#' --- 
#' title: Two way tables 
#' author: Carolyn J. Anderson
#' date: May 2018
#' --- 
# Modification of Friendly & Meyer 2-way R tutorial
# http://euclid.psych.yorku.ca/www/psy6136/tutorials/twoway.pdf
#

# Packages needed:
#   vcd
#   MASS
#   

library(vcd)

data("Hospital",package="vcd")
Hospital

# 1. Find marginal frequencies

margin.table(Hospital,1)     # row margins frequencies
margin.table(Hospital,2)     # column margins frequencies

# 2. Add marginal frequencies to table

addmargins(Hospital)

# 3. Find marginal proportions

prop.table(Hospital,1)       # row marginal proportions
prop.table(Hospital,2)       # column marginal proportions

# 4. Perform Pearson chi-square test (asympotic)

chisq.test(Hospital)

# 5. Perform Monte Carlo chi-square test (non-asympotic)

chisq.test(Hospital, simulate.p.value=TRUE)

# For more information about the simulated tests,
?chisq.test

# 6. Use loglm (log-linear model) to do chi-square test

library(MASS)
( model.loglm <- loglm(~ 1 + 2, Hospital) )
 
# 7. Use glm (generalized linear model) to test association (this will be used for many models)

#  a. Turn table into data.frame
 
( hospital <- as.data.frame(Hospital) )

#  b. Use glm,
 
model.glm <- glm(Freq ~ Visit.frequency + Length.of.stay, data=hospital,family=poisson) 
summary(model.glm)
  
#  c. The "Residual Deviance" is the likelihood-ratio goodness-of-fit statistic.
#     Compare this to value given by loglm

# 8. Compute association statistics

assocstats(Hospital)


############### Figures Showing association in table ##################
# A nice web-site for colors:  
# http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf
# and for palettes
# https://www.r-bloggers.com/palettes-in-r/
#
#

par=(mfrow=c(2,2)) 

# 9. Bar chart

bar.colors <- c("red","blue","green")  # I defined pallette
par(cex=1.2)
barplot(Hospital, 
        beside=TRUE, 
		legend=TRUE,col=bar.colors,
		main="Hospital Data from vcd Package",
		xlab="Length of Stay in Days",
		ylab="Frequency",
		)

# 10. Tile plot

tile(Hospital)
 
# 11. Plot

plot(Hospital,col="cornflowerblue")

# 12. Spine plot

spineplot(Hospital,col="cornflowerblue")

box.colors=rainbow(6, s=0.6)           # pre-defined palette           
spineplot(Hospital,col=box.colors)

# 13. Mosaic

mosaic(Hospital)