Dear list,

I apologize if my question is inappropriate for this list but I am having
some doubts concerning my specification of a mixed model. I am trying to do
a sort of repeated measures ANOVA. I have searched the list and found some
clues , but I am still uncertain whether it is correct or not. 

I have collected zooplankton at two different depths (2-level factor
(Habitat)) at two sites (2-level factor (Station)) and have stable isotope
data from two tissues (2-level factor).  

My problem, as I see it is that the two samples within a site will be
dependent. So this should be accounted for. Moreover, the data is not
balanced as there are fewer samples for one tissue as individuals had to be
pooled to obtain enough material for analysis. 

I am interested to see if there are isotopic differences between habitats.

Here is what my data looks like

>  str(mydata)

'data.frame':   102 obs. of  11 variables:

$ X15N   : num  -8.35 -8.58 -8.71 -8.2 -8.36 ...

$ X13C   : num  -21.9 -21.7 -21.7 -21.8 -21.5 ...

$ Habitat: Factor w/ 2 levels "Benthic","Pelagic": 2 2 2 2 2 1 1 1 1 1 ...

$ Station: Factor w/ 2 levels "S1","S2": 1 1 1 1 1 1 1 1 1 1 ...

$ Tissue : Factor w/ 2 levels "Chitin","Muscle": 1 1 1 1 1 1 1 1 1 1 ...

 

>   mydata

         X15N      X13C Habitat Station Tissue 

1   -8.345805 -21.93032 Pelagic      S2 Muscle

2   -8.580251 -21.69129 Pelagic      S2 Muscle

3   -8.714043 -21.68784 Pelagic      S1 Chitin 

4   -8.204448 -21.79203 Pelagic      S1 Chitin 

5   -8.358542 -21.46521 Pelagic      S1 Chitin 

6   -8.869785 -21.75084 Benthic      S2 Chitin 

7   -8.727968 -21.79578 Benthic      S2 Chitin 

8   -9.210613 -21.64822 Benthic      S1 Chitin 

9   -8.731536 -21.40997 Benthic      S1 Chitin 

 

This is the model I have specified:

M1<-(lme(X15N~Habitat+Station,random=list(Tissue=pdCompSymm(~Habitat-1)),dat
a=mydata,method="REML"))

I am really a beginner at this, but I hope someone will be able to give me a
clue if this is correct or not. 

Best regards/ Martin

 

 


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