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/
