Dear All, I am running into a known and unresolved issue in lme() having to do with how phylogenetic correlation structures (specifically corPagel with co-estimation of phylogenetic signal within the regression) interact with the formula-based way of specifying random effects: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2012q1/015015.html I have a randomized block design in which the block factor is "plate" and multiple measurements per individual (specified by ID), which are nested within "plate" blocks. So, the random formula I am using is: ~ 1 | plate / ID. It turns out that an lme() model with just ~ 1 | ID is slightly favored by AIC and BIC. I am now trying to account for phylogeny and I've been able to get the model to run with gls() with the above two alternative random effects formulas. However, when I try including either random effect formula and corPagel in lme() I get the error mentioned in the linked r-sig-me archived post, i.e.: Error in corFactor.corStruct(object) : NA/NaN/Inf in foreign function call (arg 1) From Simon Blomberg's post I get that when using corPagel specifying the random effects using pdMat constructors is more robust than doing so with a formula. However, I have read parts of Pinheiro & Bates and other resources on the web, but I cannot seem to properly specify a either "~ 1 | plate / ID" nor "~ 1 | ID" with pdMat constructors and I keep on getting a variety of errors when I do so. So, can someone please help me specify "~ 1 | plate / ID" and "~ 1 | ID" with pdMat constructors? Thanks! Dan.
Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2220 Life Sciences Addition, One Shields Ave. Davis, CA 95616