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/
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 at 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.
Possibly Parallel Threads
- Manipulation involving arrays
- multiplying multidimensional arrays (was: Re: [R] Manipulation involving arrays)
- mcmcsamp shortening variable names; how can i turn this feature off?
- New version of lme4 and new mailing list R-SIG-mixed-models
- New version of lme4 and new mailing list R-SIG-mixed-models