Hello, I have a question about the simulate character command in geiger. I want to generate simulations of trait evolution under different models to estimate variance around the estimate of evolutionary parameters for that trait. I've seen in previous posts in the list that characters can be simulated under distinct evolutionary models by transforming the phylogenetic tree prior to the simulation. I was wondering if the same could be done by instead adjusting the model matrix. Specifically I was wondering if ape's corPagel or corMartins could be used to specify different matrices adjusted to distinct values of lambda or alpha instead of transforming the tree. Would this be an appropriate alternative to tree transformation prior to simulations? For example I was thinking of doing something of this sort for a model with alpha of 2.5 with a phylo object called tree and table with a trait called data:
cp<-corMartins(2.5, tree, fixed=TRUE) C<-corMatrix(Initialize(cp, data)) sim.char(tree, model.matrix=C, nsims=100, model="brownian") Cheers, Alejandro __________________________________ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS & NEW E-MAIL Estación Biológica de Doñana (CSIC) Avenida Américo Vespucio s/n 41092 Sevilla Spain E-mail: alejandro.gonza...@ebd.csic.es Tel: +34- 954 466700, ext 1749 Website (From my previous position): http://www.iee.uu.se/zooekol/default.php?type=personalpage&lang=en&id=146 [[alternative HTML version deleted]]
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