[R] ANCOVA/glm missing/ignored interaction combinations

[ONKELINX, Thierry]

Lara,

The first category is nor missing, nor ignored. It is used as the
reference. So the temperature effect for semio1 is only temperature. The
temperature effect for semio2 is temperature + temperature:semio2. For
semio3 it is temperature + temperature:semio3. Hence the main effect of
temperature is NOT the overall effect of temperature but the effect for
the reference category (in your case semio1).

It looks like you need to do some reading on ?contrasts and
?contr.treatment

HTH,

Thierry


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

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-----Oorspronkelijk bericht-----
Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org]
Namens lara harrup (IAH-P)
Verzonden: woensdag 3 september 2008 10:47
Aan: r-help op r-project.org
Onderwerp: [R] ANCOVA/glm missing/ignored interaction combinations

Hi

I am using R version 2.7.2. on a windows XP OS and have a question
concerning an analysis of covariance with count data I am trying to do,
I will give details of a scaled down version of the analysis (as I have
more covariates and need to take account of over-dispersion etc etc) but
as I am sure it is only a simple problem but I just can't see how to fix
it.

I have a data set with count data as the response (total) and two
continuous covariates and one categorical explanatory variable (semio).
When I run the following lines, after loading the data and assigning
'semio' as a factor, taking into account that I want to consider two way
interactions:

> model.a<-glm(total~(temperature+humidity+semio)^2,family=poisson)
> summary(model.a)

I get the output below. But not all interactions are listed there are 4
semio categories, 1,2,3 and 4 but only 2,3,and 4 are listed in the
summary (semio2,semio3,semio4). And I cant for the life of me work out
why category one (semio1) is being ignored, missing etc.

Any help or suggestions would be most appreciated. Thanks in advance

Lara
lara.harrup op bbsrc.ac.uk

Call:
glm(formula = total ~ (temperature + humidity + semio)^2, family =
poisson)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-22.212   -5.132   -2.484    3.200   18.793 

Coefficients:
                      Estimate Std. Error z value Pr(>|z|)    
(Intercept)          23.848754   2.621291   9.098  < 2e-16 ***
temperature          -1.038284   0.150465  -6.901 5.18e-12 ***
humidity             -0.264912   0.033928  -7.808 5.81e-15 ***
semio2               22.852664   1.291806  17.690  < 2e-16 ***
semio3                3.699901   1.349007   2.743   0.0061 ** 
semio4               -1.851163   1.585997  -1.167   0.2431    
temperature:humidity  0.012983   0.001983   6.545 5.94e-11 ***
temperature:semio2   -0.870430   0.037602 -23.149  < 2e-16 ***
temperature:semio3   -0.060846   0.038677  -1.573   0.1157    
temperature:semio4    0.055288   0.046137   1.198   0.2308    
humidity:semio2      -0.114718   0.013369  -8.581  < 2e-16 ***
humidity:semio3      -0.031692   0.013794  -2.298   0.0216 *  
humidity:semio4       0.008425   0.016020   0.526   0.5990    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 10423.5  on 47  degrees of freedom Residual deviance:
2902.2  on 35  degrees of freedom
AIC: 3086.4

Number of Fisher Scoring iterations: 7

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