[R-sig-ME] lme/lmer and random effects correlation parameters

Antoine PACCARD antoine.paccard at unine.ch
Mon Nov 12 15:51:15 CET 2012


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. 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"


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:

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


Any advice and help would be very appreciated. 

Many thanks,
Antoine


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