Hi Jarod, In fact you can either choose a fixed root, or a draw from a multivariate normal with the stationary covariance (random root).
I will change the name of the options in an upcoming release (and on gitHub) to make it more explicit and make it homogeneous with univariate implementations HTH, Julien For instance for the univariate case, you will also find both parameterizations in the phylolm package (Ho & Ané, 2014): library(mvMORPH) library(phylolm) set.seed(123) tre = pbtree(n=100, scale=1) # with phylolm x <- rTrait(n=1, phy=tre, model="OU", parameters=list(optimal.value=2,sigma2=1,alpha=0.1)) phylolm(x~1,phy=tre,model="OUrandomRoot") phylolm(x~1,phy=tre,model="OUfixedRoot") # with mvMORPH mvOU(tre, x,model="OU1", param=list(vcv="ouch")) mvOU(tre, x,model="OU1", param=list(vcv="mvmorph")) ________________________________________ De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Jarrod Hadfield <j.hadfi...@ed.ac.uk> Envoyé : vendredi 4 mars 2016 07:45 À : r-sig-phylo@r-project.org Objet : [R-sig-phylo] root in mvOU Hi, I am unclear what assumptions are being made about the root values in mvOU, and was wondering if someone could clarify? For ease, imagine an OU1 model where there is one optimum per trait and so theta is a vector. Is the root value assumed to be theta, or a draw from a multivariate normal with expectation theta, and covariance matrix equal to the stationary covariance? Thanks for any help, Jarrod -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ 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/
