R help - Jul 2004 - confint.glm in a function

I can't get confint.glm to work from within a function.  Consider 
the following (using R 1.9.1, Windows 2000): 

# FIRST: SOMETHING THAT WORKS FROM A COMMAND PROMPT
DF <- data.frame(y=.1, N=100)
(fit <- glm(y~1, family=binomial, data=DF,
            weights=DF[,"N"]))
Call:  glm(formula = y ~ 1, family = binomial, data = DF, weights = 
DF[,      "N"])

Coefficients:
(Intercept) 
     -2.197 

Degrees of Freedom: 0 Total (i.e. Null);  0 Residual
Null Deviance:        0
Residual Deviance: -1.11e-14     AIC: 6.052

confint(fit)
 > confint(fit)
            2.5 % 97.5 %
(Intercept)   NaN    NaN
Warning message:
NaNs produced in: qt(p, df, lower.tail, log.p)
# The default confint thinks it knows glm, but doesn't.  This is fixed 
with: 
library(MASS)
confint(fit)
Waiting for profiling to be done...
    2.5 %    97.5 %
-2.915193 -1.594401
# This is on the logit space.  For proportions: 
Waiting for profiling to be done...
    2.5 %    97.5 %
0.0514076 0.1687655

# PUT IT IN A FUNCTION: 
confint.binom <- function(y="y", size="N", data.=DF){
  fit <- glm(y~1, family=binomial, data=data.,
             weights=data.[,size])
  CI <- confint(fit)
  CI
}
 > confint.binom()
Waiting for profiling to be done...
Error in model.frame.default(formula = y ~ 1, data = data., weights = 
data.[,  :
    Object "data." not found

##To get around this, assign both data. and size to some place where 
confint.glm can find them
confint.binom.pos <- function(y="y", size="N", data.=DF,
            pos=0){
  assign("data.", data., pos)
  assign("size", size, pos)
  fit <- glm(y~1, family=binomial, data=data.,
             weights=data.[,size])
  CI <- confint(fit)
  CI
}
 > confint.binom.pos()
Error in as.environment(pos) : invalid argument

 > confint.binom.pos(pos=-1)
Waiting for profiling to be done...
Error in model.frame.default(formula = y ~ 1, data = data., weights = 
data.[,  :
    Object "data." not found
 > confint.binom.pos(pos=1)
Waiting for profiling to be done...
    2.5 %    97.5 %
-2.915193 -1.594401
# This works. 
#  HOWEVER, THIS ASSIGNS data. AND size TO THE WORKING DIRECTORY. 
# HOW CAN I GET AROUND THIS? 

      If I had "confint.glm", I could modify it so it could find data.
and size.  However, its hidden. 

      Thanks for your help. 
      Spencer Graves

At 19:02 2004-07-12 -0700, you wrote:
>     If I had "confint.glm", I could modify it so it could find
data. and
> size.  However, its hidden.
Try

library(MASS)
MASS:::confint.glm

or navigate to /.../library/MASS/R and open the MASS file in your favourite 
editor.

HTH,
Henric

You actually don't need to load the package first:
> MASS:::confint.glm
function (object, parm, level = 0.95, trace = FALSE, ...) 
{
    pnames <- names(coef(object))
    if (missing(parm)) 
        parm <- seq(along = pnames)
    else if (is.character(parm)) 
        parm <- match(parm, pnames, nomatch = 0)
    cat("Waiting for profiling to be done...\n")
    object <- profile(object, which = parm, alpha = (1 - level)/4, 
        trace = trace)
    confint(object, parm = parm, level = level, trace = trace, 
        ...)
}
<environment: namespace:MASS>
> search()
[1] ".GlobalEnv"       "package:methods" 
"package:stats"
"package:graphics"
[5] "package:utils"    "Autoloads"       
"package:base"

Andy

> From: Henric Nilsson
> 
> At 19:02 2004-07-12 -0700, you wrote:
> 
> >     If I had "confint.glm", I could modify it so it could 
> find data. and 
> > size.  However, its hidden.
> 
> Try
> 
> library(MASS)
> MASS:::confint.glm
> 
> or navigate to /.../library/MASS/R and open the MASS file in 
> your favourite 
> editor.
> 
> HTH,
> Henric
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
>