Introduction to Programming in R

Course Website: http://bcb.dfci.harvard.edu/˜aedin/courses/R/

C ENTERS FOR D ISEASE C ONTROL AND P REVENTION

26-28 TH J UNE 2012

Aedin Culhane
Email: aedin@jimmy.harvard.edu
http://bcb.dfci.harvard.edu/˜aedin
http://www.hsph.harvard.edu/research/aedin-culhane/
Contents

1 Introduction to R Software 2
1.1 Obtaining R and RStudio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 The default R interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.1 Default R Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.2 Default R Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.3 R Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 RStudio Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.1 console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.2 Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3.3 Workspace, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3.4 Files, Plots, Packages, Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.5 Projects, SVN in RStudio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4 Starting out - setting a working directory . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.1 Managing and accessing folders in R . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.5 First R Encounter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.6 Getting help with functions and features . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.7 R as a big calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.8 A few important points on R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.8.1 Use Arrows to key browse command history . . . . . . . . . . . . . . . . . . . . . 15
1.9 Basic operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.9.1 Comparison operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.9.2 Logical operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.10 Data sets in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.11 R sessions (workspace) and saving session history . . . . . . . . . . . . . . . . . . . . . . . 18
1.12 R Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.13 Installing new R libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.14 Customizing Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2 Objects in R 24
2.1 Using ls and rm to managing R Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.2 Types of R objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3 Attributes of R Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.4 Creating and accessing objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.5 Modifying elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.5.1 Sorting and Ordering items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5.2 Missing Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.5.3 Creating empty vectors and matrices . . . . . . . . . . . . . . . . . . . . . . . . . . 36

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 2.6 Quick recap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
2.7 Exercise 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

3 Reading and writing data to and from R 40

3.1 Importing and reading text files data into RStudio . . . . . . . . . . . . . . . . . . . . . . . 40
3.2 Importing data using R command read.table() . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.2.1 Using read.table() and read.csv() . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.3 Exercise 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.3.1 Importing text files Using scan() . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.4 Reading data from Excel into R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.5 Import/Export from other statistical software . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.5.1 Reading data from SAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.5.2 S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.5.3 Stata or Systat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.6 From a Database Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.6.1 Parsing each line - Readlines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.7 Writing Data table from R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.7.1 Other considerations when reading or writing data . . . . . . . . . . . . . . . . . . 51
3.8 Exercise 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.9 Sampling and Creating simulated data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.10 Exercise 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

4 Introduction to programming and writing Functions in R 56

4.1 Why do we want to write functions? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.2 Conditional statements (if, ifelse, switch) . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.2.1 Repetitive execution: For and While loops . . . . . . . . . . . . . . . . . . . . . . . 58
4.3 Viewing Code of functions from R packages . . . . . . . . . . . . . . . . . . . . . . . . . . 59
4.4 The Apply Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4.5 Exercise 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
4.5.1 Efficient For Loop in R (Use apply) . . . . . . . . . . . . . . . . . . . . . . . . . . 65
4.6 Functions for parsing text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.7 missing values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.8 Exercise 6: Parsing Real Data - World Population Data from Wikipedia . . . . . . . . . . . 69
4.8.1 Writing functions: More on arguments . . . . . . . . . . . . . . . . . . . . . . . . . 70
4.9 Writing functions: more technical discussion -Scoping . . . . . . . . . . . . . . . . . . . . 71
4.10 Options for Running memory or CPU intensive jobs in R . . . . . . . . . . . . . . . . . . . 72
4.10.1 Distributed computing in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.10.2 Running R in the Cloud . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.11 Efficient R coding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.11.1 What is an R script . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.11.2 What a script should look like ;-) . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.11.3 Coding Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
4.11.4 Debugging R Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.11.5 End-User Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.11.6 system.time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.11.7 Etiquette when emailing the R mailing list . . . . . . . . . . . . . . . . . . . . . . . 76

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5 Introduction to graphics in R 79
5.1 The R function plot() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.2 Exercise 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
5.2.1 Arguments to plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
5.2.2 Other useful basic graphics functions . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.3 Editing the default plot with low-level plotting commands . . . . . . . . . . . . . . . . . . . 96
5.4 Default parameters - par . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5.4.1 Interactive plots in R Studio - Effect of changing par . . . . . . . . . . . . . . . . . 100
5.4.2 R Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
5.5 Interacting with graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
5.5.1 Exercise 8 - Plotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.6 Saving plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.6.1 Rstudio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.6.2 Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.6.3 Difference between vector and pixel images . . . . . . . . . . . . . . . . . . . . . . 108
5.7 Useful Graphics Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

6 Advanced Graphics 110

6.1 Advanced plotting using Trellis; ggplots2, Lattice . . . . . . . . . . . . . . . . . . . . . . . 110
6.1.1 ggplots2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
6.1.2 lattice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
6.1.3 Examples that Present Panels of Scatterplots using xyplot() . . . . . . . . . . . . . . 120
6.1.4 Simple use of xyplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
6.2 GoogleVis and GoogleMaps visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
6.3 Graph theory and Network visualization using R packages network and igraph . . . . . . . . 133
6.4 Tag Clouds, Literature Mining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.5 Other visualization resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
6.6 Summary on plotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

7 Statistical Analysis, linear models and survival analysis in R 141

7.1 This section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
7.2 Basic Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
7.2.1 Continuous Data: t test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
7.2.2 adjusting for multiple testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
7.2.3 Continuous Data: One- and two-way analysis of variance . . . . . . . . . . . . . . . 145
7.2.4 Discrete Data: Contingency Table . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
7.2.5 Common statistical Tests in R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.3 Model formulae and model options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7.3.1 Model formulae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.3.2 Example of linear regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
7.3.3 Contrasts, model.matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
7.4 Exercise 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
7.5 Output and extraction from fitted models . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
7.6 Exercise 10 :Multivariate linear regression . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
7.6.1 Residual plots, diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
7.6.2 ANOVA and updating models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
7.6.3 Model selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
7.7 Cross-validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

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 7.8 Statistical models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
7.8.1 Linear Regression: Weighted Models, Missing Values . . . . . . . . . . . . . . . . 169
7.8.2 Generalized linear modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
7.8.3 Other packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
7.9 Survival modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
7.9.1 Censored Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
7.9.2 Kaplan-Meier curve estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
7.9.3 Cox proportional hazards model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
7.10 Exercise 11: Survival Anlaysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182

8 Solutions to Exercises 183

8.1 Solution to Exercise 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
8.2 Solution to Exercise 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
8.3 Solution to Exercise 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
8.4 Solution to Exercise 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
8.5 Solution to Exercise 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
8.6 Solution to Exercise 6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
8.7 Solution to Exercise 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
8.8 Solution to Exercise 8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
8.9 Solution to Exercise 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
8.10 Solution to Exercise 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
8.11 Solution to Exercise 11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
8.12 sessionInfo() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

iv
 R set up script for this manual

We will run this course with R>2.15 and RStudio 096.

