lme/lmer and random effects correlation parameters
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