Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Dear Alejandro, Paolo, and Liam, thanks so much for your feedback on this - I was able to get Liam's method to work on my trees and data. Very useful to be able to do! Alejandro is right about BayesTraits, but indeed my data is continuous, so I was disappointed to find out that BayesTraits only takes discrete values. But of course, everything is possible with R! The only thing that I'm still curious about is whether it would be possible to set a range of values for this ancestral state, rather than a single value. As Liam points out, we have to be quite confident in this ancestor and the value that we assign to it in order to have some confidence in our reconstructions. Of my ancestor I'm quite sure as there is historical data pointing to its existence. However, I think it would increase my confidence in the analysis if I could assign a range of values, i.e. something like 0.3-0.5, to this taxon. Or even better, a range of values associated with a normal distribution, so 0.3-0.5 would all be equally likely, with 'sloping' sides on both sides of the range that indicate increasingly less likely values. Since my data is continuous, this somehow seems like a more realistic analysis to me. However, I don't know whether this is even possible, as I can imagine it would increase the complexity of the ancestral state reconstruction immensely. If you have any ideas on this, I would be very happy to hear them - and thanks again for the earlier feedback! Annemarie Liam J. Revell wrote: Hi Annemarie, I do think this makes sense - *if* (and this may be a big if, depending on your data) we have a value for a hypothetical ancestor for which we are very confident and which we are sure belongs at a particularly ancestral node. In that case, you could indeed use ace() by assigning attaching a zero length tip edge to the internal node of interest. To illustrate this using an example, let's do the following: # first generate a pure-birth tree using birthdeath.tree in geiger tree-drop.tip(birthdeath.tree(b=1,d=0,taxa.stop=21),21) # now plot the tree with internal node numbers plot(tree); nodelabels(length(tree$tip)+1:tree$Nnode) # now let's simulate on the tree using fastBM() from my phytools package # (not on CRAN, but http://anolis.oeb.harvard.edu/~liam/R-phylogenetics) # in this case we know the ancestral states if we set internal=TRUE x-fastBM(tree,internal=T) y-x[1:length(tree$tip)] # only the tip states # now, let's say we want to attach the tip to node 22 in this case tip-list(edge=matrix(c(2L,1L),1,2),tip.label=22,edge.length=0,Nnode=1L) class(tip)-phylo atree-multi2di(bind.tree(tree,tip,where=22)) z-c(y,x[22]) # now let's estimate ancestral states - we can do this using # method=gls res.gls-ace(z,atree,method=GLS,corStruct=corBrownian(1,atree)) Keep in mind that the node numbers in tree and atree are different (because the latter has a different number of tips) *and* we have a different number of them (because we used multi2di() to fully resolve our multifurcating tree after we attached the extra tip). Hope this helps. - Liam -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Dear phylo-sig list people, I want to do ancestral state reconstruction (preferably with ace) with one (or more) of the internal nodes 'fixed' for a range / a distribution of values. For instance, I want a node leading to one particular clade that is present a subset of my trees to have a value from 0.2-0.5, and then do the ancestral state reconstruction with this restriction on that node. I have been searching the archives and the net for discussion of this (but maybe with the wrong search terms), and I cannot find anything about it - not how to do it in R or in any other package. Thanks for your input! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Hi AnneMarie, I dont really know if this makes sense; in fact ancestral state reconstruction is an ** a posteriori estimation ** of nodal values starting from tips observations. A trick could be to add a false taxon lnked to that node and giving to it a 0 branch length (i.e. plitomized - you can then resolve this during computation using multi2di() ) and assigning your desired trait value. I'm not sure if this helps Best Paolo Dear phylo-sig list people, I want to do ancestral state reconstruction (preferably with ace) with one (or more) of the internal nodes 'fixed' for a range / a distribution of values. For instance, I want a node leading to one particular clade that is present a subset of my trees to have a value from 0.2-0.5, and then do the ancestral state reconstruction with this restriction on that node. I have been searching the archives and the net for discussion of this (but maybe with the wrong search terms), and I cannot find anything about it - not how to do it in R or in any other package. Thanks for your input! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ 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
Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Hi AnneMarie, The way Paolo suggests would be the best/right way to do this. We're working on some methods for incorporating fossil info in comparative methods and I have some code that will do this that i can send you off-list if you would like. I should add that, at least based on what we've found so far, doing this probably won't make much difference to your reconstructed ancestral states, simply because under BM, your CIs are so wide without constraining nodes that doing so has little effect. best, Graham On 06/30/2011 09:40 AM, ppi...