To ensure you have all of the packages needed to run this course, either

1. install course R package (available on the course website)

2. source the following commands into your R session

pkgs <- list("lme4", "xtable", "xlsx", "RODBC", "Hmisc", "SAScii",

"R2HTML", "BiocInstaller", "RColorBrewer", "lattice", "ggplot2",
"googleVis", "plyr", "network", "igraph", "vcd", "MASS",
"survival")
Biocpkgs <- c("parallel")

checkPkg <- function(x) {

print(x)
if (!require(x, character.only = TRUE))
install.packages(x)
}
checkBioCPkg <- function(x) {
print(x)
if (!require(x, character.only = TRUE))
biocLite(x)
}

lapply(pkgs, checkPkg)
lapply(Biocpkgs, checkBioCPkg)

search()

1
Chapter 1

Introduction to R Software

1.1 Obtaining R and RStudio

R can be downloaded from the website: http://cran.r-project.org/. See additional online notes
which give a very detailed description on downloading and installing R (and Bioconductor). R is available
for all platforms: Unix/Linux, Windows and Mac.
When you download R, its default editor and console are relatively basic (we describe it below). In this
course we will call R using RStudio which provides a richer interface and nicer editor of R code. RStudio
can be obtained from www.rstudio.org). RStudio is available as a desktop program for all platforms
Unix/Linux, Windows and Mac.
If you don’t want to install R on your own machine, or tie up your own machine, with a memory or CPU
intensive task. You can run R through web server or even in the Cloud. Its really simple to run R jobs in the
Amazon cloud as described in Section 4.10 and these can be run through the RStudio interface, which looks
exactly as it does on the desktop version.
In this course, we will concentrate on the Windows implementation of R. The differences between the
platforms are minor, so most of the material (R, Rstudio) is applicable to the other platforms.

1.2 The default R interface

When you click on the R icon, you will open the basic R interface

• On the menu bar, there are the menus:

– File - load script, load/save session (workspace) or command history. Change Directory
– Edit - Cut/Paste. GUI preferences
– View
– Misc - stop computations, list/remove objects in session
– Packages - allows one to install new, update packages
– Windows
– Help - An essential resource!

• The icons below will allow one to

– open script (.R file),

2
 Figure 1.1: R interface with windows installation of R

– load image (previous R session, .RData file)

– save .R script
– copy and paste
– stop a computation (this can be an important button, but the ESC also works!)
– print.

1.2.1 Default R Console

The main window that you see in the R Console. This is where you type R commands. Note it says type
demo() or help() or q() to view example R in code, to see R help or to quit R respectively.
Within the R console, you can
• Type at the prompt > symbol.

• If the prompt instead show the continuation prompt is ’+’, it means the command you typed is in-
complete and R is waiting for it to complete (usually its missing a closing quote or bracket)

• Use up and down arrow keys to scroll through previous commands. This is useful if you would like
to repeat a previous command

• R also includes basic automatic completions for function names and filenames. Type the ”tab” key to
see a list of possible completions for a function or filenames.

1.2.2 Default R Editor

• Within R, one can open an editor using the menu command File -> New script

• Can type commands in the editor

3
 • Highlight the commands and type CtrlˆR to submit the commands for R evaluation

• Evaluation of the commands can be stopped by pressing the Esc key or the Stop button

• Saving (CtrlˆS) and opening saved commands (CtrlˆO)

• Can open a new editor by typing CtrlˆN

1.2.3 R Shortcuts
Keyboard Shortcuts for traditional R GUI

• Ctrl + A: gets you to the beginning of the line

• Ctrl + E: gets you to the end

• Ctrl + K: wipes everything to the right of your cursor

• Esc: kills the current comment and takes you back to ¿

• Up Arrow: brings back last command you typed

• Down Arrow: brings back the next command (Up and down basically scrolls up and down through
your history)

Keyboard shortcuts for RStudio are listed online at http://www.rstudio.org/docs/using/

keyboard_shortcuts.

4
1.3 RStudio Interface
RStudio is a free and open source integrated development environment for R. Those familiar with matlab
will recognize the layout as its pretty similar. RStudio have a brief 2 minute guide to the interface on their
website http://rstudio.org/ which I recommend watching.
On startup R Studio brings up a window with 3 or 4 panels. If you only see 3 panels, click on File
-> New -> New R Script.

Figure 1.2: RStudio v0.96 interface with 4 panels

The first thing to notice, is that the bottom left panel ”console” is the exact same as the standard R
console. RStudio just loads your local version of R. You can specify a different version of R (if you have
multiple versions of R running on your machine) by clicking on Tools -> Options and selecting R
version.

1.3.1 console
RStudio has a nice console features

• start typing a command, for example fi, press the TAB key, it will suggest function that begin with
fi

• Select fis for sher.test. Type

fisher.test(

5
Figure 1.3: Tab not only auto-completes, but also suggests parameters and input to the function. Note it says
press F1 for further help on this function

and then press the TAB key. You will notice it bring up help on each parameter, you can browse these
and it will help you get familiar with R.

• Press F1, it will bring up a help document about the function in the help panel (right bottom)

• Press F2, it will show the source code for the function

There are many useful keyboard shortcuts in RStudio for a full list of these see http://rstudio.org/
docs/using/keyboard_shortcuts

1.3.2 Editor
The top left panel is an editor which can be used to edit R scripts (.R), plain text (.txt), html web files or
Sweave (rnw) or markdown (md), the latter two of these can be converted to pdf files. There are several nice
features to this text editor which we will describe during the course. But for now note, that it highlights R
code, and that the code is searchable (click Control-F to search)
In the menu code, you can set preferences to highlight, indent or edit code.

1.3.3 Workspace, history

On the top right there is a tab menu workspace and history. We will talk about these in detail.

• Workspace list the objects in the current R session. You can load, save or ”Clear All” object for a
workspace

• Note that under the workspace panel there is the option to Import Dataset

• The history panel lists all of the command that have been typed or input in the console. There are
options to load, save, search or delete history

• One can easily repeat a command by highlighting one or more line(s) and sending these To Console

• One can easily copy a command to a new R script or text file, by highlighting one or more line(s) and
sending these To Source

6
1.3.4 Files, Plots, Packages, Help
On the bottom right there is a tab menu Files, Plots, Packages and Help.

• Files is a file browser, which allows you to create a new folder, rename a folder or delete a folder.
Click on the triple dot icon (...) on the far right on the menu to browse folders. Under the More menu
you can set your current working directory (more about that below). If you double click on a text, .R,
Sweave or html file it will automatically open in the Editor.

• The Plots window displays plots generated in R. Simply type the following command into the Console
window

plot(1:10)
plot(rnorm(10), 1:10)

It will create 2 plots. Use the arrows keys to browse plots, click on zoom, export or delete to manage
plots.

• Packages list all of the packages installed in your computer. The packages with tick marked are those
loaded in your current R session. Click on a package name to view help on that package. Note you
can install packages or check for updates. You can also search for a package or search package
descriptions using the search window.

• The Help menu provides an extensive R help. The arrows button go forward or back through recent
help pages you have viewed. You can go home (house icon), print or open help in new window. You
can search help, use the search window. Help can also be browsed through main menu bar at the open
of the page

1.3.5 Projects, SVN in RStudio

RStudio provides an easy approach to managing projects. In the main menu there is a Projects menu which
which will create folder for your project and retain all data files and command history for your project. It
is also possible to set up a backup subversion management control system for your code as RStudio will
directly communicate with your SVN or github account.

1.4 Starting out - setting a working directory

Setting up a RStudio project folder is a great way to start a new project. It aids with managing R code, data
and results. However if you don’t use the project option or are accessing R through the default or another
interface, you will need to be able to set a current working directory (in which all your output files are
saved).
The first thing to do when starting an R session, is to ensure that you will be able to find your data
and also that your output will be saved to a useful location on your computer hard-drive. Therefore, set a
”working directory”
This maybe set by default to the depths of the operating system (C:/program files/R), which is a
poor ”working” location.
There are numerous way to set the working directory. To change directory:

1. In the classic R interface. Use the file menu, to change directory File − > Change dir

7
 2. If you start R by clicking on an R icon. You may wish to change the default start location by right
mouse clicking on the R icon on the desktop/start menu and changing the ”Start In” property. For
example make a folder ’C:/work’, and make this as a ”Start in” folder
3. In RStudio Tools − > Set Working Directory
4. Or in RStudio click on the Files tab (on the bottom right panel). Use the File browser window to view
the contents of a directory and navigate to the directory you wish to set as your home directory.

