Re: [R-sig-phylo] simulating rate shifts
Hi Liam, Yes, the idea would be to stochastically change, say, the speciation rate, so that the rate of diversification will shift in certain subclades, but not all (or at least not all at once). But, as you say, it won’t be possible to tell the shifts where on the tree to occur and, for this reason, I think the pruning-grafting approach is preferable. Regards, Eric On 01 Aug 2015, at 21:50, Liam J. Revell wrote: > Hi Eric. > > If you want to do a "process-based simulation", what is the process that you > want to simulate? If you want to simulate a process in which the rate of > diversification changes randomly in the tree as a continuous-time Markov > process, or by some other related process, then this it may be equivalent to > BiSSE or related state-dependent diversification model which I believe can > all be simulated using the package diversitree. > > The problem with this is that if you simulate trees in which the rate of > diversification changes stochastically, then you might have one change, or > two, or none at all, and there is no way of predicting a priori where those > changes will occur on the tree. Does this make sense? > > If, on the other hand, you want to simulate a tree in which there was first > one rate of diversification, then a single shift occurred to a second rate on > one lineage or at some point in the past, then this is the way to do that. > > 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 8/1/2015 4:12 AM, Eric wrote: >> Hi Liam, >> >> Yes, this is what I meant. I’m a little surprised that no process-based >> simulation - rather than prune-and-graft - method exists. In any case, thank >> you for the example, it is very helpful. >> >> Regards, >> Eric >> >> >>> On Jul 31, 2015, at 8:07 PM, Liam J. Revell wrote: >>> >>> Hi Emmanuel & Eric. >>> >>> I think it's possible that Eric is interested in simulating shifts in the >>> lineage diversification (speciation and/or extinction) rate, rather than >>> the rate of phenotypic trait evolution. >>> >>> It is possible to simulate various scenarios of trait-based diversification >>> in the package diversitree, I believe; however if you are merely interested >>> in taking (or simulating some tree) and then imagining (and simulating) a >>> different diversification process for part of that tree, then this is >>> exactly the same as simulating first one tree under process 1 - then >>> pruning a subtree, simulating a replacement subtree under process 2, and >>> attaching the new subtree from whence the previous subtree was removed. >>> >>> Since this is easier said then done, I posted a more detailed worked >>> example on my blog here: >>> http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. >>> >>> 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : > Hello, > > There are several functions available for simulating rate shifts in > trees (e.g., SimTree, TESS), but these implement tree-wide shifts, > which are somewhat unrealistic, rather than shifts descending from a > particular node. Is it possible to implement a more realistic rate > shifted tree? Has such a thing already been implemented? > > Thanks. >[[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/ > > > Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : > http://f.security-mail.net/301iAWLdbwV > > ___ 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-ph
Re: [R-sig-phylo] simulating rate shifts
Hi Eric. If you want to do a "process-based simulation", what is the process that you want to simulate? If you want to simulate a process in which the rate of diversification changes randomly in the tree as a continuous-time Markov process, or by some other related process, then this it may be equivalent to BiSSE or related state-dependent diversification model which I believe can all be simulated using the package diversitree. The problem with this is that if you simulate trees in which the rate of diversification changes stochastically, then you might have one change, or two, or none at all, and there is no way of predicting a priori where those changes will occur on the tree. Does this make sense? If, on the other hand, you want to simulate a tree in which there was first one rate of diversification, then a single shift occurred to a second rate on one lineage or at some point in the past, then this is the way to do that. 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 8/1/2015 4:12 AM, Eric wrote: Hi Liam, Yes, this is what I meant. I’m a little surprised that no process-based simulation - rather than prune-and-graft - method exists. In any case, thank you for the example, it is very helpful. Regards, Eric On Jul 31, 2015, at 8:07 PM, Liam J. Revell wrote: Hi Emmanuel & Eric. I think it's possible that Eric is interested in simulating shifts in the lineage diversification (speciation and/or extinction) rate, rather than the rate of phenotypic trait evolution. It is possible to simulate various scenarios of trait-based diversification in the package diversitree, I believe; however if you are merely interested in taking (or simulating some tree) and then imagining (and simulating) a different diversification process for part of that tree, then this is exactly the same as simulating first one tree under process 1 - then pruning a subtree, simulating a replacement subtree under process 2, and attaching the new subtree from whence the previous subtree was removed. Since this is easier said then done, I posted a more detailed worked example on my blog here: http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? Thanks. [[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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/301iAWLdbwV ___ 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] simulating rate shifts
