[R] help with glmmPQL

[Spencer Graves]

HI, DOUG & JOSE: 

      Is there some reason that "anova.lme" should NOT accept an object 
of class "glmmPQL" in the example below?  If you don't see one either, 
then I suggest you consider modifying the code as described below. 

HI, ANDREW: 

      I couldn't find your data "learning" in my Windows installation of 
R 2.0.0pat, which meant that I had to take the time to find another 
example before I could get the error message you described.  I got it 
from modifying the example in the documentation for "glmmPQL" as follows: 

fit1 <- glmmPQL(y ~ trt, random = ~ 1 | ID,
                     family = binomial, data = bacteria)
fit2 <- glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,
                     family = binomial, data = bacteria)
anova(fit1, fit2)
    Error in anova.lme(fit1, fit2) : Objects must inherit from classes 
"gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls"

      I then checked the class of fit1 and fit2: 
 > class(fit1)
[1] "glmmPQL" "lme"   
 > class(fit2)
[1] "glmmPQL" "lme"   

      As an experiment, I changed the class of fit1 and fit2: 
 > class(fit1) <- "lme"
 > class(fit2) <- "lme"
 > anova(fit1, fit2)
     Model df      AIC      BIC    logLik   Test  L.Ratio p-value
fit1     1  5 1054.623 1071.592 -522.3117                       
fit2     2  6 1113.622 1133.984 -550.8111 1 vs 2 56.99884  <.0001

      Unless someone like Doug or Jose tells us, "Don't do that", I 
would use these answers. 

      I looked briefly at the code for "anova.lme", and it looks to me 
like "glmmPQL" could be added to the list of allowed options in the 
following test roughly half way through the code: 

       if (!all(match(termsClass, c("gls", "gnls", "lm", "lmList",
            "lme", "nlme", "nlsList", "nls"), 0))) {
            stop(paste("Objects must inherit from classes \"gls\", 
\"gnls\"",
                "\"lm\",\"lmList\", \"lme\",\"nlme\",\"nlsList\", or 
\"nls\""))
        }

      hope this helps. 
      spencer graves

A.J. Rossini wrote:

>For better or worse, it's holidays in the states.  Very amusing for me
>being in a non-Thanksgiving celebrating country.
>
>In addition, it's not a problem.  The complaint is valid.  Probably no
>one has coded up the right solution yet for comparison.
>
>I can't recall if one would want those statistics for a binomial
>random effects model, but I do recall some issues with model
>comparison in that setting, though they are a bit dated (say, 2 years
>or so).
>
>On Fri, 26 Nov 2004 09:31:40 +0700, Andrew Criswell
><r-stats at arcriswell.com> wrote:
>  
>
>>Hello:
>>
>>Will someone PLEASE help me with this problem. This is the third time
>>I've posted it.
>>
>>When I appply anova() to two equations estimated using glmmPQL, I get a
>>complaint,
>>
>>    
>>
>>>anova(fm1, fm2)
>>>      
>>>
>>Error in anova.lme(fm1, fm2) : Objects must inherit from classes "gls",
>>"gnls" "lm","lmList", "lme","nlme","nlsList", or "nls"
>>
>>    
>>
>>The two equations I estimated are these:
>>
>>    
>>
>>>fm1 <- glmmPQL(choice ~ day + stereotypy,
>>>      
>>>
>>+                random = ~ 1 | bear, data = learning, family = binomial)
>>
>>    
>>
>>>fm2 <- glmmPQL(choice ~ day + envir + stereotypy,
>>>      
>>>
>>+                random = ~ 1 | bear, data = learning, family = binomial)
>>
>>Individually, I get results from anova():
>>
>>    
>>
>>>anova(fm1)
>>>      
>>>
>>          numDF denDF   F-value p-value
>>(Intercept)     1  2032   7.95709  0.0048
>>day             1  2032 213.98391  <.0001
>>stereotypy      1  2032   0.42810  0.5130
>>
>>    
>>
>>>anova(fm2)
>>>      
>>>
>>          numDF denDF   F-value p-value
>>(Intercept)     1  2031   5.70343  0.0170
>>day             1  2031 213.21673  <.0001
>>envir           1  2031  12.50388  0.0004
>>stereotypy      1  2031   0.27256  0.6017
>>
>>    
>>
>>I did look through the archives but didn't finding anything relevant to
>>my problem.
>>
>>Hope someone can help.
>>
>>ANDREW
>>____________________________
>>       _
>>platform i586-mandrake-linux-gnu
>>arch     i586
>>os       linux-gnu
>>system   i586, linux-gnu
>>status
>>major    2
>>minor    0.0
>>year     2004
>>month    10
>>day      04
>>language R
>>
>>--
>>Andrew R. Criswell, Ph.D.
>>Graduate School, Bangkok University
>>
>>______________________________________________
>>R-help at stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>>    
>>
>
>
>  
>

-- 
Spencer Graves, PhD, Senior Development Engineer
O:  (408)938-4420;  mobile:  (408)655-4567