# Chapter 5 Descriptive Syntax in R.

# Read in Rat Brain data in long format.
rat.brain <- read.table("C:\\temp\\rat_brain.dat", h = T)

# Attach rat brain data to working memory. 
attach(rat.brain) 
 
# Define region and treatment factors.
region.f <- region
region.f[region == 1] <- 1
region.f[region == 2] <- 2
region.f[region == 3] <- 0
region.f <- factor(region.f)
treat <- treatment
treat[treatment == 1] <- 0
treat[treatment == 2] <- 1
treat <- factor(treat)
rat.brain <- data.frame(rat.brain, region.f, treat)
 
###table report on page 221######
###overall ###

dim(rat.brain)  #obs


summary(rat.brain$activate) #mean

sqrt(var(rat.brain$activate)) #stdev

###by treatment group###
summary(treat)     #obs


by(rat.brain$activate,list(treat),summary) #mean
 
sqrt(by(rat.brain$activate,list(treat),var))   #stdev
 
###by region group###
summary(region.f) #obs

by(rat.brain$activate,list(region.f),summary) #mean

sqrt(by(rat.brain$activate,list(region.f),var))   #stdev

###by treat and region group###
table(treat,region.f)  #obs

by(rat.brain$activate,list(treat, region.f),summary)  #mean

sqrt(by(rat.brain$activate,list(treat, region.f),var)) #stdev

library(lattice)  # Load the library for trellis graphics.
trellis.device(color=F) # Make sure color is turned off.
 
# Load the nlme library, which is required for the 
# plots below as well as for subsequent models.
library(nlme)
 
rat.brain.g1 <- groupedData(activate ~ region | animal, outer = ~ treat, data = rat.brain)
 
plot(rat.brain.g1, display = "animal", outer = TRUE, aspect = 2, key = F, xlab = "region", ylab = "mean activate", main="treatment")