Nlme prediction intervals confidence intervals multiple comparison query
Hi, I am using nlme to fit LMM to a fish acoustic telemetry dataset and it is working very well, however I am using the following very useful code (which I got from http://glmm.wikidot.com/faq) library(nlme) fm1 <- lme(distance ~ age*Sex, random = ~ 1 + age | Subject, data = Orthodont) plot(Orthodont) newdat <- expand.grid(age=c(8,10,12,14), Sex=c("Male","Female")) newdat$pred <- predict(fm1, newdat, level = 0) Designmat <- model.matrix(eval(eval(fm1$call$fixed)[-2]), newdat[-3]) predvar <- diag(Designmat %*% fm1$varFix %*% t(Designmat)) newdat$SE <- sqrt(predvar) newdat$SE2 <- sqrt(predvar+fm1$sigma^2) newdat$upperCI<-newdat$predict+(2*newdat$SE2) newdat$lowerCI<-newdat$predict-(2*newdat$SE2) to obtain confidence intervals from predictions from an lme model. Which works well....however I would like to know; a) what method of confidence interval prediction has been used here?- I dont fully understand how this code (especially the designmat) works- does this code correct for multiple comparisons- and if so which method is used, how does it extract degrees of freedom from the model? b) if the method used is a conservative bonferroni type correction can anyone point me in the right direction to change this code to a less conservative method e.g FDR or something similar? Thanks in advance for any help Philip Harrison MSc PhD student (Fisheries Ecology) Department of Biology University of Waterloo 200 University Avenue West Waterloo, Ontario, Canada N2L 3G1 Cell:226-808-2309 Email:pharriso at uwaterloo.ca