• click on the triple dot icon on the top right. Navigate to the correct directory
• Once you are in the correct directory and see your data files click on the More (blue cogwheel),
and select ”Set as Working Directory”

Figure 1.4: Note the triple dot icon on the far right and the blue cog wheel

5. The commands to set the working directory.

 What is my current directory

getwd()

To change the directory:

 Set working directory

setwd("C:/work")

To see folders or files in the working directory, use the command dir() (or browse the files using the
Files Browser panel in RStudio)

dir()
dir(pattern = ".txt")

1.4.1 Managing and accessing folders in R

I can create a new working directory for an R session for example, I try to include a project Name Date in
my folder names eg colonJan13.

 check if the directory or file exisits

file.exists("colonJan13")
 Create a directoryfolder
dir.create("colonJan13")
setwd("colonJan13")

8
 To create a full directory or more complex directory path. A path can be relative to the current location,
in this case two dots mean ”the directory above”

setwd("../../RWork/colonJan13")

Or you can specific a full directory path. For cross-platform compatibility, its best to use file.path() to
create paths. for example

wkdir <- getwd()

newdir <- "MyNewDir"
subdir <- "Project1"
newdirPath <- file.path(wkdir, newdir, subdir)

if (file.exists(wkdir)) dir.create(newdirPath)
dir(pattern = "My")

Important side note: R doesn’t like windows a back slash (\) that separate folders in a file path. Indeed
it will return a rather cryptic error

> setwd("C:\Users\aedin\Documents\Rwork\colonJan13")
Error: "\U" used without hex digits
in character string starting "C:\U"

There are a couple of ways to prevent this, either replace backslash (\) with forward (/) slash or double
back slash (\\) The first back slash tells R to treat the character literally, it is called an escape character
which invokes an alternative interpretation on subsequent characters.

setwd("C:/Users/aedin/Documents/Rwork/colonJan13")
setwd("C:\\Users\\aedin\\Dropbox\\Talks\\CDC\\Notes")

This can be rather tedious.A nice way to make scripts work across platform is to use the command
path.expand, le.path. The tilde symbol ( ˜ ) is a shortcut to your home drive (on any operating system)

path.expand("˜ ")
myhome <- path.expand("˜ ")
newdir <- file.path(path.expand("˜ "), "Rwork", " colonJan13")
setwd(newdir)

In my case, I work on several windows boxes, each have fairly different directory structures, but by
setting the home directory properly I can sync code between computers and have them run properly on each
one since where I run my R projects have similar directory structures.
Advanced Side Note: What is your system home directory
Your system HOME (˜ ) is set by your operating system. To view or change it, type

Sys.getenv("HOME")

## [1] "C:/Users/aedin/Documents"

9
Sys.setenv(HOME = "path")  path is the directory you wish to set as
your new home directory

10
1.5 First R Encounter
When you start R, and see the prompt > , it may appear as if nothing is happening. But this prompt is
now awaiting commands from you. This can be daunting to the new user, however it is easy to learn a few
commands and get started

demo()

Note we place round brackets after all functions ALWAYS. Note if the command is not complete on
one line (missing close bracket or quote), R will use continuation prompt is ’+’.
If the brackets are empty () it runs the function with default parameters. To specify a parameters these
are inserted into the brackets. For example to run a demo on a specific topics we give that parameters to
demo

demo(graphics)
demo(nlm)

Type q() to quit the program

To find out more about parameters and options for the function demo, lets look at help for demo.

1.6 Getting help with functions and features

There are many resources for help in R. Within R, you can find help on any command (or find commands)
using the follow:

• If you know the command (or part of it)

 help or ? will open a help page

help(lm)

 ?matrix
?(matrix)

 The functions find() or apropos() will search for a command

apropos("mean")

 The function example will run example of a command

example(rep)

The last command will run all the examples included with the help for a particular function. If we
want to run particular examples, we can highlight the commands in the help window and submit them
by typing CtrlˆV

• If you don’t know the command and want to do a keyword search for it.

help.search("combination")
help.start()

11
 help.search will open a html web browser or a MSWindows help browser (depending on the your
preferences) in which you can browse and search R documentation.

• Finally, there is a large R community who are incredibly helpful. There is a mailing list for R,
Bioconductor and almost every R project. It is useful to search the archives of these mailing lists.
Frequently you will find someone encountered the same problem as you, and previously asked the R
mailing list for help (and got a solution!).

– The R search engine http://www.Rseek.org

– R bloggers website http://www.r-bloggers.com/

• There numerous useful resources for learning R on the web including the R project http://www.
r-project.org and its mailing lists but also I recommend the following:

– Emmanuel Paradis has an excellent beginners guide to R available from http://cran.

r-project.org/doc/contrib/Paradis-rdebuts_en.pdf
– There is an introduction to R classes and objects on the R website
http://cran.r-project.org/doc/manuals/R-intro.html
– also see Tom Guirkes manual at
http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual
– Tom Short’s provides a useful short R reference card at http://cran.r-project.org/
doc/contrib/Short-refcard.pdf

• Coming from SAS or SPSS background?

– In the December 2009 issue of the R Journal. Transitioning to R: Replicating SAS, Stata, and
SUDAAN Analysis Techniques in Health Policy Data. Anthony Damico http://journal.
r-project.org/archive/2009-2/RJournal_2009-2_Damico.pdf
– SAS and R. A blog devoted to examples of tasks (and their code) replicated in SAS and R
http://sas-and-r.blogspot.com/
– R for SAS and SPSS Users. Download a free 80 page document, http://rforsasandspssusers.
com/
R for SAS and SPSS Users which contains over 30 programs written in all three languages.

1.7 R as a big calculator

Type the following into an R session (or copy and paste from this document).

2 + 2

## [1] 4

2 * 2

## [1] 4

2 * 100/4

12
## [1] 50

2 * 100/4 + 2

## [1] 52

2 * 100/(4 + 2)

## [1] 33.33

210

## [1] 1024

log(2)

## [1] 0.6931

Note even in the simple use of R as a calculator, it is useful to store intermediate results. For example
lets store the value of (tmpVal=log(2)).

tmpVal <- log(2)

print(tmpVal)

## [1] 0.6931

tmpVal

## [1] 0.6931

exp(tmpVal)

## [1] 2

In this case, we assigned a symbolic variable tmpVal. Note when you assign a value to such a variable,
there is no immediate visible result. We need to print(tmpVal) or just type tmpVal in order to see
what value was assigned to tmpVal

1.8 A few important points on R

• Elementary commands: expressions are evaluated, printed and value lost; assignments evaluate ex-
pressions, passes value to a variable, but not automatically printed

2 * 52

## [1] 50

x <- 2 * 52
print(x)

13
 ## [1] 50

• Assignment operators are: <-, =, ->

2 * 52

## [1] 50

y <- 2 * 52
z <- 2 * 52
z <- 2 * 52
print(y)

## [1] 50

x == y

## [1] TRUE

y == z

## [1] TRUE

• <- is the most popular assignment operator, and = is a recent addition.

