[R] dropterm, binomial.glm, F-test

[Andrew Beckerman]

Hi there -

I am using R1.5.1 on WinNT and the latest MASS (Venables and Ripley) library.

Running the following code:

 >minimod<-glm(miniSF~gtbt*f.batch+log(mxjd),data=gtbt,family="binomial")

 >summary(minimod,cor=F)
Coefficients:
                 Estimate Std. Error z value Pr(>|z|)
(Intercept)      0.91561    0.32655   2.804 0.005049 **
gtbtgt           0.47171    0.23614   1.998 0.045766 *
f.batch2         0.48332    0.31159   1.551 0.120866
log(mxjd)       -0.26675    0.06889  -3.872 0.000108 ***
gtbtgt:f.batch2 -0.92483    0.37244  -2.483 0.013023 *
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1

(Dispersion parameter for binomial family taken to be 1)

     Null deviance: 4117.4  on 14  degrees of freedom
Residual deviance: 4053.1  on 10  degrees of freedom
AIC: 4131.3

 >anova(minimod,test="Chisq")
 >anova(minimod,test="F")
 >dropterm(minimod,test="Chisq")
 >dropterm(minimod,test="F")

produces the following, suggesting that the anova function does not deal 
with the F-test for quasibinomial family.... should it or is dropterm() 
doing something odd?

cheers,
andrew

 > anova(minimod,test="Chisq")
Analysis of Deviance Table

---
Terms added sequentially (first to last)


              Df Deviance Resid. Df Resid. Dev P(>|Chi|)
NULL                            14     4117.4
gtbt          1     40.3        13     4077.1 2.225e-10
f.batch       1      8.5        12     4068.6 3.541e-03
log(mxjd)     1      9.4        11     4059.3 2.217e-03
gtbt:f.batch  1      6.2        10     4053.1 1.301e-02
 > anova(minimod,test="F")

Analysis of Deviance Table
---
Terms added sequentially (first to last)


              Df Deviance Resid. Df Resid. Dev       F    Pr(>F)
NULL                            14     4117.4
gtbt          1     40.3        13     4077.1 40.2588 2.225e-10 ***
f.batch       1      8.5        12     4068.6  8.5053  0.003541 **
log(mxjd)     1      9.4        11     4059.3  9.3605  0.002217 **
gtbt:f.batch  1      6.2        10     4053.1  6.1678  0.013009 *
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
 > dropterm(minimod,test="Chisq")
Single term deletions

Model:
miniSF ~ gtbt * f.batch + log(mxjd)
              Df Deviance    AIC    LRT   Pr(Chi)
<none>            4053.1 4131.3
log(mxjd)     1   4068.0 4144.2   14.9 0.0001139 ***
gtbt:f.batch  1   4059.3 4135.4    6.2 0.0130093 *
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
 > dropterm(minimod,test="F")
Single term deletions

Model:
miniSF ~ gtbt * f.batch + log(mxjd)
              Df Deviance    AIC F value  Pr(F)
<none>            4053.1 4131.3
log(mxjd)     1   4068.0 4144.2  0.0367 0.8518
gtbt:f.batch  1   4059.3 4135.4  0.0152 0.9043
Warning message:
F test assumes quasibinomial family in: dropterm.glm(minimod, test = "F")
----------------------------------------------------------
Dr. Andrew Beckerman
Institute of Biological Science
University of Stirling
Stirling FK9 4LA
+44 (0)1786 then wk-467808 fx-464994
(APB is not responsible for anything below this)

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