
 
 
I am using mixed effect models (library lmer) to evaluate factors that influence the catch rate of hake (set by set) in a fishery. I have some empty cells when I include some of the interactions between the fixed factors (e.g. year:area)  and interactions in the random effects (e.g. year:vessel, where vessel is a random effect) . While empty cell were not the problem when all factors were treated as fixed using lm or glm, the estimation failed when I used lme4 and treated some of the factors (the vessel id) as random.  
 
My models is :
Fixed=lmer(merlkg~observer + vessel + area + year +area*year + vessel*year, data=y)
 
The table  area*year is the following:

                2001 2002 2003 2006 2007
  AVJM CAM         5  609  112   10   67
  AVJM CH        365  438  843  497  217
  AVJM RW        614   40   17    0    0
  AVJM SC          1  520  745   29   59
  AVJM TOMBO     601  263   28   48    0
  CENTRO          50  630   31  647  253
  CENTRO LIMITE  216 1436 1160  943  409
  CENTRO ZEPR      0  328   15  215   29
  PAN                   517  683  674  187  389
  QUINTANO        85  680  306   65   81
  RASA                332 1028 1097  137  439
  ROBREDO        553  808  379  164  202
  SC                         5  667   78   64  125
  SCLIMITE       781 3462 2534 1543 1218
 
The desbalance in the interaccion year*vessel is very important.
 
Mixed=lmer(merlkg~area+area*year+(1|observer)+(1|vessels)+(1|vessels*year)
 
In the help site of the package said that the functions for default is na.fail, and na.action so it works as a function lm. But I can´t find  the right sintaxis about how to incorporate the function na.omit in the model mixed, and then run model with all factors. 
Thanks
Maria Eva 
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