#   This code examines association between
#   myocardinal infarction and diabetes in
#   1:1 matched case-control study
#   First enter the counts as a matrix.

m <- matrix(c(9,37,16,82),2,2)
dimnames(m) <- list(c("case_E","case_NE"),c("control_E","control_NE"))
m


# Evaluate McNemar's test

mcnemar.test(m) 



# Evaluate McNemar's test without 
# using the continuity correction

mcnemar.test(m, correct=F) 


# Evaluate an exact p-value based on a
# binomial distirbution for the 
# discordant pairs

binom.test(m[1,2], (m[1,2]+m[2,1]), p=.5)


#  Conditional logistic regression

mdat <- read.table("c:/Documents and Settings/kkoehler.IASTATE/My Documents/courses/st565/R/midiab.matched.txt",
           header=F, col.names=c("group","MI","diabetes"))
mdat$time <- 1
mdat

# Attach the library of survival analysis functions

library(survival)

conlogit.out <- coxph(Surv(time,MI) ~ diabetes + strata(group),data=mdat)  
conlogit.out