# t test paired data

# following to obtain my sample data:

# http://www.robin-beaumont.co.uk/virtualclassroom/book2data/ttest_paired_hindmarsh_1987.dat
mydataframe <-read.delim("http://www.robin-beaumont.co.uk/virtualclassroom/book2data/ttest_paired_hindmarsh_1987.dat")

### local copy ignore:
# mydataframe <- read.delim("D:\\web_sites_mine\\HIcourseweb 
# new\\book2data\\ttest_paired_hindmarsh_1987.dat", header=TRUE)
###
names(mydataframe)
attach(mydataframe)
str(mydataframe)
mydataframe
# create the difference variable
mydataframe$difference <- mydataframe$X1_year - mydataframe$baseline_std
#or as  created by R Commander:
# mydataframe$difference <- with(mydataframe, X1_year - baseline_std) 
# get summary stats
summary(mydataframe)

#boxplot it; two methods:
library(Rcmdr)
Boxplot( ~ difference, data=mydataframe, id.method="y")
# or just using the standard boxplot function()
boxplot(difference, data=mydataframe)

# now perform the t test
t.test(mydataframe$baseline_std, mydataframe$X1_year, 
  alternative='two.sided', conf.level=.95, paired=TRUE)
#
# effect size
effect_size <- mean(difference)/ sd(difference)
effect_size

need to delete the difference variable: 
mydataframe$difference <- NULL
# now to draw 
# install.packages("reshape2", dependencies = TRUE)
library(reshape2)
stacked_data <- melt(mydataframe, id.vars = "subject")
stacked_data
stacked_data$variable
stacked_data$value
# now we need to order the new stacked_data dataframe by 
# subject id so the display is correct
stacked_data <- stacked_data[order(stacked_data$subject),]
stacked_data
#now graph it
library(lattice)
xyplot(value ~ variable, data = stacked_data, type="b")

## more complex one

xyplot(value ~ variable, data = stacked_data, type="b", 
ylab= "standardised height cm",
xlab = "before after",
main = "standardised height changes over 1 year")

# the last line below not required is allows you the option of
# specifying which categories you want displayed.

xyplot(value ~ variable, data = stacked_data, type="b", 
ylab= "standardised height cm",
xlab = "before after",
main = "standardised height changes over 1 year",
scales = list(x = list(at = c(1,2))))