Re: [R-sig-phylo] trait correlations with PICs
Hi all, As traits may be more or less phylogenetically constraint, what about the following solution. For a given trait, first we can perform a phylogenetic regression m - gls(trait ~ 1, corr=corGrafen(0.5,tree,fixed=FALSE)) Then base on the output of the phylogenetic regression we can adjust the branch lengths of the phylogenetic tree new.tree - compute.brlen(tree,power=rho), where rho is in the output of m. Finally, we can compute the PIC based on this new phylogenetic tree. pic.trait -pic(trait,new.tree) Best, Rudolf Original Message Subject: RE: [R-sig-phylo] trait correlations with PICs Date: Wed, 17 Apr 2013 17:16:42 + From: Theodore Garland Jr theodore.garl...@ucr.edu To: Alejandro Gonzalez alejandro.gonza...@ebd.csic.es CC: Anne Kempel kem...@ips.unibe.ch, r-sig-phylo@r-project.org r-sig-phylo@r-project.org Exactly. That's why I wrote: A problem is that then the statistical model is unclear/confusing. But for nuisance variables in a multuple-regression type of model, I see no problem putting them on a star phylogeny if they are not phylogenetically distrubuted (e.g., assuming that a particular technique for measuring, say, home range size, does not tend to be applied in a clade-specific [biased] fashion). So far as I am aware, Nobody knows exactly jhow to do this, nor has tried to implement this, with PGLS or phylogenetic regression models! We mention this in Garland 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 result of ignorance... With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004). From an evolutionary point of view, what does it mean when using different sets of branch lengths for different traits? If we're testing co-evolution of traits, I would tend to think - and I may very well be wrong - that the interest would be in estimating a single rate describing this co-evolution and by employing different branch lengths would we not loose the opportunity to estimtate that rate? Cheers Alejandro On 17, Apr 2013, at 6:24 PM, Theodore Garland Jr wrote: For correlations per se, please check this paper: 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. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. I could not find any reference doing this, and I wonder whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among 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. office (not confidential) Email:tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Inquiry-based Middle School Lesson Plan: Born to Run: Artificial Selection Lab http://www.indiana.edu/~ensiweb/lessons/BornToRun.html From: r
[R-sig-phylo] trait correlations with PICs
Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne -- Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland ___ 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] trait correlations with PICs
-project.org Subject: Re: [R-sig-phylo] trait correlations with PICs Hello Anne, The problem of non-independence, from a statistical point of view, has to do with the residuals of the relationship, hence testing phylogenetic signal of the traits - and not the residuals - can be misleading. Liam Revell has a paper in Methods in Ecology and Evolution (I think) that deals with this issue. Labra et al 2009 also discuss this briefly in the introduction of their paper. Although GLS is based on regression the results can only be interpreted as correlations because we have no way of determining causality, and an advantage of PGLS is that it includes the lambda parameter which estimates the required phylogenetic correction (emphasis on the quotations) for the data (actually for the residuals of the model), also see Freckleton et al 2002 and Revell 2010. Cheers Alejandro On 17, Apr 2013, at 2:37 PM, Anne Kempel wrote: Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland ___ 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/ __ Alejandro Gonzalez Voyer Post-doc Estaci�n Biol�gica de Do�ana Consejo Superior de Investigaciones Cient�ficas (CSIC) Av Am�rico Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web site (Under construction): Personal page: http://consevol.org/members/alejandro_combo.html Group page: http://consevol.org/people.html http://csic.academia.edu/AlejandroGonzalezVoyer ___ 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] trait correlations with PICs
For correlations per se, please check this paper: 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. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. I could not find any reference doing this, and I wonder whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among 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. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Inquiry-based Middle School Lesson Plan: Born to Run: Artificial Selection Lab http://www.indiana.edu/~ensiweb/lessons/BornToRun.html From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Anne Kempel [kem...@ips.unibe.ch] Sent: Wednesday, April 17, 2013 5:37 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] trait correlations with PICs Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne -- Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland ___ 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] trait correlations with PICs
Can I risk a question here, maybe a result of ignorance... With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004). From an evolutionary point of view, what does it mean when using different sets of branch lengths for different traits? If we're testing co-evolution of traits, I would tend to think - and I may very well be wrong - that the interest would be in estimating a single rate describing this co-evolution and by employing different branch lengths would we not loose the opportunity to estimtate that rate? Cheers Alejandro On 17, Apr 2013, at 6:24 PM, Theodore Garland Jr wrote: For correlations per se, please check this paper: 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. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. I could not find any reference doing this, and I wonder whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among 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. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Inquiry-based Middle School Lesson Plan: Born to Run: Artificial Selection Lab http://www.indiana.edu/~ensiweb/lessons/BornToRun.html From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Anne Kempel [kem...@ips.unibe.ch] Sent: Wednesday, April 17, 2013 5:37 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] trait correlations with PICs Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne -- Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland ___ 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
Re: [R-sig-phylo] trait correlations with PICs
Exactly. That's why I wrote: A problem is that then the statistical model is unclear/confusing. But for nuisance variables in a multuple-regression type of model, I see no problem putting them on a star phylogeny if they are not phylogenetically distrubuted (e.g., assuming that a particular technique for measuring, say, home range size, does not tend to be applied in a clade-specific [biased] fashion). So far as I am aware, Nobody knows exactly jhow to do this, nor has tried to implement this, with PGLS or phylogenetic regression models! We mention this in Garland 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 result of ignorance... With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004). From an evolutionary point of view, what does it mean when using different sets of branch lengths for different traits? If we're testing co-evolution of traits, I would tend to think - and I may very well be wrong - that the interest would be in estimating a single rate describing this co-evolution and by employing different branch lengths would we not loose the opportunity to estimtate that rate? Cheers Alejandro On 17, Apr 2013, at 6:24 PM, Theodore Garland Jr wrote: For correlations per se, please check this paper: 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. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the signal-traits but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. I could not find any reference doing this, and I wonder whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among 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. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=enuser=iSSbrhwJ Inquiry-based Middle School Lesson Plan: Born to Run: Artificial Selection Lab http://www.indiana.edu/~ensiweb/lessons/BornToRun.html From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Anne Kempel [kem...@ips.unibe.ch] Sent: Wednesday, April 17, 2013 5:37 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] trait correlations with PICs Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate pseudo-PICs based on a star phylogeny
