Re: [R-sig-phylo] PGLS transformations
Hi Sergio. Yesterday you asked if it would be reasonable to use the tree with branch lengths simulated assuming a Yule process if the topology is known in phylogenetic regression. I wondered what would happen if, for a given tree topology, we simulated a set of trees with branches as if the tree arose under a Yule process, and then fit our regression model to each tree. We could then add the variance among fitted regression slopes to the mean variance of each slope to get the total variance, from which we could test a hypothesis that (for instance) the slope is not different from zero. Well, I tried this (details here: http://blog.phytools.org/2015/04/phylogenetic-regression-when-branch.html), and, assuming I have done so correctly, it seems as though the approach is too conservative - leading to low power and a type I error rate lower than the nominal level. Using arbitrary branch lengths (all branch lengths equal to 1.0, Grafen's branch lengths) results in elevated type I error, but not incredibly badly inflated type I error. I thought you other R-sig-phylo readers might be interested in this result (newly obtained), or could correct it if I have done something wrong. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 2:20 PM, Liam J. Revell wrote: I wouldn't go as far as to call it a suggestion - but this is one thing that you could do. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 2:04 PM, Sergio Ferreira Cardoso wrote: Hello, So what you're suggesting is that I do that and then fit-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method=ML, right? Thanks. Best regards, Sérgio. ᐧ 2015-04-13 18:42 GMT+01:00 Liam J. Revell liam.rev...@umb.edu mailto:liam.rev...@umb.edu: Hi all. I just wanted to add that it should be straightforward to sample edge lengths as if they arose under a specific process. For instance, here on my blog I show how to sample branching times edge lengths as if they arose under a pure-birth (i.e., 'Yule') process, given a particular input topology: http://blog.phytools.org/2015/__04/sampling-edge-lengths-__under-yule-process.html http://blog.phytools.org/2015/04/sampling-edge-lengths-under-yule-process.html. For things like the phylogenetic (contrasts) regression, this may be preferable to Grafen's edge lengths, which tend to make recent edge lengths very short, giving very high weight to the associated contrasts. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.__revell/ http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote: Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr mailto:emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a
Re: [R-sig-phylo] PGLS transformations
Thank you Liam. I'll check it now. Best regards, Sérgio. 2015-04-14 18:27 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi Sergio. Yesterday you asked if it would be reasonable to use the tree with branch lengths simulated assuming a Yule process if the topology is known in phylogenetic regression. I wondered what would happen if, for a given tree topology, we simulated a set of trees with branches as if the tree arose under a Yule process, and then fit our regression model to each tree. We could then add the variance among fitted regression slopes to the mean variance of each slope to get the total variance, from which we could test a hypothesis that (for instance) the slope is not different from zero. Well, I tried this (details here: http://blog.phytools.org/2015/ 04/phylogenetic-regression-when-branch.html), and, assuming I have done so correctly, it seems as though the approach is too conservative - leading to low power and a type I error rate lower than the nominal level. Using arbitrary branch lengths (all branch lengths equal to 1.0, Grafen's branch lengths) results in elevated type I error, but not incredibly badly inflated type I error. I thought you other R-sig-phylo readers might be interested in this result (newly obtained), or could correct it if I have done something wrong. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 2:20 PM, Liam J. Revell wrote: I wouldn't go as far as to call it a suggestion - but this is one thing that you could do. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 2:04 PM, Sergio Ferreira Cardoso wrote: Hello, So what you're suggesting is that I do that and then fit-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method=ML, right? Thanks. Best regards, Sérgio. ᐧ 2015-04-13 18:42 GMT+01:00 Liam J. Revell liam.rev...@umb.edu mailto:liam.rev...@umb.edu: Hi all. I just wanted to add that it should be straightforward to sample edge lengths as if they arose under a specific process. For instance, here on my blog I show how to sample branching times edge lengths as if they arose under a pure-birth (i.e., 'Yule') process, given a particular input topology: http://blog.phytools.org/2015/__04/sampling-edge-lengths-__ under-yule-process.html http://blog.phytools.org/2015/04/sampling-edge-lengths- under-yule-process.html. For things like the phylogenetic (contrasts) regression, this may be preferable to Grafen's edge lengths, which tend to make recent edge lengths very short, giving very high weight to the associated contrasts. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.__revell/ http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu mailto:liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote: Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards,
Re: [R-sig-phylo] PGLS transformations
