Hi,

I've got a strange behaviour with lme4a::lmer in combination with 
lme4a::profile()

profile() seems to change the merMod object it has been calculating the 
profile for. The variance components and standard errors on fixed effects 
as returned by summary() are different before and after running profile() 
as you can see in the example below.
>From the profile itself, the first run seems to be the correct one.

Output and sessionInfo below. I can provide the data set on request.

Anybody an idea what is going wrong?
Thanks
Joris



> modL1.2 <- lmer(data=RPD15L1, value ~ transgenity + 
(transgenity|event),REML=FALSE)
> summary(modL1.2)
Linear mixed model fit by maximum likelihood ['summary.mer']
Formula: value ~ transgenity + (transgenity | event) 
   Data: RPD15L1 
      AIC       BIC    logLik  deviance 
 500.6290  520.7116 -244.3145  488.6290 

Random effects:
 Groups   Name                Variance Std.Dev. Corr 
 event    (Intercept)         0.4475   0.6690 
          transgenityPositive 0.9615   0.9806   0.295
 Residual                     0.2971   0.5450 
Number of obs: 210, groups: event, 36

Fixed effects:
                    Estimate Std. Error t value
(Intercept)          23.2766     0.1235  188.50
transgenityPositive   1.0607     0.1801    5.89

Correlation of Fixed Effects:
            (Intr)
trnsgntyPst 0.115 
> pr.modL1.2 <- profile(modL1.2)
> summary(modL1.2)
Linear mixed model fit by maximum likelihood ['summary.mer']
Formula: value ~ transgenity + (transgenity | event) 
   Data: RPD15L1 
      AIC       BIC    logLik  deviance 
 500.6290  520.7116 -244.3145  488.6290 

Random effects:
 Groups   Name                Variance Std.Dev. Corr 
 event    (Intercept)         0.1964   0.4432 
          transgenityPositive 0.4376   0.6615   0.523
 Residual                     0.2971   0.5450 
Number of obs: 210, groups: event, 36

Fixed effects:
                    Estimate Std. Error t value
(Intercept)         23.27657    0.09092  256.01
transgenityPositive  1.06065    0.13364    7.94

Correlation of Fixed Effects:
            (Intr)
trnsgntyPst 0.119 


> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252 
[3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C 
[5] LC_TIME=Dutch_Belgium.1252 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

other attached packages:
[1] boot_1.2-43        lme4a_0.999375-63  MatrixModels_0.2-1 minqa_1.1.14  
 
[5] Rcpp_0.9.0.2       Matrix_0.999375-46 lattice_0.19-13    rj_0.5.0-5   

loaded via a namespace (and not attached):
[1] codetools_0.2-6 grid_2.12.1     nlme_3.1-98     rJava_0.8-8 
[5] splines_2.12.1  stats4_2.12.1   tools_2.12.1 
	[[alternative HTML version deleted]]


