Re: [R-sig-phylo] statistically test whether two characters evolve dependently
Thanks, Liam. good to know. I think extending the tools to analyze traits of ordered/unordered multistates can be very useful. There are many interesting traits such as oxygent requirement (anaerobic, facultative, aerobic) of microbes, which is ordered multistates, and habitats (water, air, soil), which is unordered. Best, Peter On Mon, Apr 8, 2013 at 7:00 PM, Liam J. Revell liam.rev...@umb.edu wrote: Peter - I realized that this is not very clear. Threshml can analyze multiple continuous discrete characters, but the discrete characters must be binary. threshBayes has the same limitation, but is also limited to only two traits (binary-binary, binary-continuous, or continuous-continuous). - 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 blog: http://blog.phytools.org On 4/8/2013 8:27 PM, Liam J. Revell wrote: Hi Peter. I'm not sure if this is what you mean, but Felsenstein (2005, 2012) has a method for estimating the correlation between discrete characters or a discrete and a continuous character in which the discrete trait is modeled using the threshold model from quantitative genetics. There is a stand-alone program for this called Threshml (http://evolution.gs.**washington.edu/phylip/**download/threshml/http://evolution.gs.washington.edu/phylip/download/threshml/). I have a Bayesian MCMC version in the phytools package called threshBayes (http://blog.phytools.org/**search?q=threshBayeshttp://blog.phytools.org/search?q=threshBayes). So far, threshBayes only allows binary discrete characters two traits; Threshml can analyze more than two traits - but I believe is still limited to binary discrete characters. Please let me know if it would be helpful to your research to extend threshBayes to allow for multistate (ordered, naturally) discrete characters. 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 blog: http://blog.phytools.org On 4/7/2013 6:35 PM, New Bio wrote: Dear all, Just started studying phylogeny. I know BayesTraits program can calculate the likelihood of the observed data given the model of two charaters evolve dependently or independently. I am wondering how to do it with R packages or functions for discrete and continuous characters? Best, Peter [[alternative HTML version deleted]] __**_ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/**listinfo/r-sig-phylohttps://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-**sig-ph...@r-project.org/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-phylohttps://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-**sig-ph...@r-project.org/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] statistically test whether two characters evolve dependently
New Bio wrote: Thanks, Liam. good to know. I think extending the tools to analyze traits of ordered/unordered multistates can be very useful. There are many interesting traits such as oxygent requirement (anaerobic, facultative, aerobic) of microbes, which is ordered multistates, and habitats (water, air, soil), which is unordered. For approaches like the threshold model, it is not simple to see how to handle multistate characters. Should we assume one scale? If so, how far from the 0/1 threshold should we place the 1/2 threshold? That becomes an additional parameter to be estimated. Or should we have an additional axis, so that 0/1 is on the x axis, while [01]/2 is on another axis? And then what do we do about state 3 if it also exists? That way lies madness ... or perhaps a good Ph.D. thesis topic. (This is in some way related to Transformation Series Analysis, which was an issue with parsimony methods. One imagined one's states arranged in a character transformation series which could even be a tree, the Character State Tree. Then one wanted to infer the phylogeny and at the same time also the CST, using parsimony as the criterion. In a sense what I am raising is the likelihood and modeling equivalent problem.) Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 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] statistically test whether two characters evolve dependently
Thanks for clarifying this, Joe. My function for ancestral character estimation under the threshold model (ancThresh) allows multistate data - but the order of the states along the liability axis needs to be specified a priori by the user.** The relative positions of the thresholds are sampled (along with the liabilities of tips nodes) from their joint posterior probability distribution using MCMC. This method is still undergoing peer review, but it seems to work fairly well in simulations - so this also might be a viable approach for estimating the correlation between multistate threshold characters. (**In my manuscript about ancThresh I suggest that an information criterion like DIC could be used to identify the correct order - but a single true order must exist.) As for unordered multistate characters, I'm not sure how the threshold model could be used. Several people have made suggestions about this to me but I'm not sure I understand them. 