Oh yes! I forgot OUwie! This is definitely the easiest way for this kind of simulations with make.era.map. But I think that fitting OU models on several time bin is not the best idea with ultrametric trees.
Julien Envoyé de mon iPad > Le 5 nov. 2014 à 18:30, "Liam J. Revell" <liam.rev...@umb.edu> a écrit : > > Hi Lara. > > I have not tried this myself, but theoretically you should be able to use > make.era.map in phytools to paint different regimes to different time > periods; and then OUwie.sim (with simmap.tree=TRUE) in the OUwie package to > simulate different OU process in different regimes. Let us know if this works. > > 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 11/5/2014 12:21 PM, Lara Budic wrote: >> Hi Julien, >> >> thank you for your suggestions! I also thought of using make.era.map. >> As I understand it, it is possible to transform each slice according to >> different rates by multiplying the branch lengths, but I am still struggling >> to transform different time-periods according to a different alpha value. >> >> Basically I would like to visualize trait evolution in which each time >> period has a different alpha and sigma2. >> I still haven't find a way but I will explore the options in phytools then, >> thanks. >> >> >> Lara >> >> >>> On 3 Nov 2014, at 19:44, Julien Clavel wrote: >>> >>> Hi Lara, >>> >>> You can use the make.era.map function in phytools to slice your tree in >>> simmap like format. Then you multiply the mapped time slices by the >>> required rate (eg, tree$mapped.edge[,1]*sigma) and then use >>> tree$edge.length<-rowSum(tree$mapped.edge) or something like that. >>> >>> HTH >>> >>> Julien >>> >>>> From: lara.bu...@biom.uni-freiburg.de >>>> To: r-sig-phylo@r-project.org >>>> Date: Mon, 3 Nov 2014 18:36:34 +0100 >>>> Subject: [R-sig-phylo] Rescaling trees >>>> >>>> Hello R Phylo list >>>> >>>> I have a question regarding rescaling trees. >>>> >>>> "rescale" function in geiger has an option to rescale the >>>> tree in which different time slices have a different rate >>>> of evolution. >>>> >>>> I would like to rescale each time slice with a different >>>> rate but also with a specific alpha parameter (for a >>>> time-dependent OU model). >>>> >>>> Do you know if that would be possible somehow? >>>> >>>> I will greatly appreciate any thoughts and suggestions. >>>> >>>> >>>> >>>> Lara Budic >>>> PhD student at Biometry and Environmental System Analysis >>>> Faculty of Environment and Natural Resources >>>> University of Freiburg >>>> Tennenbacherstr. 4 >>>> 79106 Freiburg i. Br. >>>> >>>> _______________________________________________ >>>> 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/ >> >> >> [[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/
