[R-sig-ME] Fwd: lme4::mcmcsamp + coda::HPDinterval

Douglas Bates bates at stat.wisc.edu
Tue Apr 1 22:04:14 CEST 2008

I replied to Sundar including code and a plot then found that the plot
was too large for the mailing list software.  I have left the plot at
http://www.stat.wisc.edu/~bates/Sundar.pdf or you can run the code to
produce your own copy of the plot.

---------- Forwarded message ----------
From: Douglas Bates <bates at stat.wisc.edu>
Date: Tue, Apr 1, 2008 at 1:40 PM
Subject: Re: [R-sig-ME] lme4::mcmcsamp + coda::HPDinterval
To: Sundar Dorai-Raj <sundar.dorai-raj at pdf.com>
Cc: r-sig-mixed-models at r-project.org

May I suggest that you repeat the experiment in the development
 version of the lme4 package?  In that version the HPDinterval function
 has been moved to lme4 and it is no longer necessary to attach the
 coda package.

 I think it is easier to see what is happening when you use that
 version of the package because you can use the xyplot method to
 examine the evolution of the sampler.  I enclose a modified version of
 your code.  Running this version produces the enclosed plot.  You will
 see that the (relative) standard deviation of A (labelled 'ST2') gets
 stuck near zero.  This is a known problem with MCMC sampling of
 variance components.  The prior distribution corresponds to a "locally
 constant" uninformative prior on log(sigma_A).  As long as the
 likelihood at sigma = zero is sufficiently small to prevent the MCMC
 sampler getting near there the sampler proceeds happily.  However, if
 the likelihood is not sufficiently small then the MCMC sampler may
 wander into the "sigma near zero" region where the posterior density
 of log(sigma) is essentially flat and it gets stuck there.  The recent
 paper by Gelman et al. (JCGS, 2008) provides a suggestion of avoiding
 this problem by overparameterizing the model for the MCMC sampler but
 I haven't yet implemented.

 On Tue, Apr 1, 2008 at 12:50 PM, Sundar Dorai-Raj
 <sundar.dorai-raj at pdf.com> wrote:
 > Hi, lmer+coda Users,
 >  (reproducible code at end)
 >  I have a question regarding confidence intervals on the random effects.
 >  The data I'm working with is a highly unbalanced, nested design with two
 >  random effects (say, A/B), where the B variance is expected to be larger
 >  than A variance. I need to compute confidence bounds on the standard
 >  deviations of each effect (A and A:B). To do this, I use lme4::mcmcsamp
 >  with coda::HPDinterval. As in,
 >  f <- lmer(...)
 >  m <- mcmcsamp(f, n = 1000)
 >  (s <- sqrt(exp(HPDinterval(m))))
 >  However, one of the point estimates falls below the lower bound of the
 >  confidence interval. My guess is that this is due to the correlation
 >  between A and A:B (due to imbalance? relative magnitude of A vs. A:B?)
 >  leading to an unstable model fit. Are the point estimates completely
 >  untrustworthy? In this case, should I simply remove the offending random
 >  effect and refit? Is there a reference that describes situations such as
 >  these (point estimates outside the C.I.)?
 >  Also, this may be an example where the nlme:::intervals.lme function
 >  produces intervals that are nonsensical (at least to me) if you change
 >  sd.A below to, say, 0.5.
 >  Thanks,
 >  --sundar
 >  <code>
 >  set.seed(2)
 >  ## simulate data
 >  A <- factor(rep(1:10, each = 4))
 >  n <- length(A)
 >  B <- factor(rep(1:2, 20))
 >  sd.A <- 5
 >  sd.B <- 10
 >  sd.e <- 0.5
 >  rA <- rnorm(nlevels(A), 0, sd.A)
 >  rB <- rnorm(nlevels(A:B), 0, sd.B)
 >  e <- rnorm(n, 0, sd.e)
 >  y <- 0.5 + rA[A] + rB[A:B] + e
 >  ## create unbalance
 >  out <- seq(length(y)) %in% sample(length(y), 20)
 >  ## fit model
 >  library(lme4)
 >  library(coda)
 >  f <- lmer2(y ~ (1 | A) + (1 | A:B), subset = !out)
 >  m <- mcmcsamp(f, 1000)
 >  v <- VarCorr(f)
 >  s.lmer <- cbind(sqrt(exp(HPDinterval(m[, -1]))),
 >                  est. = c(attr(v, "sc"), sqrt(sapply(v, as.matrix))),
 >                  true = c(sd.e, sd.B, sd.A))
 >  s.lmer <- s.lmer[, c("lower", "est.", "upper", "true")]
 >  rownames(s.lmer) <- c("sigma", "A:B", "A")
 >  print(zapsmall(s.lmer), digits = 4)
 >  </code>
 >  _______________________________________________
 >  R-sig-mixed-models at r-project.org mailing list
 >  https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

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