[R] post hoc comparison following with multcomp?

[Spencer Graves]

	  Your use of the multcomp package looks plausible to me (though I 
certainly did not check every detail).

	  Do you have any specific concerns?  [Also, have you reviewed 
vignette("Rmc")?]  And have you considered the plotting, e.g.:

	  plot(csimint(coefglm1,df=27,covm=vc.trait,cmatrix=CM))

	  hope this helps.
	  spencer graves

Michaël Coeurdassier wrote:

> Dear R community,
> 
> I would like to check differences between treatment (Trait) following a 
> glm. From R help list, I tried in the following way using the multcom 
> library. Please, is it a correct manner to do post hoc comparison with 
> the data below.
> 
> Thank you in advance. Sincerely
> 
> *> tabp<-read.delim("ponteM1.txt")*
> *> tabp*
>    Trait totponte
> 1      T       10
> 2      T       11
> 3      T       11
> 4      T        9
> 5      T        7
> 6      T        7
> 7      T        9
> 8      T       12
> 9      T        9
> 10     T       10
> 11     M        9
> 12     M       10
> 13     M        8
> 14     M        8
> 15     M       10
> 16     M        8
> 17     M        8
> 18     M        9
> 19     M       11
> 20     M        7
> 21     F        8
> 22     F        8
> 23     F        5
> 24     F        9
> 25     F        5
> 26     F        7
> 27     F        5
> 28     F        7
> 29     F        6
> 30     F        3
>  
> *> attach(tabp)*
> *> glm1<-glm(totponte~Trait,family=poisson)* **
> *> anova(glm1,test="F")*
> Model: poisson, link: log
> Response: totponte
> Terms added sequentially (first to last)
>  
>       Df Deviance Resid. Df Resid. Dev      F  Pr(>F) 
> NULL                     29    16.3879                
> Trait  2   7.1770        27     9.2109 3.5885 0.02764 *
> * *
> *> library(multcomp)*
> *> (coefglm1<-coef(glm1))*
>  (Intercept)      TraitM      TraitT
>   1.8405496   0.3342021   0.4107422
>  
> *> (vc.trait<-vcov(glm1))*
>             (Intercept)      TraitM      TraitT
> (Intercept)  0.01587301 -0.01587301 -0.01587301
> TraitM      -0.01587301  0.02723665  0.01587301
> TraitT      -0.01587301  0.01587301  0.02639933
>  
> *> (CM<-contrMat(table(tabp$Trait),type="Tukey"))*
>      F  M T
> M-F -1  1 0
> T-F -1  0 1
> T-M  0 -1 1
> * *
> *> csimint(coefglm1,df=27,covm=vc.trait,cmatrix=CM)*
> Simultaneous confidence intervals: user-defined contrasts
>         95 % confidence intervals
>  
>     Estimate  2.5 % 97.5 %
> M-F   -1.506 -2.177 -0.836
> T-F   -1.430 -2.097 -0.763
> T-M    0.077 -0.286  0.439
> 
> 
> ---------------
> Michaël COEURDASSIER, PhD
> Department of Environmental Biology
> UsC INRA EA3184MRT
> Institute for Environmental Sciences and Technology
> 
> University of Franche-Comte
> Place Leclerc
> 25030 Besançon cedex
> FRANCE
> Tel : +33 (0)381 665 741
> Fax : +33 (0)381 665 797
> 
> E-m at il: michael.coeurdassier at univ-fcomte.fr
> http://lbe.univ-fcomte.fr/
> 
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