[R-sig-eco] aov vs. glm

[Lara R. Appleby 04]

Below are the results obtained from doing a two way anova using glm (Method 1)  
and aov (Method 2).

##Method 1
>  summary(glm(clutchsize~treatment*species))

Call:
glm(formula = clutchsize ~ treatment * species)

Deviance Residuals:
     Min       1Q   Median       3Q      Max
-4.6223  -1.3917   0.0171   1.3777   6.6974

Coefficients:
                   Estimate Std. Error t value Pr(>|t|)
(Intercept)         7.7095     1.2679   6.080 8.23e-09 ***
treatment          -0.2480     0.5845  -0.424 0.671891
species            -3.0463     0.8837  -3.447 0.000721 ***
treatment:species   0.5677     0.4069   1.395 0.164874
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for gaussian family taken to be 4.166879)

     Null deviance: 854.72  on 166  degrees of freedom
Residual deviance: 679.20  on 163  degrees of freedom
AIC: 718.21

Number of Fisher Scoring iterations: 2

##Method 2
>  summary(aov(clutchsize~treatment*species))
                    Df Sum Sq Mean Sq F value   Pr(>F)
treatment           1  29.26  29.264  7.0230  0.00884 **
species             1 138.14 138.143 33.1526 4.13e-08 ***
treatment:species   1   8.11   8.110  1.9464  0.16487
Residuals         163 679.20   4.167
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

--- Chris Howden <chris at trickysolutions.com.au> wrote:
It would help if u posted the results so we know how different.

But have a look at the defaults for a call to glm. Are they the same as for lm?

There are some differences in the output for glm and lm objects when
using summary.

Chris Howden
Founding Partner
Tricky Solutions
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On 11/11/2011, at 10:25, "Lara R. Appleby 04"
<Lara.R.Appleby.04 at alum.dartmouth.org> wrote:

>  I'm trying to basically do a two way ANOVA on the dependent variable (clutchsize)  
>with the two independent variables (treatment and species). It seems that there  
>are three ways I can say this in R:
>
>  1. glm(clutchsize~treatment*species)
>  2. aov(clutchsize~treatment*species)
>  3. anova(lm(clutchsize~treatment*species)
>
>  Methods 2 and 3 yield equivalent results, but Method 1 is completely different!
>
>  Any idea why?
>
>  Lara Appleby
>
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>  R-sig-ecology at r-project.org
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--- end of quote ---