[R-sig-ME] lme/lmer and random effects correlation parameters
Ben Bolker
bbolker at gmail.com
Mon Nov 12 17:09:46 CET 2012
Antoine PACCARD <antoine.paccard at ...> writes:
> Dear Mix modelers,
>
> I am trying to run the following models:
>
> m1 <- lme(A ~ treatment * lat, random= ~ 1 + treatment | population/family)
>
> or with lmer
>
> m2 <- lmer(A ~ treatment * lat + (treatment |population/family))
> Unfortunately m1 won't converge and I always get the following
> message: "iteration limit reached without convergence (10)". I
> understand this comes from random correlation parameters and this
> issue has been previously discussed in the past. However, I can't
> find a way to make it work and I was wondering if anybody had found
> a way to fix this problem.
> lmer will work and converge properly.
I would be very careful about this statement. Are you *sure* it
has converged properly? Do the results make sense? Do you get
non-trivial (not zero, not very very small, correlations not
equal to +/- 1.0) estimates for the variance-covariance matrix?
Does centering the covariates help?
> Unfortunately the following function to extract p-values won't work
> because of the same reason explained above: pvals.fnc(m2, nsim =
> 10000) "Error in pvals.fnc(m2, nsim = 10000) : MCMC sampling is not
> implemented in recent versions of lme4 for models with random
> correlation parameters"
http://glmm.wikidot.com/faq offers some alternatives.
I would consider parametric bootstrapping or Kenward-Roger
(perhaps using the functions in the pbkrtest package)
> I believe my models are correct since each family and each
> population have experienced treatment (when I get rid of "treatment"
> in the random parameters, the models work fine). Here is a sample of
> the data set:
What are the missing (blank) values in the A column?
Is that a glitch in the display, or are there really lots
of missing values?
> population lat family treatment A
> AA 37.724 35 AB 124
> LLL 37.419 14 AB 249
> AAJ 46.114 8 AB
> XXX 43.356 1 CD
> OOO 40.441 27 CD 244.5
> FFF 36.418 6 CD 240
> OOO 40.441 11 AB
> AA 37.724 28 AB
> AAF 46.114 17 CD 116.5
> QQQ 39.491 19 CD 93.5
> QQQ 39.491 21 AB 247
> AAF 46.114 10 CD
> OOO 40.441 20 CD 227
> UUU 42.996 25 AB 95.5
> XXX 43.356 22 CD 209
> AA 37.724 15 AB
> QQQ 39.491 29 AB 186
> UUU 42.996 19 AB 110
> UUU 42.996 3 AB 247
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