[R] post hoc comparison following with multcomp?

[Michaël Coeurdassier]

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/