[R] Repeated measures ANOVA

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From: GIDEON WASSERBERG (wasserberg@wisc.edu)
Date: Thu 20 May 2004 - 15:11:46 EST


Message-id: <8e1e48d815.8d8158e1e4@wiscmail.wisc.edu>


  
 
Dear friends

I am not sure that I am conducting this analysis correctly. I would really appreciate if someone can verify what I've done.
I conducted repeated measures ANOVA for some bugs data. These bugs were measured repeatedly over 32 weeks at the same trapping plots. I want to test a full model for the effect of time ("week") (the "within subject" variable), and the main effects are: place, station,species, and all the interactions thereof.

Below, I pasted the commands I used, the analysis output, and a segment of my data (2 out of the 32 weeks) in order to show how I coded the data.

> Rep1<-read.csv("C:/Documents and Settings/Gideon/My Documents/Vasily-Alon paper/Seasonal2.csv")
> summary(aov(Total~Place*Station*Species*Week+Error(Subject/Week),data=Rep1)
+ )

Output:

Error: Subject
      Df Sum Sq Mean Sq
Place 1 2570.3 2570.3

Error: Subject:Week
     Df Sum Sq Mean Sq
Week 1 977.08 977.08

Error: Within
                             Df Sum Sq Mean Sq F value Pr(>F)
Place 2 9764 4882 45.4435 < 2.2e-16 ***
Station 3 7120 2373 22.0930 5.068e-14 ***
Species 4 35145 8786 81.7883 < 2.2e-16 ***
Week 1 5 5 0.0421 0.8374211
Place:Station 3 1355 452 4.2048 0.0056664 **
Place:Species 10 44468 4447 41.3934 < 2.2e-16 ***
Station:Species 15 20277 1352 12.5833 < 2.2e-16 ***
Place:Week 2 1674 837 7.7894 0.0004298 ***
Station:Week 3 2617 872 8.1194 2.286e-05 ***
Species:Week 4 4104 1026 9.5500 1.244e-07 ***
Place:Station:Species 15 6155 410 3.8196 9.862e-07 ***
Place:Station:Week 3 457 152 1.4188 0.2355024
Place:Species:Week 10 5830 583 5.4268 5.984e-08 ***
Station:Species:Week 15 4484 299 2.7826 0.0002802 ***
Place:Station:Species:Week 15 3363 224 2.0867 0.0084501 **
Residuals 1620 174033 107

---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
> 

Data:

Subject Place Station Species Week Total 1 Amnun Garden Aa 1 1 2 Amnun Garden As 1 0 3 Amnun Garden Lp 1 0 4 Amnun Garden Ls 1 0 5 Amnun Garden Lt 1 1 6 Amnun Garden Ps 1 0 7 Amnun Grass Aa 1 0 8 Amnun Grass As 1 0 9 Amnun Grass Lp 1 0 10 Amnun Grass Ls 1 0 11 Amnun Grass Lt 1 0 12 Amnun Grass Ps 1 0 13 Amnun Rocks Aa 1 1 14 Amnun Rocks As 1 0 15 Amnun Rocks Lp 1 0 16 Amnun Rocks Ls 1 0 17 Amnun Rocks Lt 1 0 18 Amnun Rocks Ps 1 0 19 Korazim 1 Garden Aa 1 0 20 Korazim 1 Garden As 1 0 21 Korazim 1 Garden Lp 1 0 22 Korazim 1 Garden Ls 1 0 23 Korazim 1 Garden Lt 1 0 24 Korazim 1 Garden Ps 1 0 25 Korazim 1 Grass Aa 1 0 26 Korazim 1 Grass As 1 0 27 Korazim 1 Grass Lp 1 0 28 Korazim 1 Grass Ls 1 0 29 Korazim 1 Grass Lt 1 0 30 Korazim 1 Grass Ps 1 0 31 Korazim 1 Rocks Aa 1 0 32 Korazim 1 Rocks As 1 0 33 Korazim 1 Rocks Lp 1 0 34 Korazim 1 Rocks Ls 1 0 35 Korazim 1 Rocks Lt 1 3 36 Korazim 1 Rocks Ps 1 0 37 Korazim 2 Garden Aa 1 0 38 Korazim 2 Garden As 1 0 39 Korazim 2 Garden Lp 1 0 40 Korazim 2 Garden Ls 1 0 41 Korazim 2 Garden Lt 1 0 42 Korazim 2 Garden Ps 1 0 43 Korazim 2 Ochard Aa 1 0 44 Korazim 2 Ochard As 1 0 45 Korazim 2 Ochard Lp 1 0 46 Korazim 2 Ochard Ls 1 0 47 Korazim 2 Ochard Lt 1 0 48 Korazim 2 Ochard Ps 1 0 49 Korazim 2 Rocks Aa 1 0 50 Korazim 2 Rocks As 1 0 51 Korazim 2 Rocks Lp 1 0 52 Korazim 2 Rocks Ls 1 0 53 Korazim 2 Rocks Lt 1 4 54 Korazim 2 Rocks Ps 1 0 1 Amnun Garden Aa 2 0 2 Amnun Garden As 2 0 3 Amnun Garden Lp 2 0 4 Amnun Garden Ls 2 0 5 Amnun Garden Lt 2 1 6 Amnun Garden Ps 2 0 7 Amnun Grass Aa 2 0 8 Amnun Grass As 2 0 9 Amnun Grass Lp 2 0 10 Amnun Grass Ls 2 0 11 Amnun Grass Lt 2 0 12 Amnun Grass Ps 2 0 13 Amnun Rocks Aa 2 0 14 Amnun Rocks As 2 0 15 Amnun Rocks Lp 2 0 16 Amnun Rocks Ls 2 0 17 Amnun Rocks Lt 2 0 18 Amnun Rocks Ps 2 0 19 Korazim 1 Garden Aa 2 0 20 Korazim 1 Garden As 2 0 21 Korazim 1 Garden Lp 2 0 22 Korazim 1 Garden Ls 2 0 23 Korazim 1 Garden Lt 2 0 24 Korazim 1 Garden Ps 2 0 25 Korazim 1 Grass Aa 2 0 26 Korazim 1 Grass As 2 0 27 Korazim 1 Grass Lp 2 0 28 Korazim 1 Grass Ls 2 0 29 Korazim 1 Grass Lt 2 0 30 Korazim 1 Grass Ps 2 0 31 Korazim 1 Rocks Aa 2 0 32 Korazim 1 Rocks As 2 0 33 Korazim 1 Rocks Lp 2 0 34 Korazim 1 Rocks Ls 2 0 35 Korazim 1 Rocks Lt 2 1 36 Korazim 1 Rocks Ps 2 0 37 Korazim 2 Garden Aa 2 0 38 Korazim 2 Garden As 2 0 39 Korazim 2 Garden Lp 2 0 40 Korazim 2 Garden Ls 2 0 41 Korazim 2 Garden Lt 2 0 42 Korazim 2 Garden Ps 2 0 43 Korazim 2 Ochard Aa 2 0 44 Korazim 2 Ochard As 2 0 45 Korazim 2 Ochard Lp 2 0 46 Korazim 2 Ochard Ls 2 0 47 Korazim 2 Ochard Lt 2 0 48 Korazim 2 Ochard Ps 2 0 49 Korazim 2 Rocks Aa 2 0 50 Korazim 2 Rocks As 2 0 51 Korazim 2 Rocks Lp 2 0 52 Korazim 2 Rocks Ls 2 0 53 Korazim 2 Rocks Lt 2 4 54 Korazim 2 Rocks Ps 2 0

Very Much obliged

Gideon Wasserberg Wildlife research unit, Department of wildlife ecology, University of Wisconsin 218 Russell labs, 1630 Linden dr., Madison, Wisconsin 53706, USA. Tel.:608 265 2130, Fax: 608 262 6099

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