@uniroma3.it wrote: Hi AnneMarie, I dont really know if this makes sense; in fact ancestral state reconstruction is an ** a posteriori estimation ** of nodal values starting from tips observations. A trick could be to add a false taxon lnked to that node and giving to it a 0 branch length (i.e. plitomized - you can then resolve this during computation using multi2di() ) and assigning your desired trait value. I'm not sure if this helps Best Paolo Dear phylo-sig list people, I want to do ancestral state reconstruction (preferably with ace) with one (or more) of the internal nodes 'fixed' for a range / a distribution of values. For instance, I want a node leading to one particular clade that is present a subset of my trees to have a value from 0.2-0.5, and then do the ancestral state reconstruction with this restriction on that node. I have been searching the archives and the net for discussion of this (but maybe with the wrong search terms), and I cannot find anything about it - not how to do it in R or in any other package. Thanks for your input! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ 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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Hi Annemarie, I do think this makes sense - *if* (and this may be a big if, depending on your data) we have a value for a hypothetical ancestor for which we are very confident and which we are sure belongs at a particularly ancestral node. In that case, you could indeed use ace() by assigning attaching a zero length tip edge to the internal node of interest. To illustrate this using an example, let's do the following: # first generate a pure-birth tree using birthdeath.tree in geiger tree-drop.tip(birthdeath.tree(b=1,d=0,taxa.stop=21),21) # now plot the tree with internal node numbers plot(tree); nodelabels(length(tree$tip)+1:tree$Nnode) # now let's simulate on the tree using fastBM() from my phytools package # (not on CRAN, but http://anolis.oeb.harvard.edu/~liam/R-phylogenetics) # in this case we know the ancestral states if we set internal=TRUE x-fastBM(tree,internal=T) y-x[1:length(tree$tip)] # only the tip states # now, let's say we want to attach the tip to node 22 in this case tip-list(edge=matrix(c(2L,1L),1,2),tip.label=22,edge.length=0,Nnode=1L) class(tip)-phylo atree-multi2di(bind.tree(tree,tip,where=22)) z-c(y,x[22]) # now let's estimate ancestral states - we can do this using # method=gls res.gls-ace(z,atree,method=GLS,corStruct=corBrownian(1,atree)) Keep in mind that the node numbers in tree and atree are different (because the latter has a different number of tips) *and* we have a different number of them (because we used multi2di() to fully resolve our multifurcating tree after we attached the extra tip). Hope this helps. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 6/30/2011 12:40 PM, ppi...@uniroma3.it wrote: Hi AnneMarie, I dont really know if this makes sense; in fact ancestral state reconstruction is an ** a posteriori estimation ** of nodal values starting from tips observations. A trick could be to add a false taxon lnked to that node and giving to it a 0 branch length (i.e. plitomized - you can then resolve this during computation using multi2di() ) and assigning your desired trait value. I'm not sure if this helps Best Paolo Dear phylo-sig list people, I want to do ancestral state reconstruction (preferably with ace) with one (or more) of the internal nodes 'fixed' for a range / a distribution of values. For instance, I want a node leading to one particular clade that is present a subset of my trees to have a value from 0.2-0.5, and then do the ancestral state reconstruction with this restriction on that node. I have been searching the archives and the net for discussion of this (but maybe with the wrong search terms), and I cannot find anything about it - not how to do it in R or in any other package. Thanks for your input! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ 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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)
Hi Graham, I, too, have done this under Brownian motion and squared-change parsimony reconstructions. In my experience (which was a while ago, and memory fades ...), the confidence intervals for nodes near to the one you constrain (near in terms of the length of the branches connecting the nodes) should be reduced, and sometimes substantially, if the constrained node is close by. Right? Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 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 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 Graham Slater [gsla...@ucla.edu] Sent: Thursday, June 30, 2011 10:09 AM To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s) Hi AnneMarie, The way Paolo suggests would be the best/right way to do this. We're working on some methods for incorporating fossil info in comparative methods and I have some code that will do this that i can send you off-list if you would like. I should add that, at least based on what we've found so far, doing this probably won't make much difference to your reconstructed ancestral states, simply because under BM, your CIs are so wide without constraining nodes that doing so has little effect. best, Graham On 06/30/2011 09:40 AM, ppi...@uniroma3.it wrote: Hi AnneMarie, I dont really know if this makes sense; in fact ancestral state reconstruction is an ** a posteriori estimation ** of nodal values starting from tips observations. A trick could be to add a false taxon lnked to that node and giving to it a 0 branch length (i.e. plitomized - you can then resolve this during computation using multi2di() ) and assigning your desired trait value. I'm not sure if this helps Best Paolo Dear phylo-sig list people, I want to do ancestral state reconstruction (preferably with ace) with one (or more) of the internal nodes 'fixed' for a range / a distribution of values. For instance, I want a node leading to one particular clade that is present a subset of my trees to have a value from 0.2-0.5, and then do the ancestral state reconstruction with this restriction on that node. I have been searching the archives and the net for discussion of this (but maybe with the wrong search terms), and I cannot find anything about it - not how to do it in R or in any other package. Thanks for your input! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes ___ 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 ___ 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
