# 3-way table:   marignal dependence, conditional independence (boy scout data)
# Edps 589
# Fall 2018
# C.J.Anderson
#

library(vcd)
library(vcdExtra)
library(MASS)
library(DescTools)

setwd("D:\\Dropbox\\edps 589\\3 Way")
( bs.dat <- read.table("bs_data.txt",header=TRUE) )


# 2-way marginal table
delin.by.bs <- xtabs(count~delin+bs,data=bs.dat) 
addmargins(delin.by.bs)

# 2-way marginal analysis:  
assocstats(delin.by.bs)                  # Compute G2 and X2
OR <- oddsratio(delin.by.bs)             # Compute odds ratio
summary(OR)                              # signficant test for odds ratio -- don't really 
                                         #   need because have X2 and G2 from assocstats()
exp(-.5790339)                           # Convert log odds ratio to odds ratio
exp(confint(OR) )                        # Confidnece interval of odds ratio



# 3-way  Table of data
#  -- partial or conditional tables
bs.tab <- xtabs(count ~ delin + bs + ses, data=bs.dat)
addmargins(bs.tab)

# 3-way contitional/partial table analysis 
assocstats(bs.tab)                        # Compute X2 and G2
OR <- oddsratio(bs.tab)                   # Compute odds ratio
summary(OR)                               # Signficant test for odds ratios
exp( confint(OR) )                        # Confidnece interval of odds ratios



# Test for homogenity (shouldn't be significant...p should = 1
# Breslow-Day test of homogeneity
BreslowDayTest(bs.tab, OR = NA, correct = FALSE)


WoolfTest(bs.tab)

# Test for conditional independence
CMHtest(bs.tab)

# MH estimate of common odds ratio
mantelhaen.test(bs.tab,alternative = c("two.sided"),
                correct = TRUE, exact = FALSE, conf.level = 0.95)