[R] error in ordgee

[David Winsemius]

On Jul 26, 2011, at 12:28 PM, Anera Salucci wrote:

> I am trying to used "ordgee" from "geepack" for an ordinal dataset.
> When I write the code it returns
> "Warning message:In binomial(link) : use of binomial(link=link) is  
> deprecated" ,
> but the program runs.
>
>>   fit <- ordgee(ordered(phy) ~ age+BMI++convert, id=id,  
>> data=newdata, int.const=FALSE)
> Warning message:
> In binomial(link) : use of binomial(link=link) is deprecated
>> summary (fit)
> Call:
> ordgee(formula = ordered(lim_phy) ~ age + BMI + +convert, id = id,
>     data = newdata, int.const = FALSE)
> Mean Model:
>  Mean Link:                 logit
>  Variance to Mean Relation: binomial
>  Coefficients:
>                estimate     san.se         wald          p
> Inter:1:0  -0.200293725 1.16194316 0.0297142603 0.86314017
> Inter:1:25 -0.516243875 1.16840224 0.1952203377 0.65860683
> Inter:1:50 -0.924611635 1.18123668 0.6126957419 0.43377462
>
>
> Even when I run the R code  example for "ohio" and "respdis", it  
> returns the same error.
>
> why  the package returns this error and how to solve it?

As Prof Ripley has emphasized, this is not an error. Furthermore it is  
not even a warning from the ordgee function, but rather from the  
binomial function, as becomes clear after the invocation of warn=2 and  
traceback()

 > options(warn=2)
 > fit <- ordgee(ordered(resp) ~ trt, id=id, data=resp.l,  
int.const=FALSE)
Error in binomial(link) :
   (converted from warning) use of binomial(link=link) is deprecated
 > traceback()
8: doWithOneRestart(return(expr), restart)
7: withOneRestart(expr, restarts[[1L]])
6: withRestarts({
        .Internal(.signalCondition(simpleWarning(msg, call), msg,
            call))
        .Internal(.dfltWarn(msg, call))
    }, muffleWarning = function() NULL)
5: .signalSimpleWarning("use of binomial(link=link) is deprecated\n",
        quote(binomial(link)))
4: warning("use of binomial(link=link) is deprecated\n", domain = NA)
3: binomial(link)
2: glm.fit(xmat, Y, w, family = binomial(link))
1: ordgee(ordered(resp) ~ trt, id = id, data = resp.l, int.const =  
FALSE)

You can easily reproduce the behavior outside of ordgee:

 > link="logit"
 > binomial(link = link)
Error in binomial(link = link) :
   (converted from warning) use of binomial(link=link) is deprecated

This doesn't make sense to me, but maybe there is a valid reason to  
throw a warning when the object name is "link". It's a bit like a  
fortune("dog") gotcha.

-- 
David Winsemius, MD
West Hartford, CT