Dear all,

I am analyzing data regarding the effects of introduced fish on the  
biodiversity of 12 alpine lakes. I have 6 lakes with fish and 6  
without and my dependent variables are various repeated density  
measurements of zooplankton taxa.
As we repeated the biodiversity measurements twice a year for two  
years (2006 and 2007) I am analyzing this data with  the lme function  
of the nlme package with lake identity as random grouping factor  
(random = ~1|as.factor(Cod)), and the presence/absence of fish as  
fixed effect. I included also the year and month of sampling as fixed  
effects.
The full model specification is the following:

zoopcrost.lme<-lme(Logcrostacei~as.factor(year)+as.factor(month) 
+as.factor(fish),method="ML", random=~1|as.factor(Cod),  
data=zooplankton, na.action=na.omit)

Now, I have a doubt....
The lakes differ among each other for some physical characteristics  
such as altitude, maximum depth etc....Obviously these parameters do  
not vary within each sampling as they are specific for each lake  
(they do not vary from one year to the next or from one month to the  
next) but they may have an influence on the densities of zooplankton  
taxa, regardless of the presence/absence of introduced fish. Should I  
nonetheless consider these variables among the fixed effects? Or  
should the fact that I impose the lake identity as grouping factor  
take care of the fact that there are individual differences among the  
lakes?

Sorry for possibly a naive question and thank you for your help!

Dr. Achaz von Hardenberg
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Centro Studi Fauna Alpina - Alpine Wildlife Research Centre
Servizio Sanitario e della Ricerca Scientifica
Parco Nazionale Gran Paradiso, Degioz, 11, 11010-Valsavarenche (Ao),  
Italy
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