Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Dear Marguerite and everyone, thank you very much for your considerate postings. I have reconsidered my analyses and excluded the zero values, because they indicate absence of the trait rather than are part of the continuum of values. Instead, I analyzed the data as a 1) discrete trait: presence/absence of trait, and 2) continuous trait, where trait present. In the absence of zeros, the continuous data log-transform to normality where sufficient variability exists. Thank you again, Nina On 2012-04-25, at 9:13 PM, Marguerite Butler wrote: Hi Nina and everyone, One thing to consider is that not all zero data are the same. Zeros under a model of continuous trait evolution with a gaussian process as assumed under Brownian motion and OU processes would occasionally cross zero, maybe go negative, etc. For example if you were modeling something like the deviation from average height. You may have a lot of individuals that are at zero because they are all average, but their offspring will quickly move off zero as some will be taller, some shorter than average. On the other hand, many of us measure traits which disappear, for example scale counts on fish. Numbers of scale rows vary while there are scales, but once they disappear, those lineages will be at zero, perhaps for a very long time. In this case it is no longer behaving as a gaussian process with small changes expected every time period. We usually think of these more as a threshold trait. Maybe there is some hormone or something else (a hidden variable) underlying the determination of scales or no scales, and once it goes below threshhold the scales disappear. The hidden variable may fit model assumptions, but not the scale counts (what we can see and measure). For example, the scale counts can never go negative. With a value like height, it also never goes negative, but usually we are far away from that zero boundary so we can casually ignore that problem:). Or we can do a log-transform, or something else that transforms the data onto a different scale. Anyway, the! absorbing boundary zeros are, I think, an example of what Ted is talking about. So it depends on the nature of your data. On the other hand, for the other variable, if there is just not much variation, but it's not stuck on any particular value (doesn't appear to have any absorbing boundary), I think that's less of a problem. HTH, Marguerite On Apr 25, 2012, at 7:17 AM, Theodore Garland Jr wrote: Read over the Blomberg et al. (2003) paper. K is intended for continuous-valued traits and/or those evolving similar to Brownian motion. You could report it if you wished, but I would add that caveat if you do. The randomization test should be robust in any case. Cheers, Ted From: Nina 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) Thanks all for your helpful contributions! I will use phylosignal. Ted, I'm not sure I understand your last comment, when the data are not though of as continuous-valued and/or evolving similar to Brownian motion. What do you mean by that? Also, are you suggesting that I report the presence/absence of phylogenetic signal, but not the value of the K statistic? Many thanks again, Nina On 2012-04-25, at 5:54 PM, Theodore Garland Jr wrote: However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however. Cheers, Ted [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 South Africa [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I 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://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 South Africa [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo 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.html Group page: http://consevol.org/index.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however. Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 25, 2012 8:46 AM To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I 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://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 South Africa [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo __ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo 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.html Group page: http://consevol.org/index.html For PDF copies of papers see: 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
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Thanks all for your helpful contributions! I will use phylosignal. Ted, I'm not sure I understand your last comment, when the data are not though of as continuous-valued and/or evolving similar to Brownian motion. What do you mean by that? Also, are you suggesting that I report the presence/absence of phylogenetic signal, but not the value of the K statistic? Many thanks again, Nina On 2012-04-25, at 5:54 PM, Theodore Garland Jr wrote: However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however. Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 25, 2012 8:46 AM To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I 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://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 South Africa ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Read over the Blomberg et al. (2003) paper. K is intended for continuous-valued traits and/or those evolving similar to Brownian motion. You could report it if you wished, but I would add that caveat if you do. The randomization test should be robust in any case. Cheers, Ted From: Nina 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) Thanks all for your helpful contributions! I will use phylosignal. Ted, I'm not sure I understand your last comment, when the data are not though of as continuous-valued and/or evolving similar to Brownian motion. What do you mean by that? Also, are you suggesting that I report the presence/absence of phylogenetic signal, but not the value of the K statistic? Many thanks again, Nina On 2012-04-25, at 5:54 PM, Theodore Garland Jr wrote: However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however. Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 25, 2012 8:46 AM To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I 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://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Dear fellow list users, I would like to assess the magnitude of phylogenetic signal in two sets of continuous data. Set 1 contains numerous zeros and is therefore non-normal. Set 2 contains very little variation and is non-normal due to underdispersion. Given that both data sets are largely immune to transformations to normality, I am wondering whether the lambda estimates for untransformed data derived from phylosig and fitContinuous will be meaningful? If not, can you recommend transformations or other methods of phylogenetic-signal assessment that would be preferable? Thank you very much, Nina Dr. Nina Hobbhahn Post-doctoral fellow Lab of Prof. S. D. Johnson School of Life Sciences University of KwaZulu-Natal Private Bag X01 Scottsville, Pietermaritzburg, 3201 South Africa ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)
Hi Nina and everyone, One thing to consider is that not all zero data are the same. Zeros under a model of continuous trait evolution with a gaussian process as assumed under Brownian motion and OU processes would occasionally cross zero, maybe go negative, etc. For example if you were modeling something like the deviation from average height. You may have a lot of individuals that are at zero because they are all average, but their offspring will quickly move off zero as some will be taller, some shorter than average. On the other hand, many of us measure traits which disappear, for example scale counts on fish. Numbers of scale rows vary while there are scales, but once they disappear, those lineages will be at zero, perhaps for a very long time. In this case it is no longer behaving as a gaussian process with small changes expected every time period. We usually think of these more as a threshold trait. Maybe there is some hormone or something else (a hidden variable) underlying the determination of scales or no scales, and once it goes below threshhold the scales disappear. The hidden variable may fit model assumptions, but not the scale counts (what we can see and measure). For example, the scale counts can never go negative. With a value like height, it also never goes negative, but usually we are far away from that zero boundary so we can casually ignore that problem:). Or we can do a log-transform, or something else that transforms the data onto a different scale. Anyway, the a! bsorbing boundary zeros are, I think, an example of what Ted is talking about. So it depends on the nature of your data. On the other hand, for the other variable, if there is just not much variation, but it's not stuck on any particular value (doesn't appear to have any absorbing boundary), I think that's less of a problem. HTH, Marguerite On Apr 25, 2012, at 7:17 AM, Theodore Garland Jr wrote: Read over the Blomberg et al. (2003) paper. K is intended for continuous-valued traits and/or those evolving similar to Brownian motion. You could report it if you wished, but I would add that caveat if you do. The randomization test should be robust in any case. Cheers, Ted From: Nina 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) Thanks all for your helpful contributions! I will use phylosignal. Ted, I'm not sure I understand your last comment, when the data are not though of as continuous-valued and/or evolving similar to Brownian motion. What do you mean by that? Also, are you suggesting that I report the presence/absence of phylogenetic signal, but not the value of the K statistic? Many thanks again, Nina On 2012-04-25, at 5:54 PM, Theodore Garland Jr wrote: However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however. Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 25, 2012 8:46 AM To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation. Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr wrote: I would suggest the randomization test in Blomberg et al. (2003). This will give a valid significance test of the null hypothesis of no phylogenetic signal. By itself, it does not give a measure of the strength (or amount) of phylogenetic signal. Not sure if it is implented in r. If not, I 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://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From:
