Hi everyone,

I'm using lmer and estimable (from packages lme4 and gmodels respectively) and have the disconcerting happening that when I run exactly the same code, I get different results!  In checking this out by running the code 50x, it seems to be that answers may be randomly deviating around those which I get from another stats package (GenStat, using the linear mixed models functionality in this).  As such, my guess is that perhaps there is a random seed involved somewhere in the estimable function, and that the answer is simply converging to a slightly different place each time, based on a slightly different starting place.  But this is only a guess - if anyone could either confirm or otherwise explain this unexpected-to-me happening, that'd be fantastic!!

The code that I'm running is:

design.1 = rbind(c(0,0,0,1,0,0,0,0,0,0,0,0))

lme1 <- lmer(var_x~AGE*GENDER*DAM_DIET + (1|CHIP) + (1|LITTER),x_temp)

 est <- estimable(lme1,design.1)
 print(est)
 est <- estimable(lme1,design.1)  # Repeat of code
 print(est)
 est <- estimable(lme1,design.1)  # Another repeat of code
 print(est)

And this is the output - you can see in this that the results vary each time the code is run...

>    print(est)
                            Estimate Std. Error p value
(0 0 0 1 0 0 0 0 0 0 0 0) 0.02241752  0.2185279   0.902
>    est <- estimable(lme1,design.1)
>    print(est)
                             Estimate Std. Error p value
(0 0 0 1 0 0 0 0 0 0 0 0) 0.001824573  0.2106973   0.974
>    est <- estimable(lme1,design.1)
>    print(est)
                            Estimate Std. Error p value
(0 0 0 1 0 0 0 0 0 0 0 0) 0.01276941  0.2154196   0.938

My SessionInfo is as follows:

R version 2.9.2 (2009-08-24)
i386-pc-mingw32

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

other attached packages:
[1] lme4_0.999375-32   Matrix_0.999375-31 lattice_0.17-25    multcomp_1.1-2     survival_2.35-7    mvtnorm_0.9-7      gmodels_2.15.0     svIDE_0.9-5

loaded via a namespace (and not attached):
[1] gdata_2.4.2  grid_2.9.2   gtools_2.6.1 MASS_7.2-48  svMisc_0.9-5

Many thanks for any help or advice that anyone can provide :)

Cheers,
Zaneta

____________________________
Zaneta Park
Biometrician
T +64 6 351 8008
E zaneta.park-ng@agresearch.co.nz
AgResearch Limited
Grasslands Research Centre
Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
T  +64 6 356 8019   F  +64 6 351 8032  www.agresearch.co.nz
Farming Food and Health. First
Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi


=======================================================================
Attention: The information contained in this message and...{{dropped:15}}


