More problems. If I run sim(fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) from the lmer() help page.
I get the error Error in mvrnorm(n.sims, bhat[j, ], V.beta) : 'Sigma' is not positive definite On Mar 7, 2007, at 1:30 PM, Michael Kubovy wrote: > Dear r-helpers, > > I can run the examples on the mcsamp help page. For example: > **************************************** >> M1 <- lmer (y1 ~ x + (1|group)) >> (M1.sim <- mcsamp (M1)) > fit using lmer, > 3 chains, each with 1000 iterations (first 500 discarded) > n.sims = 1500 iterations saved > mean sd 2.5% 25% 50% 75% 97.5% Rhat > n.eff > beta.(Intercept) 0.1 0.7 -1.2 -0.3 0.1 0.5 1.4 1.0 > 1500 > beta.x 2.5 0.4 1.7 2.2 2.5 2.7 3.2 1.0 > 1500 > sigma.y 3.8 0.3 3.3 3.6 3.7 3.9 4.3 > 1.0 61 > sigma.grop.(In) 1.5 0.8 0.0 1.0 1.4 1.9 3.3 > 1.4 12 > eta.group.(Intercept)[1] 0.0 1.0 -2.1 -0.5 0.0 0.6 2.0 1.0 > 1500 > eta.group.(Intercept)[2] 1.0 1.1 -0.9 0.2 0.9 1.7 3.4 > 1.0 59 > eta.group.(Intercept)[3] -1.3 1.2 -4.0 -2.0 -1.3 -0.4 0.5 > 1.0 66 > eta.group.(Intercept)[4] 1.3 1.1 -0.6 0.4 1.1 2.0 3.7 > 1.1 43 > eta.group.(Intercept)[5] -0.7 1.0 -3.0 -1.4 -0.6 0.0 1.2 1.0 > 120 > eta.group.(Intercept)[6] 1.5 1.2 -0.3 0.6 1.4 2.2 4.0 > 1.0 49 > eta.group.(Intercept)[7] 0.3 1.0 -1.7 -0.3 0.1 0.8 2.5 1.0 > 440 > eta.group.(Intercept)[8] -1.6 1.2 -4.0 -2.4 -1.5 -0.6 0.3 > 1.1 41 > eta.group.(Intercept)[9] 0.4 1.0 -1.6 -0.2 0.2 0.9 2.7 1.0 > 180 > eta.group.(Intercept)[10] -1.0 1.1 -3.3 -1.6 -0.9 -0.2 0.8 > 1.0 86 > > For each parameter, n.eff is a crude measure of effective sample size, > and Rhat is the potential scale reduction factor (at convergence, > Rhat=1). > **************************************** > But when I try to do this with my own data I get an error: > **************************************** >> display(e7.lmer2) > lmer(formula = baLO ~ I(baRatio - 0.985) + delta + (1 + I(baRatio - > 0.985) + delta | subject), data = e7) > coef.est coef.se > (Intercept) -0.19 0.06 > I(baRatio - 0.985) -4.95 0.74 > delta 0.41 0.06 > Error terms: > Groups Name Std.Dev. Corr > subject (Intercept) 0.13 > I(baRatio - 0.985) 2.57 0.45 > delta 0.22 -0.12 -0.94 > Residual 0.39 > number of obs: 494, groups: subject, 13 > deviance = 551.4 > >> e7.sim <- mcsamp(e7.lmer2) > Error in as.bugs.array(sims, program = "lmer", n.iter = n.iter, > n.burnin = n.burnin, : > error in parameter sigma. in parameters.to.save > **************************************** > I would appreciate a pointer to what the problem might be. > _____________________________ > Professor Michael Kubovy > University of Virginia > Department of Psychology > USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 > Parcels: Room 102 Gilmer Hall > McCormick Road Charlottesville, VA 22903 > Office: B011 +1-434-982-4729 > Lab: B019 +1-434-982-4751 > Fax: +1-434-982-4766 > WWW: http://www.people.virginia.edu/~mk9y/ > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.