pgls.Ives(tree, X, y, Vx=NULL, Vy=NULL, Cxy=NULL, lower=c(1e-8,1e-8))"phylo".X can contain the species means, or a single long vector containing the sample of values for each species. In the latter case the names(X) will be repeating - all samples from the same species should have the same name.X.X. If NULL, then the within-species variance is computed from the data assuming that individual samples, not species means, have been provided in X.y. If NULL, then the within-species variance is computed from the data assuming that individual samples, not species means, have been provided in y.X and y. This will also be computed from the data if Cxy==NULL. Note than in this case - but not for the calculation of Vx and Vy, the same number of observations and the same ordering must be provided for X and y. If this is not the case, then it is assumed that different individuals have been sampled for X and y and thus Cxy is assumed to be zero for all species.sig2x and sig2y, respectively. (Must be >0.)optim(...,method="L-BFGS-B") for optimization. Note that some problems have been reported with the optimization algorithm for this model, which is simple and thus may fail to find the ML solution.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
brownie.lite, phylosig, phyl.resid