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 4/9/2013 7:22 PM, Joe Felsenstein wrote: New Bio wrote: Thanks, Liam. good to know. I think extending the tools to analyze traits of ordered/unordered multistates can be very useful. There are many interesting traits such as oxygent requirement (anaerobic, facultative, aerobic) of microbes, which is ordered multistates, and habitats (water, air, soil), which is unordered. For approaches like the threshold model, it is not simple to see how to handle multistate characters. Should we assume one scale? If so, how far from the 0/1 threshold should we place the 1/2 threshold? That becomes an additional parameter to be estimated. Or should we have an additional axis, so that 0/1 is on the x axis, while [01]/2 is on another axis? And then what do we do about state 3 if it also exists? That way lies madness ... or perhaps a good Ph.D. thesis topic. (This is in some way related to Transformation Series Analysis, which was an issue with parsimony methods. One imagined one's states arranged in a character transformation series which could even be a tree, the Character State Tree. Then one wanted to infer the phylogeny and at the same time also the CST, using parsimony as the criterion. In a sense what I am raising is the likelihood and modeling equivalent problem.) Joe Joe Felsenstein j...@gs.washington.edu mailto:j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ 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] statistically test whether two characters evolve dependently
Hi Peter. I'm not sure if this is what you mean, but Felsenstein (2005, 2012) has a method for estimating the correlation between discrete characters or a discrete and a continuous character in which the discrete trait is modeled using the threshold model from quantitative genetics. There is a stand-alone program for this called Threshml (http://evolution.gs.washington.edu/phylip/download/threshml/). I have a Bayesian MCMC version in the phytools package called threshBayes (http://blog.phytools.org/search?q=threshBayes). So far, threshBayes only allows binary discrete characters two traits; Threshml can analyze more than two traits - but I believe is still limited to binary discrete characters. Please let me know if it would be helpful to your research to extend threshBayes to allow for multistate (ordered, naturally) discrete characters. 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 4/7/2013 6:35 PM, New Bio wrote: Dear all, Just started studying phylogeny. I know BayesTraits program can calculate the likelihood of the observed data given the model of two charaters evolve dependently or independently. I am wondering how to do it with R packages or functions for discrete and continuous characters? Best, Peter [[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] statistically test whether two characters evolve dependently
Peter - I realized that this is not very clear. Threshml can analyze multiple continuous discrete characters, but the discrete characters must be binary. threshBayes has the same limitation, but is also limited to only two traits (binary-binary, binary-continuous, or continuous-continuous). - 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 4/8/2013 8:27 PM, Liam J. Revell wrote: Hi Peter. I'm not sure if this is what you mean, but Felsenstein (2005, 2012) has a method for estimating the correlation between discrete characters or a discrete and a continuous character in which the discrete trait is modeled using the threshold model from quantitative genetics. There is a stand-alone program for this called Threshml (http://evolution.gs.washington.edu/phylip/download/threshml/). I have a Bayesian MCMC version in the phytools package called threshBayes (http://blog.phytools.org/search?q=threshBayes). So far, threshBayes only allows binary discrete characters two traits; Threshml can analyze more than two traits - but I believe is still limited to binary discrete characters. Please let me know if it would be helpful to your research to extend threshBayes to allow for multistate (ordered, naturally) discrete characters. 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 4/7/2013 6:35 PM, New Bio wrote: Dear all, Just started studying phylogeny. I know BayesTraits program can calculate the likelihood of the observed data given the model of two charaters evolve dependently or independently. I am wondering how to do it with R packages or functions for discrete and continuous characters? Best, Peter [[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 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] statistically test whether two characters evolve dependently
Dear all, Just started studying phylogeny. I know BayesTraits program can calculate the likelihood of the observed data given the model of two charaters evolve dependently or independently. I am wondering how to do it with R packages or functions for discrete and continuous characters? Best, Peter [[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/