There is no space between < and −
It is <- (less than and a minus symbol)
When assigning a value spaces are ignored so z<-3 is equivalent to z <- 3
• R is case sensitive, i.e. myData and Mydata are different names
x

## [1] 50

## [1] 50

Z <- 20
x == z

## [1] TRUE

x == Z

## [1] FALSE

14
 • ’==’ and ’=’ have very different uses in R. == is a binary operator, which test for equality (A==B
determines if A ’is equal to’ B ).

• Missing values called represented by NA

• Comments can be put anywhere. To comment text, insert a hashmark #. Everything following it to
end of the line is commented out (ignored, not evaluated).

print(y) # Here is a comment

• Quotes, you can use both ” double or ’ single quotes, as long as they are matched.

• For names, normally all alphanumeric symbols are allowed plus . and _ Start names with a character
[Aa-Zz] not a numeric character [0-9]. Avoid using single characters or function names t, c, q, diff,
mean, plot etc.

• Arguments (parameters) to a function calls f(x), PROC are enclosed in round brackets. Even if no
arguments are passed to a function, the round brackets are required.

print(x)
getwd()

• Commands can be grouped together with braces ({ and }).

• Note on brackets. It is very important to use the correct brackets.

Bracket Use
() To set priorities 3*(2+4). Function calls f(x)
[] Indexing in vectors, matrices, data frames
{} Creating new functions. Grouping commands {mean(x); var(x)}
[[]] Indexing of lists

1.8.1 Use Arrows to key browse command history

Note you can recover or browser previous commands using the up and down arrow keys.
For example rnorm generates 10 random numbers from a normal distribution. Type this a few times
(hint: the up arrow key is useful).

rnorm(5)

If you wish to generate the same set of random numbers each time, you could set.seed(10)
You can view previous expressions entered into the R session (default 25) using the function

history()

(this is discussed in more detail later on) You can also view the history of R commands in the history
tab on top right panel in RStudio

15
1.9 Basic operators
We already saw that == tests for equality or a match between 2 objects. Other operators are:

1.9.1 Comparison operators

• equal: ==

• not equal: !=

• greater/less than: > <

• greater/less than or equal: >= <=

1 == 1

## [1] TRUE

1.9.2 Logical operators

• AND & Returns TRUE if both comparisons return TRUE.

x <- 1:10
y <- 10:1
x > y  x > 5

## [1] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE

• OR — Returns TRUE where at least one comparison returns TRUE.

x == y | x != y

## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

• NOT ! The ’!’ sign returns the negation (opposite) of a logical vector.

!x > y

## [1] TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE

These return a logical vector of TRUE or FALSE and can be useful for filtering (we will see this later)

1.10 Data sets in R

Both the R core installation and contributed R package contain data sets, which are useful example data
when learning R. To list all available data sets:

16
data()

To load a dataset, for example, the dataset women which gives the average heights and weights for 15
American women aged 30-39.

data(women)
ls()
ls(pattern = "w")

Figure 1.5: The Workspace windows lists the object currently in the R workspace. You can click on each
item to view or edit it. Note women is a data table with dimensions 15 rows x 2 columns, you can click on
the table icon to view it. Z and y are a single value (50). x and y are integer vectors of length 10.

17
1.11 R sessions (workspace) and saving session history
To finish up today, we will save our R session and history
1. R session One can either save one or more R object in a list to a file using save() or save the entire R
session (workspace) using save.image().

save(women, file = "women.RData")

save.image(file = "entireL2session.RData")

To load this into R, start a new R session and use the load()

rm(women)
ls(pattern = "women")
load("women.RData")
ls(pattern = "women")

2. R history R records the commands history in an R session. To view most recent R commands in a
session

history()
help(history)
history(100)

To search for a particular command, for example ”save”

history(pattern = "save")

To save the commands in an R session to a file, use savehistory()

savehistory(file = "L2.Rhistory")

3. Note you can also browse and search history in RStudio, really easily in the history window. A really
nice feature of this window is the ease of sending command either to the console (to execute code
again) or to Source (to a text file or script you are writing in the editor)

Figure 1.6: You can easily save or search command history, send commands to the R console or a source
(script) file

4. Default saving of RData and Rhistory

By default, when you quit q() an R session, it will ask if you wish to save the R workspace image. If
you select yes, it will create two file in the current working directory, there are .RData and .Rhistory.
These are hidden system files, unless you choose to ”Show Hidden Files” in the folder options. There
are output files are the same as running save.image(file=”.RData”) and savehistory(file=”.Rhistory”)
respectively.

18
1.12 R Packages
By default, R is packaged with a small number of essential packages, however as we saw there are many
contributed R packages.

1. Some packages are loaded by default with every R session. The libraries included in the Table are
loaded on the R startup.

Table 1.1: Preloaded packages

Package Description
base Base R functions
datasets Base R datasets
grDevices Graphics devices for base and grid graphics
graphics R functions for base graphics
methods Formally defined methods and classes for R objects,
plus other programming tools
stats R statistical functions.
utils R utility functions

2. To see which packages are currently loaded, use

search()
sessionInfo()

3. To see which packages are installed on your computer, issue the command

library()

Within RStudio installed packages can be view in the Package Tab of the lower right panel. You
can tick or select a library to load it in R.
You will very likely want to install additional packages or libraries.

1.13 Installing new R libraries

There are several thousand R packages and >500 Bioconductor packages (also called libraries) available.
These are not installed by default, so we have to select and install additional packages that will be of use to
us. Not all of them, actually a small subset, will be useful to us. R users are free to selected which libraries
to install.
On windows, sometimes I have encoutered problems with program installation using RStudio. This is
normally when R tries to write to a folder and doesn’t have write permission to this folder. In this case,
either

1. Run RStudio as administrator

19
 Figure 1.7: The list is all installed packages. A tick marked indicates its loaded into the current R session.
Clicking on the package name will open help for that package

2. check you have write permission to the path where it will write the files (use the following R function
to list your RStudio Paths) ¡¡rsPref, eval=FALSE¿¿= .rs.defaultUserLibraryPath() Path where RStu-
dio installs packages .rs.rpc.getp ackagei nstallc ontext()Otherusef ulRStudioconf igurationinf o@

3. Install packages using the basic R GUI using the drop-down menu Packages or command line (in-
stall.packages). First Click on “Packages” and “Set CRAN mirror” and choose an available mirror (choose
one close by, it’ll be faster hopefully). Then If you know the name of the package you want to install, or if
you want to install all the available packages, click on “install Packages”

4. Open a CMD shell and type R CMD INSTALL packageName.tar.gz. You can open a CMD shell from
RStudio Tools -> Shell

Installing packages using RStudio

Figure 1.8: Click on Install Packages

This will open an install window:

Commands to install packages

20
Figure 1.9: Type the name of the package. Unfortunately RStudio does not display a list of all available
packages

 Installing and updating R libraries

install.packages("lme4")
update.packages("lme4")

Installation of all packages takes some time and space on your computer. If the name of the package is
not known, you could use taskviews help or archives of the mailing list to pinpoint one. Also look on the R
website Task views description of packages (see Additional Notes in Installation which I have provided).
To get an information on a package, type

library(help = lme4)

Once you have installed a package, you do NOT need to re-install it. But to load the library in your
current R session use the commands

library(lme4)  Load a package

 Or the alternative
require(lme4)

sessionInfo() List all packages loaded in the current R session

library()  List all installed packages

You can unload the loaded package pkg by

search()
detach(package:lme4)
search()

21
 NOTE: Packages are often inter-dependent, and loading one may cause others to be automatically
loaded.

1.14 Customizing Startup

To customize your R environment, you can change options through RStudio File -> Tools -> Options

Figure 1.10: Within the options window you can change the version of R, your default directory and SVN
preferences

In addition you can specify preferences for either a site or local installation in Rprofile.site. On Windows,
this file is in the C:\Program Files\R\R-x.y.z\etc directory where x.y.z is the version of R. Or
you can also place a .Rprofile file in the directory that you are going to run R from or in the user home
directory.
At startup, R will source the Rprofile.site file. It will then look for a .Rprofile file in the current working
directory. If it doesn’t find it, it will look for one in the user’s home directory.
There are two special functions you can place in these files. .First( ) will be run at the start of the R
session and .Last( ) will be run at the end of the session. These can be used to load a set of libraries that you
use most.

