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
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