Thu, Jul 16, 2015 at 2:55 PM, Theodore Garland Jr theodore.garl...@ucr.edu wrote: Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the 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.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Solomon Chak [tc...@vims.edu] Sent: Thursday, July 16, 2015 3:31 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS with non-ultrametric tree Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] PGLS with non-ultrametric tree
I really think this post could be useful for the discussion https://stat.ethz.ch/pipermail/r-sig-phylo/2010-September/000773.html best paolo Da: R-sig-phylo r-sig-phylo-boun...@r-project.org per conto di Solomon Chak tc...@vims.edu Inviato: giovedì 16 luglio 2015 23.19 A: Theodore Garland Jr Cc: r-sig-phylo@r-project.org Oggetto: Re: [R-sig-phylo] PGLS with non-ultrametric tree Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book http://www.springer.com/us/book/9783662435496ch. 2 pg. 38: most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic traits of extant species with the underlying assumption is that the time available for phenotypic evolution is the same for all taxa. I understand that the methodology of PGLS can use any tree form, I suppose there're different assumptions if I used an additive tree or an ultrametric tree. Could you guide me to some references that explicitly discuss about this? Is it necessary to use an ultrametric tree If I want to estimate lambda in the residual error of the gls and do a branch length transformation as Revell 2010 http://onlinelibrary.wiley.com/doi/10./j.2041-210X.2010.00044.x/pdf suggested? Many thanks! Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA On Thu, Jul 16, 2015 at 2:55 PM, Theodore Garland Jr theodore.garl...@ucr.edu wrote: Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the 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.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Solomon Chak [tc...@vims.edu] Sent: Thursday, July 16, 2015 3:31 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS with non-ultrametric tree Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] PGLS with non-ultrametric tree
Hi Solomon, Comparatives methods are routinely applied to non-ultrametric trees, contrary to the text you quoted. See the last chapter of that book. The phylogeny-based analyses that do generally require ultrametric trees are those that fit some form of a lineage diversification model, because these models are ultimately descended from the idea of treating the age of modern lineages as a reverse survivorship curve. Most trait-based analyses are fine. What does typically need to be done for at least some PGLS functions, is accounting for unequal tip variances with non-ultrametric trees. I usually do something like this, just using gls() and ape functions... tiph - diag( vcv.phylo(tree) ) gls(X1~X2 ,correlation=corBrownian(value=1, phy=tree), weights=varFixed(~tiph), data=data) Cheers, -Dave On Thu, Jul 16, 2015 at 3:19 PM, Solomon Chak tc...@vims.edu wrote: Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book http://www.springer.com/us/book/9783662435496ch. 2 pg. 38: most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic traits of extant species with the underlying assumption is that the time available for phenotypic evolution is the same for all taxa. I understand that the methodology of PGLS can use any tree form, I suppose there're different assumptions if I used an additive tree or an ultrametric tree. Could you guide me to some references that explicitly discuss about this? Is it necessary to use an ultrametric tree If I want to estimate lambda in the residual error of the gls and do a branch length transformation as Revell 2010 http://onlinelibrary.wiley.com/doi/10./j.2041-210X.2010.00044.x/pdf suggested? Many thanks! Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA On Thu, Jul 16, 2015 at 2:55 PM, Theodore Garland Jr theodore.garl...@ucr.edu wrote: Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the 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.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Solomon Chak [tc...@vims.edu] Sent: Thursday, July 16, 2015 3:31 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS with non-ultrametric tree Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- David W. Bapst, PhD Adjunct Asst
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-ultrametric tree I really think this post could be useful for the discussion https://stat.ethz.ch/pipermail/r-sig-phylo/2010-September/000773.html best paolo Da: R-sig-phylo r-sig-phylo-boun...@r-project.org per conto di Solomon Chak tc...@vims.edu Inviato: giovedì 16 luglio 2015 23.19 A: Theodore Garland Jr Cc: r-sig-phylo@r-project.org Oggetto: Re: [R-sig-phylo] PGLS with non-ultrametric tree Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book http://www.springer.com/us/book/9783662435496ch. 2 pg. 38: most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic traits of extant species with the underlying assumption is that the time available for phenotypic evolution is the same for all taxa. I understand that the methodology of PGLS can use any tree form, I suppose there're different assumptions if I used an additive tree or an ultrametric tree. Could you guide me to some references that explicitly discuss about this? Is it necessary to use an ultrametric tree If I want to estimate lambda in the residual error of the gls and do a branch length transformation as Revell 2010 http://onlinelibrary.wiley.com/doi/10./j.2041-210X.2010.00044.x/pdf suggested? Many thanks! Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA On Thu, Jul 16, 2015 at 2:55 PM, Theodore Garland Jr theodore.garl...@ucr.edu wrote: Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the 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.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Solomon Chak [tc...@vims.edu] Sent: Thursday, July 16, 2015 3:31 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS with non-ultrametric tree Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares in which gls(y ~ x, correlation=corPagel(value=0.1, phy=phy, fixed=F), weights=varFixed(~tip.heights), data=dat) Cheers, Solomon Chak --- *Solomon **Tin Chi **Chak* Ph.D. Candidate Tel: (804) 684-7484 Marine Biodiversity Laboratory http://www.vims.edu/research/units/labgroups/marine_biodiversity/index.php Virginia Institute of Marine Science http://www.vims.edu/ College of William and Mary http://www.wm.edu/ PO Box 1346 / Rt. 1208 Greate Rd., Gloucester Pt, VA 23062, USA [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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 http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r