 Sample Rprofile.site file

 Things you might want to change options(papersize=a4)

 options(editor=notepad) options(pager=internal)

 R interactive prompt options(prompt=> ) options(continue=+ )

22
 General options
options(tab.width = 2)
options(width = 100)
options(digits = 5)

.First <- function() {

library(lme4)
library(design)
library(xtable)
cat("\nWelcome at", date(), "\n")
}

.Last <- function() {

cat("\nGoodbye at ", date(), "\n")
}

For more help on this see http://www.statmethods.net/interface/customizing.html

23
Chapter 2

Objects in R

• Everything (variable, functions etc) in R is an object

• Every object has a class

2.1 Using ls and rm to managing R Objects

R creates and manipulates objects: variables, matrices, strings, functions, etc. objects are stored by name
during an R session.
During a R session, you may create many objects, if you wish to list the objects you have created in the
current session use the command

objects()
ls()

The collection of objects is called workspace.

If you wish to delete (remove) objects, issue the commands:

rm(x, y, z, junk)

where x, y, junk were the objects created during the session.

Note rm(list=ls()) will remove everything. Use with caution

2.2 Types of R objects

Objects can be thought of as a container which holds data or a function. The most basic form of data is
a single element, such as a single numeric or a character string. However one can’t do statistics on single
numbers! Therefore there are many other objects in R.

• A vector is an ordered collection of numerical, character, complex or logical objects. Vectors are
collection of atomic (same data type) components or modes. For example

 Numeric
vec1 <- 1:10
vec1

24
 ## [1] 1 2 3 4 5 6 7 8 9 10

 Character
vec2 <- LETTERS[1:10]
vec2

## [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J"

 logical
vec3 <- vec2 == "D"
vec3

## [1] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE

In each case above, these vectors have 10 elements, and are of length=10.

• A matrix is a multidimensional collection of data entries of the same type. Matrices have two
dimensions. It has rownames and colnames.

mat1 <- matrix(vec1, ncol = 2, nrow = 5)

print(mat1)

## [,1] [,2]
## [1,] 1 6
## [2,] 2 7
## [3,] 3 8
## [4,] 4 9
## [5,] 5 10

dim(mat1)

## [1] 5 2

colnames(mat1) <- c("A", "B")

rownames(mat1) <- paste("N", 1:5, sep = "")
print(mat1)

## A B
## N1 1 6
## N2 2 7
## N3 3 8
## N4 4 9
## N5 5 10

25
• A list is an ordered collection of objects that can be of different modes (e.g. numeric vector, array,
etc.).

a <- 20
newList1 <- list(a, vec1, mat1)
print(newList1)

## [[1]]
## [1] 20
##
## [[2]]
## [1] 1 2 3 4 5 6 7 8 9 10
##
## [[3]]
## A B
## N1 1 6
## N2 2 7
## N3 3 8
## N4 4 9
## N5 5 10
##

newList1 <- list(a = a, myVec = vec1, mat = mat1)

print(newList1)

## $a
## [1] 20
##
## $myVec
## [1] 1 2 3 4 5 6 7 8 9 10
##
## $mat
## A B
## N1 1 6
## N2 2 7
## N3 3 8
## N4 4 9
## N5 5 10
##

• Though a data.frame is a restricted list with class data.frame, it maybe regarding as a matrix
with columns that can be of different modes. It is displayed in matrix form, rows by columns. (Its like
an excel spreadsheet)

df1 <- as.data.frame(mat1)

df1

26
 ## A B
## N1 1 6
## N2 2 7
## N3 3 8
## N4 4 9
## N5 5 10

• A factor is a vector of categorical variables, it can be ordered or unordered.

charVec <- rep(LETTERS[1:3], 10)

print(charVec)

## [1] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A"
## [17] "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C"

table(charVec)  Tabulate charVec

## charVec
## A B C
## 10 10 10

fac1 <- factor(charVec)

print(fac1)

## [1] A B C A B C A B C A B C A B C A B C A B C A B C A B C A B C
## Levels: A B C

attributes(fac1)

## $levels
## [1] "A" "B" "C"
##
## $class
## [1] "factor"
##

levels(fac1)

## [1] "A" "B" "C"

• array An array in R can have one, two or more dimensions. I find it useful to store multiple related
data.frame (for example when I jack-knife or permute data). Note if there are insufficient objects to
fill the array, R recycles (see below)

27
array(1:24, dim = c(2, 4, 3))

## , , 1
##
## [,1] [,2] [,3] [,4]
## [1,] 1 3 5 7
## [2,] 2 4 6 8
##
## , , 2
##
## [,1] [,2] [,3] [,4]
## [1,] 9 11 13 15
## [2,] 10 12 14 16
##
## , , 3
##
## [,1] [,2] [,3] [,4]
## [1,] 17 19 21 23
## [2,] 18 20 22 24
##

array(1:23, dim = c(2, 4, 3))

## , , 1
##
## [,1] [,2] [,3] [,4]
## [1,] 1 3 5 7
## [2,] 2 4 6 8
##
## , , 2
##
## [,1] [,2] [,3] [,4]
## [1,] 9 11 13 15
## [2,] 10 12 14 16
##
## , , 3
##
## [,1] [,2] [,3] [,4]
## [1,] 17 19 21 23
## [2,] 18 20 22 1
##

array(1:23, dim = c(2, 4, 3), dimnames = list(paste("Patient",

1:2, sep = ""), LETTERS[1:4], c("X", "Y", "Z")))

## , , X
##

28
 ## A B C D
## Patient1 1 3 5 7
## Patient2 2 4 6 8
##
## , , Y
##
## A B C D
## Patient1 9 11 13 15
## Patient2 10 12 14 16
##
## , , Z
##
## A B C D
## Patient1 17 19 21 23
## Patient2 18 20 22 1
##

2.3 Attributes of R Objects

1. Basic attributes
The most basic and fundamental properties of every objects is its mode and length. These are
intrinsic attributes of every object. Examples of mode are ”logical”, ”numeric”, ”character”, ”list”,
”expression”, ”name/symbol” and ”function”.
Of which the most basic of these are:
• character: a character string
• numeric: a real number, which can be an integer or a double
• integer: an integer
• logical: a logical (true/false) value

 Numeric
x <- 3
mode(x)

## [1] "numeric"

 Charachter
x <- "apple"
mode(x)

## [1] "character"

x <- 3.145
x + 2  5.145

29
## [1] 5.145

 FALSE, logical
x == 2

## [1] FALSE

x <- x == 2
x

## [1] FALSE

mode(x)

## [1] "logical"

All R objects have mode

 vectors of different modes Numeric

x <- 1:10
mode(x)

## [1] "numeric"

x <- matrix(rnorm(50), nrow = 5, ncol = 10)

mode(x)

## [1] "numeric"

 Character
x <- LETTERS[1:5]
mode(x)

## [1] "character"

 logical
x <- x == "D"
mode(x)

## [1] "logical"

30
 Quick Exercise
Repeat above, and find the length and class of x in each case.

2. Other attributes, dimension

x <- matrix(5:14, nrow = 2, ncol = 5)

x

## [,1] [,2] [,3] [,4] [,5]

## [1,] 5 7 9 11 13
## [2,] 6 8 10 12 14

attributes(x)

## $dim
## [1] 2 5
##

In summary
Object Modes Allow >1 Modes*
vector numeric, character, complex or logical No
matrix numeric, character, complex or logical No
list numeric, character, complex, logical, function, expression, ... Yes
data frame numeric, character, complex or logical Yes
factor numeric or character No
array numeric, character, complex or logical No
*Whether object allows elements of different modes. For example all elements in a vector or array have to be
of the same mode. Whereas a list can contain any type of object including a list.

