###Sample code for Lab1
#display the current working directory
getwd()
#change the directory to where the dataset is stored
setwd("C:/Users/shouhermione/Documents/TA/Nanjing/Karen")
#list all the files in the directory
list.files()
#list all the files in the work space
ls()

#logical value
3>2
(1==4)&(is.na(5))

#create a vector/matrix/array
x<-1:10
x
x<-c(0.3,-2.1,5.7)  #concatenate
summary(x)
sort(x)
mean(x)

#create a matrix
y<-matrix(1:6,nrow=2,ncol=3,byrow=FALSE)
y
y[2,1]
#matrix calculation
A<-matrix(1:6,nrow=3,ncol=2)
B<-matrix(7:10,2,2)
A%*%B
A*B

z<- array(1:9,dim=c(3,3,3))

#generate a list
x<-list(gender=c('F','M'),grade=c(98,100,90),undergrad=FALSE)

#read in data frame
dat<-read.csv('osteo.csv',header=TRUE)
dim(dat)
#output the data
write.table(dat, 'osteo2.txt',col.names=TRUE, sep='\t')
dat<-read.table('osteo2.txt', header=TRUE)

##pick the subset of the data with osteo==1, which returns the index of rows satifying the criteria in the parentheses
case<-dat[which(dat$Osteo==1),]

##plotting
op<-par(mfrow=c(2,2))
plot(dat$Age, dat$DPA,main='DPA vs. age',xlab='age',ylab='DPA',col='blue')
hist(dat$DPA,main='Histogram of DPA')
#boxplot(dat$DPA,main='Boxplot of DPA')
boxplot(dat$DPA~dat$Osteo,main='Boxplot of DPA by disease status')
qqnorm(dat$DPA)
qqline(dat$DPA)
par(op)

#stem plot
stem(dat$DPA)

#plot
x<-seq(from=0,to=1,length=50)
w<-2*cos(4*pi*x)             #true value
e<-rnorm(50,mean=0,sd=.5)     #random errors
y<-w+e
plot(x,y,type='l',ylim=c(-3,4))
lines(x,w,col='blue',lwd=2,lty='dashed')
legend('topright',legend=c('with noise','true value'),col=c('black','blue'),lty=c('solid','dashed'),lwd=c(1,2))

#loops
m=4
s<-1
for(i in 1:4){
   s=s*i
   }
print(s)

s<-4
j<-4-1
while(j>=1) {
 s=s*j
 j=j-1
 }

#define your own function
fx<-function(x){
   y=0
   if((x<=8)&(x>0)) y=2*x-1
   if((x<=10)&(x>8)) y=x
   y
}

fx(9)