# R code for chapter 51 mosaic and extended association plots.r
# Book details:
# Health Science Statistics using R and R Commander
# by Robin Beaumont
# Paperback - ISBN 9781907904318
# http://www.amazon.co.uk/Health-Science-Statistics-using-Commander/dp/190790431X
# or direct from publisher at: 
# http://www.scionpublishing.com/
# book website: http://www.robin-beaumont.co.uk/rbook
###########################################################
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# using the Amoxicillin/Erythromycin data described in the chapter
# Comparing several independent categories, section Equivalent analysis directly in R.
#
thedata <- matrix( c(144, 96, 160, 80), nrow= 2, ncol=2,  
dimnames = list(outcome = c("improved at 5 days", "NO improvement at 5 days"),  antibiotic =c("Amoxicillin", "Erythromycin")))
thedata # get a printout of the data

# now draw the moasic plot using the vcd package:
install.packages("vcd", dependencies=TRUE) 
library(vcd)

mosaic(thedata, shade=TRUE, legend=TRUE)
######## more data showing significant proportions:

thedata <- matrix( c (110, 120,160,80), ncol=2, byrow=FALSE) 
mycol_names <- c("Amoxicillin", "Erythromycin")
myrow_names <- c("improved", "no_improve")
dimnames(thedata) <- list(status = myrow_names, antibiotic = mycol_names)
thedata
myresult <- chisq.test(thedata)
myresult

# 50.2	Mosaic plot options - shading and residual types
# default; using components of Pearson’s chi-squared
mosaic(thedata, residuals_type = "pearson", gp = shading_Friendly )
# using components of the likelihood ratio chi-squared
mosaic(thedata, residuals_type = "deviance", gp = shading_Friendly )
# using Freeman-Tukey residuals
mosaic(thedata, residuals_type = "FT", gp = shading_Friendly )

############# tips
# Remember if you have raw data you need to wrap the data in the table() function:
# mosaic(thecountdata,  residuals_type = "pearson", gp = shading_Friendly )
# or
# mosaic(table(therawdata),  residuals_type = "pearson", gp = shading_Friendly )

########## end #######



















load(url("http://www.robin-beaumont.co.uk/virtualclassroom/book2data/healthwagedata.rda"))
# or
# http://www.robin-beaumont.co.uk/virtualclassroom/book2data/healthwagedata.sav