2.4 Creating and accessing objects

We have already created a few objects: x, y, junk. Will create a few more and will select, access and
modify subsets of them.

• Create vectors, matrices and data frames using seq, rep, rbind and cbind

 Vector
x.vec <- seq(1, 7, by = 2)

 The function seq is very useful, have a look at the help on seq
 (hint ?seq)

names(x.vec) <- letters[1:4]

 Matrices

31
 xMat <- cbind(x.vec, rnorm(4), rep(5, 4))
yMat <- rbind(1:3, rep(1, 3))
z.mat <- rbind(xMat, yMat)
 Data frame
x.df <- as.data.frame(xMat)
names(x.df) <- c("ind", "random", "score")

• Accessing elements
NOTE Use square brackets to access elements. The number of elements within the square bracket
must equal the dimension of the object.

1. vector [1]
2. matrix [1,1]
3. array with 3 dimensions [1,1,1]

 Access first element of x.vec

x.vec[1]

## a
## 1

 or if you know the name

x.vec["a"]

## a
## 1

 Access an element of xMat in the second row, third column

xMat[2, 3]

## [1] 5

 Display the second and third columns of matrix xMat

xMat[, c(2:3)]

##
## a -0.1267 5
## b -1.2919 5
## c 0.8820 5
## d -0.6514 5

 or
xMat[, -c(1)]

##
## a -0.1267 5
## b -1.2919 5
## c 0.8820 5
## d -0.6514 5

32
 Here -1 means everything except for the first column.

Quick Exercise What does this command do?

xMat[xMat[, 1] > 3, ]

## x.vec
## c 5 0.8820 5
## d 7 -0.6514 5

If the object has class data.frame or list, you can use the dollar symbol $ to access elements. The $
can only access columns of data.frame

 Get the vector of ind from x.df

colnames(x.df)

## [1] "ind" "random" "score"

x.dfind

## [1] 1 3 5 7

x.df[, 1]

## [1] 1 3 5 7

names(newList1)

## [1] "a" "myVec" "mat"

newList1a

## [1] 20

2.5 Modifying elements

 Change the element of xMat in the third row and first column to
 6
xMat[3, 1] <- 6
 Replace the second column of z.mat by 0s
z.mat[, 2] <- 0

33
2.5.1 Sorting and Ordering items
Frequently we need to re-order the rows/columns of a matrix or see the rank order or a sorted set elements
of a vector
The functions sort and order are designed to be applied on vectors. Sort returns a sorted vector. Order
returns an index which can be used to sort a vector or matrix.

 Simplest sort
z.vec <- c(5, 3, 8, 2, 3.2)
sort(z.vec)

## [1] 2.0 3.0 3.2 5.0 8.0

order(z.vec)

## [1] 4 2 5 1 3

Sorting the rows of a matrix. We will use an example dataset in R called ChickWeight. First have a look
at the ChickWeight documentation (help)
Lets take a subset of the matrix, say the first 36 rows.

 ?ChickWeight
ChickWeight[1:2, ]

## weight Time Chick Diet

## 1 42 0 1 1
## 2 51 2 1 1

chick.short <- ChickWeight[1:36, ]

Now order this matrix by time and weight

 by just weight
chickOrd <- chick.short[order(chick.shortweight), ]
chickOrd[1:5, ]

## weight Time Chick Diet

## 26 39 2 3 1
## 13 40 0 2 1
## 1 42 0 1 1
## 25 43 0 3 1
## 14 49 2 2 1

 By both time and weight

chick.srt <- chick.short[order(chick.shortTime, chick.shortweight),
]
chick.srt[1:5, ]

34
## weight Time Chick Diet
## 13 40 0 2 1
## 1 42 0 1 1
## 25 43 0 3 1
## 26 39 2 3 1
## 14 49 2 2 1

35
2.5.2 Missing Values
Missing values are assigned special value of ’NA’

z <- c(1:3, NA)

z

## [1] 1 2 3 NA

ind <- is.na(z)

ind

## [1] FALSE FALSE FALSE TRUE

To remove missing values from a vector

print(z)

## [1] 1 2 3 NA

x <- z[!is.na(z)]
print(x)

## [1] 1 2 3

Check to see if a vector has all, any or a certain number of missing values. These create logical vectors
which can be used to filter a matrix or data.frame

all(is.na(z))

## [1] FALSE

any(is.na(z))

## [1] TRUE

sum(is.na(z))

## [1] 1

sum(is.na(z)) > 1

## [1] FALSE

2.5.3 Creating empty vectors and matrices

To create a empty vector, matrix or data.frame

36
x1 <- numeric()
x2 <- numeric(5)
x1.mat <- matrix(0, nrow = 10, ncol = 3)

37
2.6 Quick recap
• R Environment, interface, R help and R-project.org and Bioconductor.org website

• installing R and R packages.

• assignment <-, =, ->

• operators ==, !=, <, >, Boolean operators &, |

• Management of R session, starting session, getwd(), setwd(), dir()

• Listing and deleting objects in memory, ls(), rm()

• R Objects
Object Modes Allow >1 Modes*
vector numeric, character, complex or logical No
matrix numeric, character, complex or logical No
list numeric, character, complex, logical, function, expression, ... Yes
data frame numeric, character, complex or logical Yes
factor numeric or character No
array numeric, character, complex or logical No
*Whether object allows elements of different modes. For example all elements in a vector or array have to be
of the same mode. Whereas a list can contain any type of object including a list.
There are other objects type include ts (time series) data time etc. See the R manual for more infor-
mation. All R Objects have the attributes mode and length.

• Creating objects; c(), matrix(), data.frame(), seq(), rep(), etc

• Adding rows/columns to a matrix using rbind() or cbind()

• Subsetting/Accessing elements in a vector(), matrix(), data.frame(), list() by element name or index.

38
2.7 Exercise 1
For this exercise we will work on data from a study which examined the weight, height and age of women.
Data from the women Study is available as an R dataset and information about this study can be found by
using R help (hint ?women) which we will read directly from the website URL http://bcb.dfci.
harvard.edu/˜aedin/courses/Bioconductor/Women.txt into the object women
Basic tools for reading and writing data are respectively: read.table and write.table. We will go into
further detail about each later today, but first lets read in this file by typing these commands:

myURL <-
"http://bcb.dfci.harvard.edu/˜ aedin/courses/Bioconductor/Women.txt"
women <- read.table(myURL, sep = "\t", header = TRUE)

(Or in RStudio Click on Workspace -> Import Dataset)

Tasks

1. Get help on the command colnames

2. what is the class of this dataset?

