= R code for running Agresti-Min CI for difference in paired proportions =


----citation to Agresti and Min----
Agresti, A. and Min, Y. (2005). Simple improved confidence intervals for comparing
matched proportions. Statistics in Medicine 24, 729-740.

--- a portion of a Google cached U.Fla web site, probably by Agresti----

R code for the adjustment of the Wald confidence interval for a difference 
of proportions, with matched pairs. This is the interval called Wald+2 in 
Agresti and Min, Statistics in Medicine, 2004, which adds 0.5 to each cell 
before constructing the Wald CI. The CI is truncated when it overshoots the 
boundary.

{{{
diffpropci <- function(b,c,n,conflev)
{
 z  <- qnorm(1-(1-conflev)/2)
 diff <- (c-b)/(n+2)
 sd <- sqrt((b+c+1)-(c-b)^2/(n+2))/(n+2)
 ll <- diff - z*sd
 ul <- diff + z*sd
 if(ll < -1) ll = -1
 if(ul > 1) ul = 1 
 c(ll, ul)
}
# Adjusted Wald interval for difference of proportions with matched pairs
# "conflev"=confidence coefficient, n=sample size, b,c = off-diag counts
}}}

------end extract from Agresti's site--------------------------------------