library(DAAG)
data(ais)
help(ais)

is.data.frame(ais)
plot(ais)
head(ais)
names(ais)
attach(ais)

################## star plots #########################################

x <- ais[,"bmi"]
y <- ais[,"pcBfat"]
plot(x,y,type="n",xlab="Body mass index",ylab="Percent body fat")

########### ray length corresponds to variables in star. Starts at 3 o'clock, goes counter-clockwise

sport.name <- levels(sport)
n <- length(sport.name)
for (j in 1:n) {
	I <- sport==sport.name[j]
	x <- ais[I,"bmi"]
	y <- ais[I,"pcBfat"]
	star <- matrix(unlist(ais[I,1:5]),ncol=5)
	symbols(x,y,stars=star,add=TRUE,fg=j)
}
legend(x="topleft",legend=sport.name,pch=16,col=1:n)

x <- ais[,"bmi"]
y <- ais[,"pcBfat"]
n <- length(x)
plot(x,y,type="n",xlab="Body mass index",ylab="Percent body fat")

########################## convex hull #########################

genders <- levels(sex)
n <- length(genders)
for (j in 1:n) {
	I <- sex==genders[j]
	x <- ais[I,"bmi"]
	y <- ais[I,"pcBfat"]
	star <- matrix(unlist(ais[I,1:5]),ncol=5)
	symbols(x,y,stars=star,add=TRUE,fg=j)
	hull <-chull(x,y)
	polygon(x[hull],y[hull],border=j)
}
legend(x="topleft",legend=genders,pch=16,col=1:n)

################## conditioning plots

library(lattice)
xyplot(bmi~ssf|sport,groups=sex,pch=16,col=c(2,3),data=ais,xlab="Skin-fold",ylab="Body mass")
legend(x="topleft",legend=c("Females","Males"),pch=16,col=c(2,3))
########################## 3-D perspective #########################

library(scatterplot3d)

Weight <- ais$wt
Height <- ais$ht
BMI <- ais$bmi ### kg/m^2
HG <- ais$hg
scatterplot3d(Weight,Height,BMI,type="h")
coplot(BMI~Weight|Height)
coplot(BMI~Height|Weight)

RedCells <- ais$rcc
scatterplot3d(RedCells,BMI,HG,type="h")

coplot(HG~RedCells|BMI)

####################### box plots ###########################


library(mlbench)
data(Ozone)
help(Ozone)
Ozone <- na.omit(Ozone)


names(Ozone) <- c("month","daym","dayw","ozone","pressure","windspeed",
	"humidity","tempS","tempEM","inversion","grad","inverstemp","visibility")
ozone <- Ozone$ozone

boxplot(ozone~Ozone$month,ylab="Ozone ",xlab="Month")
library(lattice)
stripplot(ozone~Ozone$month,ylab="Ozone ",xlab="Month",pch=16,col=1)
bwplot(ozone~Ozone$month,ylab="Ozone ",xlab="Month",col=1)

coplot(Ozone$ozone~Ozone$tempS|Ozone$windspeed)

coplot(Ozone$ozone~Ozone$tempS|Ozone$tempEM,
	panel=function(x,y,col,pch)panel.smooth(x,y,span=1))

########################### lowess smooth #################
n <- length(ozone)

cor(ozone[1:(n-1)],ozone[2:n]) 
acf(ts(ozone)) # plot of auto-correlation function

plot(ozone[1:(n-1)],ozone[2:n],xlab="Ozone at time t",ylab="Ozone at time t+1")
lines(lowess(ozone[2:n],ozone[1:(n-1)],f=2/3))
lines(lowess(ozone[2:n],ozone[1:(n-1)],f=1/3))
lines(lowess(ozone[2:n],ozone[1:(n-1)],f=1/6))

par(mfrow=c(2,1))
symbols(ozone[1:(n-1)],ozone[2:n],circles = Ozone$inversion[1:(n-1)],inches=0.15,xlab="Ozone, day t",
	ylab="Ozone at time t+1",main="Circles are inversion height, day t")
symbols(ozone[1:(n-1)],ozone[2:n],circles = Ozone$inversion[2:n],inches=0.15,xlab="Ozone, day t",
	ylab="Ozone at time t+1",main="Circles are inversion height, day t+1")

symbols(ozone[1:(n-1)],ozone[2:n],circles = Ozone$inversion[2:n],inches=0.15,xlab="Ozone, day t",
	ylab="Ozone at time t+1",main="Circles are inversion height, day t+1")
invers <- max(Ozone$inversion[2:n])-Ozone$inversion[2:n]
symbols(ozone[1:(n-1)],ozone[2:n],circles = invers[2:n],inches=0.15,xlab="Ozone, day t",
	ylab="Ozone at time t+1",main="Circles are inversion depth, day t+1")

par(mfrow=c(1,1))
lm.obj <- lm(ozone[2:n]~ozone[1:(n-1)])
summary(lm.obj)

residuals <- lm.obj$residuals - min(lm.obj$residuals)
symbols(Ozone$tempS[2:n],ozone[2:n],circles = Ozone$inversion[2:n],inches=0.15,xlab="Temperature at Sandburg",
	ylab="Detrended Ozone ar t+1",main="Circles are inversion height, day t+1",cex.main=0.9)

################# Count data ###################
# Outcomes from open and ultrasound surgery of kidney stones

stones <- array(c(81,6,234,36,192,71,55,25),dim=c(2,2,2),
	dimnames=list(Success=c("yes","no"),Method=c("open","ultrasound"),
	Size=c("<2cm",">2cm")))
stones

mosaicplot(stones,sort=3:1)