Chapter 1. Introduction to R

Saturday, September 27, 2014

R is, at its heart, an elegant and beautiful language, well tailored for data analysis and statistics. --- Hadley Wickham

For introduction of R language, you are recommended to read the first chapter of R in Action and the introduction part of Advanced R.

R Installation

Install R

You can follow my instruction which is described below to install and upgrade R on Windows.

First, you need to download R and RStudio and install them. After the installations, run the following codes to set up a global library.

chooseCRANmirror() # Choose XMU
source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
Old.R.RunMe()

Upgrade R

Once you have done these, from now on, whenever you want to update to a new version of R in the future, all you will need to do are the following TWO steps:

Download and install the new version of R
Open your new R and run the following codes

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
New.R.RunMe()

RStudio settings

Open up your RStudio. In RStudio, Tools --> Global Options --> Code Editing/Appearance. See Customizing RStudio for details.

Most used RStudio keyboard shortcuts:

Description	Keyboard(Windows)
Clear console	Ctrl+L
Interrupt currently executing command	Esc
Run current line/selection	Ctrl+Enter
Run current document	Ctrl+Alt+R
Find and Replace	Ctrl+F
Find in Files	Ctrl+Shift+F
Comment/uncomment current line/selection	Ctrl+Shift+C
Check Spelling	F7
Undo	Ctrl+Z
Redo	Ctrl+Shift+Z
Delete Line	Ctrl+D
Indent	Tab (at beginning of line)
Show help for function at cursor	F1
Show source code for function at cursor	F2
Attempt completion	Tab or Ctrl+Space

See Keyboard Shortcuts for more details.

Getting help

Use Ctrl+Enter to run the selected codes or the line where you cursor on. The output is shown in the Console window.

help.start()   # general help
help(plot)      # help about function plot
?plot          # same thing 
apropos("plot") # list all functions containing string plot
example(plot)   # show an example of function plot

# search for plot in help manuals and archived mailing lists
RSiteSearch("plot")

# get vignettes on using installed packages
vignette()      # show available vingettes
vignette("knitr-html") # show specific vignette

Manage your workspace

Now please create a file in you computer system as your workpalce. Such as E:\Project\WISE R Club\LearnR.

R gets confused if you use a path in your code like

c:\mydocuments\myfile.txt

This is because R sees "" as an escape character.

Instead, you should use

c:\\my documents\\myfile.txt
c:/mydocuments/myfile.txt

Either will work.

getwd() # print the current working directory - cwd 
ls()    # list the objects in the current workspace

setwd("E:/Project/WISE R Club/LearnR")  # note / instead of \ in windows 

# view and set options for the session
help(options) # learn about available options
options() # view current option settings
optio#ns(digits=3) # number of digits to print on output

# work with your previous commands
history() # display last 25 commands
history(max.show=Inf) # display all previous commands

# save your command history 
savehistory(file="myfile") # default is ".Rhistory" 

# recall your command history 
loadhistory(file="myfile") # default is ".Rhistory"

# save the workspace to the file .RData in the cwd 
save.image()

# save specific objects to a file
# if you don't specify the path, the cwd is assumed 
save(object list, file="myfile.RData")
save(x, file="mydata.RData")

# load a workspace into the current session
# if you don't specify the path, the cwd is assumed 
load("mydata.RData")

q() # quit R. You will be prompted to save the workspace.

Script input/output

By default, R provides an interactive session with input from the keyboard and output to the screen. However, you can have input come from a script file and direct output to a variety of destinations.

Input

# source a script
source("myfile.R")
source("myfile.R", print.eval = TRUE)
source("myfile.R", echo = TRUE, print.eval = TRUE)

Output

The sink( ) function defines how to print the output.

# direct output to a file 
sink("output_file", append=FALSE, split=FALSE)

# return output to the terminal 
sink()

The append option controls whether output overwrites or adds to a file. The split option determines if output is also sent to the screen as well as the output file.

Here are some examples of the sink() function.

# output directed to myfile.txt in cwd. output is appended to existing file. output also send to terminal. 
sink("output_file.txt", append=FALSE)
x <- 1:5
cat("x: \n")
x
cat("Mean: \n")
mean(x)
cat("Variance: \n")
var(x)

cat("\n")
source("myfile.R", echo = TRUE, print.eval = TRUE)

sink()

When redirecting output, use the cat( ) function to annotate the output.

Packages

Packages are collections of R functions, data, and compiled code in a well-defined format. The directory where packages are stored is called the library.

.libPaths() # get library location 
library()   # see all packages installed 
search()    # see packages currently loaded

A complete list of contributed packages is available from CRAN.

You can add packages from the Tools --> Install Packages or run code like install.packages("ggplot2"). You can update packages from Tools --> Check for Packages Updates or use update.packages()

Reusing results

One of the most useful design features of R is that the output of analyses can easily be saved and used as input to additional analyses. Please see the following examples.

lm(mpg~wt, data=mtcars)

fit <- lm(mpg~wt, data=mtcars)

str(fit) # view the contents/structure of "fit"

# plot residuals by fitted values
plot(fit$residuals, fit$fitted.values)

# produce diagnostic plots
plot(fit)

An example

An example at the end.

setwd("E:/Project/WISE R Club/LearnR")
install.packages("ggplot2")
library(ggplot2)
help(package = "ggplot2")
vignette(package = "ggplot2")
?qplot
str(diamonds)
example(qplot) # example of qplot function
qplot(color, price/carat, data = diamonds, geom="jitter", alpha = I(1/5))