#####################################################################
# R commands      STAT540 R Basic 2 
# University of South Carolina
######################################################################
# This file contains the R commands for the lab.
#
# Lines beginning with the symbol '#' are comments in R.  All other
# lines contain code.
#
# In R for Windows, you may wish to open this file from the menu bar
# (File:Display file); you can then copy commands into the command
# window.  (Use the mouse to highlight one or more lines; then
# right-click and select "Paste to console".)
######################################################################


#### Navigating and Managing the Filesystem
### working directory 
getwd()
setwd("/Users/hoyen/Desktop/STAT540")


## ------------------------------------------------------
system.file(package = "dslabs")


## ------------------------------------------------------
dir <- system.file(package = "dslabs")
list.files(dir)


## ------------------------------------------------------
dir <- system.file(package = "dslabs")
file_path <- file.path(dir, "extdata/murders.csv")


## ------------------------------------------------------
file.copy(file_path, "murders.csv")



## ------------------------------------------------------
readLines("murders.csv", n = 3)


## ------------------------------------------------------
fn <- "calificaciones.csv"
file.copy(file.path(system.file("extdata", package = "dslabs"), fn), fn)
readLines(fn, n = 1)


## ------------------------------------------------------
dat <- read.csv("murders.csv")


## ------------------------------------------------------
x <- scan("murders.csv", sep = ",", what = "c")
x[1:10]


#Section 5.1 Creating data

#Using rep
rep(1,10)
rep("Gamecocks Rule",1000)
rep("While Gamecocks Rule, cockfighting itself is banned in SC",10)


#Creating constant matrices and variables
zeromat = matrix(0,5,3)
onesvec.col = matrix(1,10,1)
rep(1,10)

#Converting a variable to a matrix
bigvec = 1:200
mat.bycols = matrix(bigvec,100,2)
mat.bycols
mat.byrows = matrix(bigvec,100,2,byrow=T)
mat.byrows

#Section 5.2

#Reading tab-delimited files with and without headers
#Reading files from working directory
brainbod = read.table("brainbod2.txt")
brainbod

brainbod = read.table("brainbod1.txt", header=T)
brainbod
is.numeric(brainbod$brainwt)

brainbod1 = read.table("brainbod1.txt")
brainbod1
is.numeric(brainbod1$brainwt)

brainbod = read.table("brainbod.txt", sep=',', header=T)
brainbod

# read.csv 
brainbod3 = read.csv("brainbod.csv")
brainbod3

#Assigning row and column names

names(brainbod)=c("Species", "Brain.Weight","Body.Weight")
brainbod

brainbod = read.table("brainbod2.txt",col.names=c("Species","Body Weight", "Brain Weight"))
brainbod # pay attention that blank spaces in the names are changed to "."

row.names(brainbod)=brainbod$Species
brainbod

# some special types of missing values
brainbod = read.table("brainbod4.txt", na.strings="*")
brainbod
is.numeric(brainbod[,2])
is.character(brainbod[,2])

brainbod[,2]<- as.numeric(brainbod[,2])
brainbod

ratio= brainbod[, 2]/brainbod[, 1]/1000
ratio=round(ratio, digit=6)
cbind(brainbod, ratio)

## try attach and detach again
brainbod$Species
Species
attach(brainbod)
#brainbod=data.frame(Brain.Weight,Body.Weight,row.names=Species)
Species
rm(brainbod)
ls()
Species
objects(2)
search()
detach(brainbod)

# read data file from non-working directory
brainbod = read.table("C:/WangFiles/Stat540_Fall2023/Rcodes/brainbod2.txt")
brainbod

is.factor(brainbod$V1)
is.character(brainbod$V1)
is.numeric(brainbod$V2)


brainbod = read.table("C:/WangFiles/Stat540_Fall2023/Rcodes/brainbod2.txt")
brainbod


brainbod = read.table("C:/WangFiles/Stat540_Fall2023/Rcodes/brainbod2.txt", col.names=c("Species","Body Weight", "Brain Weight"))
brainbod

# read data from a website
brainbod = read.table("http://people.stat.sc.edu/hitchcock/brainbod.txt")
brainbod



#Section 5.3

help(scan)

brainbod = as.data.frame(scan("brainbod2.txt",what=list(Species="",Body.Weight=0, Brain.Weight=0)))
brainbod

my.dfr <- as.data.frame(scan("Garden.txt", what=list(name="", tomato=0, grapes=0, type=""), multi.line=T))
my.dfr

# use scan to input numeric data  using keyboard
xz=scan()


##Chapter 6

#Outputting a matrix into a text file
mymat=matrix(1:15,5,3)
mymat

colnames(mymat)<- c("x1", "x2","x3")
rownames(mymat)<- c("row1", "row2", "row3", "row4", "row5")
mymat


write(mymat, "mymat.txt",ncol=ncol(mymat)) # check out what is in mymat.txt

write(t(mymat),"mymat2.txt",ncol=ncol(mymat))

write(t(mymat),"mymat3.txt")  # what if the column number is not specified?

write(t(mymat),"mymat2.txt",ncol=ncol(mymat), append=T) 

write.table(mymat, "mymat4.txt") # save the matrix together with the row and column names

# write to a designated file in the non-working directory
write(mymat, "C:/WangFiles/Stat540_Fall2023/Rcodes/mymat.txt",ncol=ncol(mymat))
write(t(mymat),"C:/WangFiles/Stat540_Fall2023/Rcodes/mymat2.txt",ncol=ncol(mymat))

# save objects in a .rdata file
help(save)
save(mymat, brainbod, file="lecture1.rdata") # save mydata and brainbod into an r workspace named "lecture1.rdata"
save.image(file="lecture.rdata") # save all objects in the current workspace into an r workspace "lecture.rdata"


# write a function into a file
myfct<-function(x){c(mean(x)-2*sd(x),mean(x)+2*sd(x) )}

a=rnorm(20) 
myfct(a)

dput
help(dput)
dput(myfct, "") # display the function on screen
dput(myfct, "try1.txt") # write the function in a file called try1.txt

fix(myfct) # open a editor window for myfct

# print results to screen 
x<-101
print(paste("this output is",x))
print(paste("the output x is ", x, " and x+1 is ", x+1 ))

a=23
b=11
xxx=paste("the score of today's game is ", a,":", b, ", Gamecocks win!!!" )
xxx
print(paste("the score of today's game is ", a,":", b, ", Gamecocks win!!!" ))

# print some results within a loop on screen 
for (i in 1:8){
x=runif(1)
print(paste("iteration =", i, ", x[", i, "]=", round(x, digit=4)) )
}