[R-sig-eco] ANOVA Output

[ONKELINX, Thierry]

Dear Katrina,

The F-value are different because you test different hypotheses since
anova yields Type I SS. It looks like you expect Type III SS.

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] Namens Katrina W. Chu
Verzonden: woensdag 12 november 2008 22:27
Aan: r-sig-ecology at r-project.org
Onderwerp: [R-sig-eco] ANOVA Output

I have a question about my R-output when I run a three-way ANOVA.  I
just plugged in the
interaction term into the formula and presto!  ANOVA!  But I noticed
that if I change
the order of the formula (or interaction term), I get slightly different
ANOVA outputs.
 I've pasted the output at the bottom of this message.  I didn't think
that this should
happen, so I would appreciate if anyone had any feedback on this
problem.

Thanks in advance, Kat.

> ANOVA <- aov(Chlorophyll.a~Treatment*SamplingPeriod*Site)
> summary(ANOVA)
                               Df  Sum Sq Mean Sq F value    Pr(>F)    
Treatment                       3   356.5   118.8  4.2878  0.005276 ** 
SamplingPeriod                  3   374.7   124.9  4.5069  0.003911 ** 
Site                            1  1016.5  1016.5 36.6791 2.629e-09 ***
Treatment:SamplingPeriod        9   467.6    52.0  1.8747  0.053284 .  
Treatment:Site                  3   167.8    55.9  2.0176  0.110424    
SamplingPeriod:Site             3  1670.2   556.7 20.0884 2.383e-12 ***
Treatment:SamplingPeriod:Site   9   277.2    30.8  1.1115  0.352455    
Residuals                     534 14799.5    27.7                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

> ANOVA <- aov(Chlorophyll.a~SamplingPeriod*Treatment*Site)
> summary(ANOVA)
                               Df  Sum Sq Mean Sq F value    Pr(>F)    
SamplingPeriod                  3   369.5   123.2  4.4437  0.004264 ** 
Treatment                       3   361.8   120.6  4.3510  0.004840 ** 
Site                            1  1016.5  1016.5 36.6791 2.629e-09 ***
SamplingPeriod:Treatment        9   467.6    52.0  1.8747  0.053284 .  
SamplingPeriod:Site             3  1662.0   554.0 19.9894 2.718e-12 ***
Treatment:Site                  3   176.0    58.7  2.1166  0.097111 .  
SamplingPeriod:Treatment:Site   9   277.2    30.8  1.1115  0.352455    
Residuals                     534 14799.5    27.7                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

> ANOVA <- aov(Chlorophyll.a~Site*SamplingPeriod*Treatment)
> summary(ANOVA)
                               Df  Sum Sq Mean Sq F value    Pr(>F)    
Site                            1  1008.9  1008.9 36.4050 2.998e-09 ***
SamplingPeriod                  3   374.1   124.7  4.4990  0.003953 ** 
Treatment                       3   364.8   121.6  4.3871  0.004607 ** 
Site:SamplingPeriod             3  1654.8   551.6 19.9026 3.050e-12 ***
Site:Treatment                  3   172.6    57.5  2.0761  0.102364    
SamplingPeriod:Treatment        9   478.2    53.1  1.9172  0.047282 *  
Site:SamplingPeriod:Treatment   9   277.2    30.8  1.1115  0.352455    
Residuals                     534 14799.5    27.7                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 


-- 
Katrina W. Chu, H.B.Sc.
M.Sc. Candidate
Canadian Rivers Institute
University of New Brunswick
10 Bailey Drive
Fredericton, NB, E3B 6E1
E-mail: katrina.chu at unb.ca

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