# R code for chapter 37 paired nominal data: mcnemars test
# Book details:
# http://www.amazon.co.uk/Health-Science-Statistics-using-Commander/dp/190790431X
#############
Basic analysis: observed, total, null hypothesis proportion  
binom.test(2,14,0.5)
######  if sample >30 can use:
x <- array(c(20,2, 12, 16), dim=c(2,2))
mcnemar.test(x)
##########
odds:
odds_ratioa <- 12/2
odds_ratioa
# or
odds_ratiob <- 2/12
odds_ratiob
probabilitya <-   odds_ratioa/(odds_ratioa +1)
probabilitya
probabilityb <-   odds_ratiob/(odds_ratiob +1)
probabilityb
############# for confidence intervals
# use mcnemar.exact in the exact2x2 package, also provides a odds ratio
install.packages("exact2x2")
library(exact2x2)
mcnemar.exact(x) 
############# for situations with more than 2 categories
install.packages("coin"); library(coin)
tablex <- as.table(x)
tablex
mh_test(tablex)
install.packages("irr"); library(irr)
stuart.maxwell.mh(x)
################ improved version of the Stuart-Maxwell statistic
# known as the marginal homogeneity statistic W of Bhapkar
# code available online
# source function sometimes problematic can use source_url() in the devtools package instead: 
# library(devtools)
# source_url("http:/www.robin-beaumont.co.uk/virtualclassroom/book2data/r_code/bhapkar_test_R.txt")
#  first approach:
### you may need to edit the "Rprofile.site" file:
# C:\Program Files\R\R-2.15.2\etc\Rprofile.site
# Open this "Rprofile.site" file in Notepad 
# and add the following line on a new line at the end of the file:
#  utils::setInternet2(TRUE)
#########
source("http://www.karlin.mff.cuni.cz/~omelka/Soubory/nmsa331/cviceni-10/bhapkar.test.R") 
# or load("http://www.karlin.mff.cuni.cz/~omelka/Soubory/nmsa331/cviceni-10/bhapkar.test.R")
source("http://www.robin-beaumont.co.uk/virtualclassroom/book2data/r_code/bhapkar_test_R.txt")

bhapkar.test(x)

######
st_result <- stuart.maxwell.mh(x)
st_result
str(st_result)
st_result$value
w <- st_result$value/(1 - st_result$value/st_result$subjects)
w
#####