Hi Julien, Liam Thanks a lot for your suggestions!
As I see it, make.era.map will define 3 different time-periods on the tree. ouwie.sim could then simulate continuous trait evolution under those time-periods, based on previously fitted alpha, sigma2 and and optima for each individual regime. And this could maybe be used to test for model adequacy (as described in Pennel et al 2014) by comparing simulated data to the original data. But I am not sure if it works correctly for era.maps. Also, I suppose this simulated evolution cannot be plotted. If the simulation gives as output only the tip values, without transforming the tree 'phenogram' will reconstruct a BM evolution. This is what I struggle with, but let me explain better my original question! I have estimates of alpha, sigma2 and theta for each regime which were fitted with OUwie.slice. I would like to visualize the trait evolution according to this model with the real data. The usual way is to rescale the tree and reconstruct the trait on it, I wonder if there is a way to rescale each slice of the era.map with different parameters? I guess this can be done with vcv matrices, but is a bit tricky given that some branches are sliced and the two halves have different set of parameters? Is this feasible somehow? Hopefully... Thanks a lot again All the best, Lara On Wed, 5 Nov 2014 23:28:55 +0100 Julien Clavel <julien.cla...@hotmail.fr> wrote: > 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/ > >> 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/
