Notes on Using R for Data Analysis and Graphics

Introduction

Using R for Data Analysis and Graphics (PDF file) is a tutorial written by John Maindonald, Centre for Bioinformation Science, Australian National University. Professor Maindonald also provides the scripts and data set that accompany Using R.

Note: John Maindonald and John Braun are coauthors of the book Data Analysis and Graphics Using R; see my notes for more information.

This page stores my notes as I work through the chapters of this book. I am using R 2.2.1 and R GUI 1.14 for Mac OS X.

Setting up a working directory

Download the Using R for Data Analysis and Graphics PDF file, the scripts, and the UsingR.RData data set to a working directory. For these notes, I have used the directory /Volumes/CHHalling/R/Tutorials/Maindonald.

Loading the UsingR.RData file

Attach the UsingR.RData data file and list the objects it contains:

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
attach( what = "UsingR.RData" )
ls( name = "file:UsingR.RData" )

A more conventional way to load the data file so that the data objects are in the user’s work space is with the following commands:

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
load( file = "UsingR.RData" )
ls()

It is also possible to load the UsingR.RData data file via a URL connection without having a local copy on your computer. The commands are:

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
con <- url( "http://www.maths.anu.edu.au/~johnm/r/dsets/usingR.RData" )
load( con )
close( con )
ls()

Chapter 1

The R script ch1-2.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

According to Data Analysis and Graphics Using R by John Maindonald and John Braun, p. 3, the elasticband data are the results of a rubber band shooting experiment, where stretch is the length that the rubber band was stretched before shooting, and distance is the distance the rubber band traveled when it was released.

These are my solutions to the exercises:

##  Set the working directory and attach the data file.

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
attach( what = "UsingR.RData" )

##  Exercise 1

elasticband <-
    data.frame(
        stretch  = c(  46,  54,  48,  50,  44,  42,  52 ),
        distance = c( 148, 182, 173, 166, 109, 141, 166 ) )

plot( distance ~ stretch, data = elasticband )

##  Exercise 2

snowCover <-
    data.frame(
        year       = 1970:1979,
        snow.cover = c( 6.5, 12.0, 14.9, 10.0, 10.7,
                        7.9, 21.9, 12.5, 14.5,  9.2 ) )

get( getOption( "device" ) )()
plot( snow.cover ~ year, data = snowCover )

get( getOption( "device" ) )()
plot( log( snow.cover ) ~ year, data = snowCover )

##  Exercise 3

damage <-
    data.frame(
        temperature = c( 53, 57, 63, 70, 70, 75 ),
        erosion     = c(  3,  1,  1,  1,  1,  0 ),
        blowby      = c(  2,  0,  0,  0,  0,  2 ),
        total       = c(  5,  1,  1,  1,  1,  2 ) )

get( getOption( "device" ) )()
plot( total ~ temperature, data = damage )

##  The entire data set is provided in data.frame orings from the
##  data file UsingR.RData. Plot these data.

get( getOption( "device" ) )()
plot( Total ~ Temperature, data = orings )

Chapter 2

The R script ch1-2.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

##  Set the working directory and attach the data file.

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
attach( what = "UsingR.RData" )

Chapter 3

The R script ch3-4.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 4

The R script ch3-4.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 5

The R script ch5.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 6

The R script ch6.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 7

The R script ch7.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 8

The R script ch8.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 9

The R script ch9.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 10

The R script ch10.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.

Chapter 11

The R script ch11.R as provided cannot be sourced successfully. Make the following change:

Change line 32 from

  library(mass)    # if needed

to

  library(MASS)    # if needed

Run the script:

setwd( dir = "/Volumes/CHHalling/R/Tutorials/Maindonald" )
attach( what = "UsingR.RData" )
source( file = "ch11.R", echo = TRUE )

R produces the following warning message when the script is sourced:

Warning message:
Error() model is singular in: aov(yield ~ block + shade + Error(block:shade),
 data = kiwishade)

Chapter 12

The R script ch12.R as provided cannot be sourced successfully. Instead, open it in a text editor and copy and paste commands into R.