Hi Eric, The thing is that it becomes very cumbersome to write user-friendly software with generalized simulation routines to allow various (unlimited?) ad hoc changes in rates of trait evolution, selection regimes (e.g., OU), rates of speciation, etc. so, the expedient approach is often called for. 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=en&user=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 Eric [eric...@hotmail.com] Sent: Saturday, August 01, 2015 1:12 AM To: Liam J. Revell Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] simulating rate shifts Hi Liam, Yes, this is what I meant. I’m a little surprised that no process-based simulation - rather than prune-and-graft - method exists. In any case, thank you for the example, it is very helpful. Regards, Eric > On Jul 31, 2015, at 8:07 PM, Liam J. Revell wrote: > > Hi Emmanuel & Eric. > > I think it's possible that Eric is interested in simulating shifts in the > lineage diversification (speciation and/or extinction) rate, rather than the > rate of phenotypic trait evolution. > > It is possible to simulate various scenarios of trait-based diversification > in the package diversitree, I believe; however if you are merely interested > in taking (or simulating some tree) and then imagining (and simulating) a > different diversification process for part of that tree, then this is exactly > the same as simulating first one tree under process 1 - then pruning a > subtree, simulating a replacement subtree under process 2, and attaching the > new subtree from whence the previous subtree was removed. > > Since this is easier said then done, I posted a more detailed worked example > on my blog here: > http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. > > 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: >> Hi Eric, >> >> See the function rTraitCont in ape: the parameters of the BM or OU model >> can be branch-specific, so it's easy to specify a change in parameter(s) >> at a given node. There's an example there: >> >> http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits >> >> >> Cheers, >> >> Emmanuel >> >> Le 30/07/2015 11:31, Eric Lewitus a écrit : >>> Hello, >>> >>> There are several functions available for simulating rate shifts in >>> trees (e.g., SimTree, TESS), but these implement tree-wide shifts, >>> which are somewhat unrealistic, rather than shifts descending from a >>> particular node. Is it possible to implement a more realistic rate >>> shifted tree? Has such a thing already been implemented? >>> >>> Thanks. >>>[[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/ >>> >>> >>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : >>> http://f.security-mail.net/301iAWLdbwV >>> >>> >> >> ___ >> 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/
Re: [R-sig-phylo] simulating rate shifts
Hi Liam, Yes, this is what I meant. I’m a little surprised that no process-based simulation - rather than prune-and-graft - method exists. In any case, thank you for the example, it is very helpful. Regards, Eric > On Jul 31, 2015, at 8:07 PM, Liam J. Revell wrote: > > Hi Emmanuel & Eric. > > I think it's possible that Eric is interested in simulating shifts in the > lineage diversification (speciation and/or extinction) rate, rather than the > rate of phenotypic trait evolution. > > It is possible to simulate various scenarios of trait-based diversification > in the package diversitree, I believe; however if you are merely interested > in taking (or simulating some tree) and then imagining (and simulating) a > different diversification process for part of that tree, then this is exactly > the same as simulating first one tree under process 1 - then pruning a > subtree, simulating a replacement subtree under process 2, and attaching the > new subtree from whence the previous subtree was removed. > > Since this is easier said then done, I posted a more detailed worked example > on my blog here: > http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. > > 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: >> Hi Eric, >> >> See the function rTraitCont in ape: the parameters of the BM or OU model >> can be branch-specific, so it's easy to specify a change in parameter(s) >> at a given node. There's an example there: >> >> http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits >> >> >> Cheers, >> >> Emmanuel >> >> Le 30/07/2015 11:31, Eric Lewitus a écrit : >>> Hello, >>> >>> There are several functions available for simulating rate shifts in >>> trees (e.g., SimTree, TESS), but these implement tree-wide shifts, >>> which are somewhat unrealistic, rather than shifts descending from a >>> particular node. Is it possible to implement a more realistic rate >>> shifted tree? Has such a thing already been implemented? >>> >>> Thanks. >>>[[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/ >>> >>> >>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : >>> http://f.security-mail.net/301iAWLdbwV >>> >>> >> >> ___ >> 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] simulating rate shifts
Hi Emmanuel & Eric. I think it's possible that Eric is interested in simulating shifts in the lineage diversification (speciation and/or extinction) rate, rather than the rate of phenotypic trait evolution. It is possible to simulate various scenarios of trait-based diversification in the package diversitree, I believe; however if you are merely interested in taking (or simulating some tree) and then imagining (and simulating) a different diversification process for part of that tree, then this is exactly the same as simulating first one tree under process 1 - then pruning a subtree, simulating a replacement subtree under process 2, and attaching the new subtree from whence the previous subtree was removed. Since this is easier said then done, I posted a more detailed worked example on my blog here: http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html. 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote: Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? Thanks. [[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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/301iAWLdbwV ___ 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] simulating rate shifts
Hi Eric, See the function rTraitCont in ape: the parameters of the BM or OU model can be branch-specific, so it's easy to specify a change in parameter(s) at a given node. There's an example there: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits Cheers, Emmanuel Le 30/07/2015 11:31, Eric Lewitus a écrit : Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? Thanks. [[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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/301iAWLdbwV ___ 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] simulating rate shifts
Hello, There are several functions available for simulating rate shifts in trees (e.g., SimTree, TESS), but these implement tree-wide shifts, which are somewhat unrealistic, rather than shifts descending from a particular node. Is it possible to implement a more realistic rate shifted tree? Has such a thing already been implemented? Thanks. [[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/
