[R] Nested design

unpeatable bjorn.robroek at gmail.com
Sat May 28 15:09:02 CEST 2011


Dear R-users, 
I have the following problem. I have performed an experiment for which I
gathered a lot of data which I now want to test. The problem is that I
cannot find an appropriate test in R (I am a starter) and someone might give
me a hand. This is what I have done: 
Across three sites (Site), I have laid out five transects (Trans)...meaning
five transects in each sites. In each transect I have five Microhabitats
(MH) which should be regarded as subplots (I think). In each transect, every
MH has the same position (so they are not randomized). I now want to test
the effect of Site and MH (nested in Trans) on my response variables. 

This is what I do now: model<-aov(Response~Site*MH+error(Trans/MH)) 

I get the following output: 

Error: Trans 
     Df   Sum Sq  Mean Sq 
Site  1 0.030294 0.030294 

Error: Trans:MH 
     Df  Sum Sq Mean Sq 
Site  1 10.8367 10.8367 
MH    3  0.2836  0.0945 

Error: Within 
          Df  Sum Sq Mean Sq F value    Pr(>F)     
Site       2 0.92504 0.46252 11.7304 5.880e-05 *** 
MH         4 1.86688 0.46672 11.8370 5.645e-07 *** 
Site:MH    8 1.17041 0.14630  3.7105  0.001615 ** 
Residuals 54 2.12917 0.03943                       
--- 
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

How do I read this? 
Any help appreciated! 

BTW: I also tried the lme function: model<-lme(Response~Site*MH,
random=~1|Trans/MH) 
but then the output is really complicated.


-----
Dr. Bjorn JM Robroek
Ecology and Biodiversity Group
Institute of Environmental Biology, Utrecht University
Padualaan 8, 3584 CH Utrecht, The Netherlands
Email address: b.j.m.robroek at uu.nl
http://www.researcherid.com/rid/C-4379-2008
Tel: +31-(0)30-253 6091
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