Than you all. Best regards, Sérgio. ᐧ 2015-04-13 22:02 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr: Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit : Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Yes! The function pic() has been in ape since its first release (ver. 0.1 in Aug 2002), and there is an option to output the contrasts scaled or not. best, Emmanuel Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr mailto:emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,__fixed=F); fit-gls(FCL~logBodymass,__correlation=gr.mammals,data=__ df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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 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 Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Monday, April 13, 2015 10:13 AM To: Emmanuel Paradis Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] PGLS transformations Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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 transformations
Hello, So what you're suggesting is that I do that and then fit-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method=ML, right? Thanks. Best regards, Sérgio. ᐧ 2015-04-13 18:42 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi all. I just wanted to add that it should be straightforward to sample edge lengths as if they arose under a specific process. For instance, here on my blog I show how to sample branching times edge lengths as if they arose under a pure-birth (i.e., 'Yule') process, given a particular input topology: http://blog.phytools.org/2015/04/sampling-edge-lengths- under-yule-process.html. For things like the phylogenetic (contrasts) regression, this may be preferable to Grafen's edge lengths, which tend to make recent edge lengths very short, giving very high weight to the associated contrasts. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote: Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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 transformations
Hi all. I just wanted to add that it should be straightforward to sample edge lengths as if they arose under a specific process. For instance, here on my blog I show how to sample branching times edge lengths as if they arose under a pure-birth (i.e., 'Yule') process, given a particular input topology: http://blog.phytools.org/2015/04/sampling-edge-lengths-under-yule-process.html. For things like the phylogenetic (contrasts) regression, this may be preferable to Grafen's edge lengths, which tend to make recent edge lengths very short, giving very high weight to the associated contrasts. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote: Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. ___ 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 transformations
Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit : Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Yes! The function pic() has been in ape since its first release (ver. 0.1 in Aug 2002), and there is an option to output the contrasts scaled or not. best, Emmanuel Reading this paper - Garland, T., Harvey, P. H., Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value. Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr mailto:emmanuel.para...@ird.fr: Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,__fixed=F); fit-gls(FCL~logBodymass,__correlation=gr.mammals,data=__df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal ___ 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 transformations
Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE all.equal(compute.brlen(tr), ts) [1] TRUE compute.brlen() transforms the branch lengths according to Grafen's model with parameter rho = 1 (by default). Some other transformations of branch lengths are available in package geiger. Best, Emmanuel Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. ___ 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 transformations
Dear Sergio, I do not use R very much, relying instead on our Matlab programs that accompany Lavin et al. (2008): Lavin S.R., W.H. Karasov, A.R. Ives, K.M. Middleton, and T. Garland Jr. 2008. Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach. Physiological and Biochemical Zoology 81:526–550. I would strongly suggest that you read the appendix to this paper regarding methods, their history, and terminology. Note that a GLS model does not inherently use any kind of branch length transformation. It uses the tree as inputted. It is mathematically equivalent to Felsenstein's (1985) phylogenetically independent contrasts. It implicitly assumes character evolution (or residual character evolution) akin to Brownian motion. Once you start estimating some branch lengths transformation along with regression parameters, 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) 827-4286 (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 Sergio Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Sunday, April 12, 2015 12:47 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS transformations Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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/
[R-sig-phylo] PGLS transformations
Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals-corGrafen(1,phylo,fixed=F); fit-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method=ML). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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/