3. How many rows and columns are in the data? (hint try using the functions str, dim, nrow and ncol))

4. Use the summary(), to view the mean height and weight of women

5. Compare the result to using the function colMeans

6. How many women have a weight under 120?

7. What is the average height of women who weigh between 124 and 150 pounds (hint: need to select
the data, and find the mean).

8. Sort the matrix women by ’weight’ hint use order

9. Give the 5th row the rowname ”Lucy”

39
Chapter 3

Reading and writing data to and from R

So far, we have only analyzed data that were already stored in R. Basic tools for reading and writing data are
respectively: read.table and write.table. We will go into further detail about each. First we will talk about
reading in simple text documents; comma and tab-delimited format text files, then Excel and import/exprot
from other statistical software.

3.1 Importing and reading text les data into RStudio

RStudio has a nice user interface to reading in file. Click on Workspace -> Import Dataset.

Figure 3.1: which provides an easy approach to read a text from a local directory or directly from a web
URL

Enter a file location (either local or on the web), and RStudio will make a ”best guess” at the file format.
There are a limited number of options (heading yes or no), separators (comma, space or tab) etc but these
should cover the most common data exchange formats (The R interfaces RCommander and RExcel also
provide rich support for data import of many different file formats into R)

40
Figure 3.2: The top panel shows the plain text of the file, and the lower panels displays how R is interpreting
the data. Black rows are the column headings

3.2 Importing data using R command read.table()

If you are calling R from a script, or are using R on a machine in which RStudio is not available, knowledge
of commands to read and write files are vital

3.2.1 Using read.table() and read.csv()

1. The most commonly used function for reading data is read.table(). It will read the data into R as a
data.frame.
By Default read.table() assumes a file is space delimited and it will fail if the file is in a different
format with the error below.

Women<-read.table("Women.txt")

In order to read files that are tab or comma delimited, the defaults must be changed. We also need to
specify that the table has a header row

 Tab Delimited
Women <- read.table("Women.txt", sep = "\t", header = TRUE)
Women[1:2, ]

## height weight age

## 1 58 115 33
## 2 59 117 34

41
 summary(Women)

## height weight age

## Min. :58.0 Min. :115 Min. :30.0
## 1st Qu.:61.5 1st Qu.:124 1st Qu.:32.0
## Median :65.0 Median :135 Median :34.0
## Mean :65.0 Mean :137 Mean :33.9
## 3rd Qu.:68.5 3rd Qu.:148 3rd Qu.:35.5
## Max. :72.0 Max. :164 Max. :39.0

class(Womenage)

## [1] "integer"

Note by default, character vector (strings) are read in as factors. To turn this off, use the parameter
as.is=TRUE
2. Important options:
header==TRUE should be set to ’TRUE’, if your file contains the column names
as.is==TRUE otherwise the character columns will be read as factors
sep=”” field separator character (often comma ’,’ or tab ”” eg: sep=”,”)
na.strings a vector of strings which are to be interpreted as ’NA’ values.
row.names The column which contains the row names
comment.char by default, this is the pound # symbol, use ”” to turn off interpre-
tation of commented text.

 Read the help file

help(read.table)

Note the defaults for read.table(), read.csv(), read.delim() are different. For example, in read.table()
function, we specify header=TRUE, as the first line is a line of headings among other parameters.
3. read.csv() is a derivative of read.table() which calls read.table() function with the following options
so it reads a comma separated file:

read.csv(file, header = TRUE, sep = ",", quote="\"", dec=".",

fill = TRUE, comment.char="", ...)

Read in a comma separated file:

 Comma Delimited
Women2 <- read.csv("Women.csv")
Women2[1:2, ]

## height weight age

## 1 58 115 33
## 2 59 117 34

42
4. Reading directly from Website You can read a file directly from the web

myURL <-
"http://bcb.dfci.harvard.edu/˜ aedin/courses/Bioconductor/Women.txt"
read.table(myURL, header = TRUE)[1:2, ]

## height weight age

## 1 58 115 33
## 2 59 117 34

43
3.3 Exercise 2
The ToothGrowth data are from a study which examined the growth of teeth in guinea pigs (n=10) in re-
sponse to three dose levels of Vitamin C (0.5, 1, and 2 mg), which was administered using two delivery
methods (orange juice or ascorbic acid). Data from the Tooth Growth Study is available as an R dataset and
information about this study can be found by using R help (hint ?ToothGrowth)

1. Download the data set ”ToothGrowth.xls” which is available on the course website. Save it in your
local directory. Open this file ”ToothGrowth.xls” in Excel.

2. Export the data as both a comma or tab delimited text files. In Excel select File -> Save as and
Tab: select the format Text (Tab delimited) (*.txt).
CSV: select the format CSV (Comma delimited) (*.csv).

1. Load each data file (.txt and .csv) into R

2. How many rows are there is ToothGrowth?

3. what is the mean and sd of Tooth length

4. Does treatment have a significant effect?

44
3.3.1 Importing text les Using scan()
NOTE: read.table() is not the right tool for reading large matrices, especially those with many columns. It
is designed to read ’data frames’ which may have columns of very different classes. Use scan() instead.
scan() is an older version of data reading facility. Not as flexible, and not as user-friendly as read.table(),
but useful for Monte Carlo simulations for instance. scan() reads data into a vector or a list from a file.

myFile <- "outfile.txt"

 Create a file
cat("Some data", "1 5 3.4 8", "9 11 23", file = myFile, sep = "\n")
exampleScan <- scan(myFile, skip = 1)
print(exampleScan)

## [1] 1.0 5.0 3.4 8.0 9.0 11.0 23.0

Note by default scan() expects numeric data, if the data contains text, either specify what=”text” or give
an example what=”some text”.
Other useful parameters in scan() are nmax (number of lines to be read) or n (number of items to be
read).

scan(myFile, what = "some text", n = 3)

## [1] "Some" "data" "1"

45
3.4 Reading data from Excel into R
There are several packages and functions for reading Excel data into R, however I normally export data as a
.csv file and use read.table().
However if you wish to directly load Excel data, here are many the options available to you. See
the section on ”Importing-from-other-statistical-systems” in the webpage http://cran.r-project.
org/doc/manuals/R-data.html for more information

1. xslx seems to be the simplest option at the moment

library(xlsx)
ww <- read.xlsx(file = "Women.xlsx", sheetIndex = 1)

read.xlsx accepts .xls and .xlsx format. You must include a worksheet name or number. It is optional
to specify a row or column index to indicate a section of a Worksheet

2. There is also a packages call XLConnect which is similar

require(XLConnect)

## Loading required package: XLConnect

## Loading required package: XLConnectJars
## Loading required package: rJava
## XLConnect 0.1-9 by Mirai Solutions GmbH
## <xlconnect@mirai-solutions.com>
## http://www.mirai-solutions.com ,
## http://miraisolutions.wordpress.com

wb <- loadWorkbook("Women.xlsx", create = TRUE)

WW <- readWorksheet(wb, sheet = 1)

Or you can read direct from a connection, calling the file directly.

Ww <- readWorksheetFromFile("Women.xlsx", name = "sheet1")

3. RExcel R can be ran from within Excel on Windows using RExcel (http://rcom.univie.ac.
at/). This add a menu to Excel that allows you to call R functions from within Excel. RExcel is part
of the much large Statconn project.

4. RODBC library. We are not sure it will not work with .xlsx files. See the vignette for more information

library(RODBC)
RShowDoc("RODBC", package = "RODBC")

The following RODBC function works under windows, but may have issues under MacOS or Linux as
may need to install ODBC drivers.

46
 channel<-odbcConnectExcel("ToothGrowth.xls")
#list the spreadsheets
sqlTables(channel)

#retrieve the contents of the Excel Sheet ToothGrowth using either of the follo
ToothGrowth<-sqlFetch(channel, "ToothGrowth")
ToothGrowth<-sqlQuery(channel, "select * from [ToothGrowth$]")
ToothGrowth[1:2,]

5. The gdata library function read.xls()

Perl must be installed on your computer in order for these to work, as it uses the Perl functions
’xls2csv’ or ’xls2tab’.

3.5 Import/Export from other statistical software

Most binary data files written by statistical software other thanR such as EpiInfo, Minitab, S-PLUS, SAS,
SPSS,Stata and Systat, can be loaded into R using the R package foreign or Hmisc. Details can be found in
the R manual: R data ImportExport.

3.5.1 Reading data from SAS

If you have SAS, you can use Frank Harrell’s ’Hmisc’ package which has functions sas.get and sasxport.get,
and other utility functions such as label,sas.get, contents,describe. For those without a SAS license, package
’foreign’ has read.ssd, lookup.xport, and read.xport.

• From SAS, save SAS dataset in trasport format

libname out xport c:/mydata.xpt;

data out.mydata;
set sasuser.mydata;
run;

In R

library(Hmisc)
mydata <- sasxport.get("c:/mydata.xpt")

• SAScii. Anthony Joseph Damico recently announced SAScii is a new packages to parse SAS in-
put code to read.fwf However although they stated the code below should work, I have been not so
successful with it in my hands.

require("SAScii")

## Loading required package: SAScii

## Loading required package: stringr

47
 # Load the 2010 National Health Interview Survey Persons file as an
# R data frame from CDC
NHIS10_personsx_SASInst <-
"ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Program_Code/NHIS/2010/PERSONSX.sas"

NHIS10_personsx_SASInst <-
"ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Datasets/NHIS/2010/personsx.zip"

 store the NHIS file as an R data frame!

NHIS10personsxdf <- read.SAScii(NHIS10personsxSASInst,
NHIS10personsxSASInst, zipped = TRUE)

 or store the NHIS SAS import instructions for use in a read.fwf

 function call outside of the read.SAScii function
NHIS10personsxsas <- parse.SAScii(NHIS10personsxSASInst)

 save the data frame now for instantaneous loading later

save(NHIS10personsxdf, file = "NHIS10personsxdata.RData")

• Recently Xin Wei of Roche Pharmaceuticals published a SAS macro called Proc_R that may poten-
tially ease integrating R and SAS (reference Xin Wei PROC_R: A SAS Macro that Enables Native
R Programming in the Base SAS Environment J. Stat Software. Vol. 46, Code Snippet 2, Jan 2012)
which allows you to put R code within a SAS macro.

%include "C:\aedin\sasmacros\Proc_R.sas";
%Proc_R (SAS2R =, R2SAS =);
Cards4;

******************************
***Please Enter R Code Here***
******************************

;;;;
%Quit;

3.5.2 S
PSS
From SPSS, save SPSS dataset in trasport format

get file=c:\mydata.sav .
export outfile=c:\mydata.por .

In R

library(Hmisc)
mydata <- spss.get("c:/mydata.por", use.value.labels = TRUE)

48
3.5.3 Stata or Systat

library(foreign)
mydata <- read.dta("c:/mydata.dta")

3.6 From a Database Connection

There is also support for database connectivity including for mySQL, Oracle and specialized file formats
including network Common Data Form (netCDF) etc. See http://cran.r-project.org/doc/
manuals/R-data.html for more details.
Note installation of RMySQL or ROracle is simple on Linux or Mac, but maybe complex on MSWin-
dows, as there is no binaray file. See the READMe associated with the package on the R website

 --------------------------------------------------------- mySQL
 ---------------------------------------------------------
library(RMySQL)
drv <- dbDriver("MySQL")

con <- dbConnect(drv, dbname = "myDB", user = "aedin", password =

"xxx",
host = "myServer.harvard.edu")
dbListTables(con)
dbWriteTable(con, "annot30", samp)

 --------------------------------------------------------- Oracle
 ---------------------------------------------------------

library(ROracle)
 create an Oracle instance and create one connection.
drv <- dbDriver("Oracle")
con <- dbConnect(drv, "username/password")
rs <- dbSendQuery(con, "select * from USERTABLES")
rel <- fetch(rs)
dbGetInfo(con)

3.6.1 Parsing each line - Readlines

There are several function in R for parsing large files. You can use the command readLine or readLines to
parse a file line by line.

49
3.7 Writing Data table from R
1. Function sink() diverts the output from the console to an external file

myPath <- getwd()

sink(file.path(myPath, "sinkTest.txt"))
print("This is a test of sink")
ls()
sin(1.5 * pi)
print(1:10)
sink()

2. Writing a data matrix or data.frame using the write.table() function write.table() has similar arguments
to read.table()

myResults <- matrix(rnorm(100, mean = 2), nrow = 20)

write.table(myResults, file = "results.txt")

This will write out a space separated file.

df1 <- data.frame(myResults)

colnames(df1) <- paste("MyVar", 1:5, sep = "")
write.table(df1, file = "results2.txt", row.names = FALSE,
col.names = TRUE)
read.table(file = "results2.txt", head = TRUE)[1:2, ]

## MyVar1 MyVar2 MyVar3 MyVar4 MyVar5

## 1 1.940 2.569 3.199 3.502 3.259
## 2 4.146 2.752 3.839 1.351 2.194

3. Important options

append = FALSE create new file

sep = ” ” separator (other useful possibility sep=”,”)
row.names = TRUE may need to change to row.names=FALSE
col.names = TRUE column header

4. Output to a webpage
The package R2HTML will output R objects to a webpage

 Write data directly to a new webpage

library(R2HTML)
HTML(df1, outdir = myPath, file = "results.html")
 Capture output to a webpage
HTMLStart(outdir = myPath, filename = "WebResults", echo = TRUE)

50
 ##
## *** Output redirected to directory: C:/Users/aedin/Dropbox/Talks/CDC/Notes
## *** Use HTMLStop() to end redirection.
## [1] TRUE

print("Capturing Output")

## [1] "Capturing Output"

df1[1:2, ]

## MyVar1 MyVar2 MyVar3 MyVar4 MyVar5

## 1 1.940 2.569 3.199 3.502 3.259
## 2 4.146 2.752 3.839 1.351 2.194

summary(df1)

## MyVar1 MyVar2 MyVar3 MyVar4

## Min. :0.546 Min. :1.03 Min. :-0.133 Min. :0.856
## 1st Qu.:1.237 1st Qu.:1.77 1st Qu.: 1.501 1st Qu.:1.696
## Median :1.914 Median :2.19 Median : 1.838 Median :2.127
## Mean :1.827 Mean :2.25 Mean : 1.929 Mean :2.176
## 3rd Qu.:2.359 3rd Qu.:2.54 3rd Qu.: 2.377 3rd Qu.:2.474
## Max. :4.146 Max. :4.24 Max. : 3.839 Max. :3.631
## MyVar5
## Min. :0.369
## 1st Qu.:1.684
## Median :2.106
## Mean :2.256
## 3rd Qu.:3.075
## Max. :4.029

print("hello and Goodbye")

## [1] "hello and Goodbye"

HTMLStop()

## [1] "C:/Users/aedin/Dropbox/Talks/CDC/Notes/Web_Results_main.html"

3.7.1 Other considerations when reading or writing data

It is often useful to create a variable with the path to the data directory, particular if we need to read and/or
write more than one dataset. NOTE: use double backslashes to specify the path names, or the forward slash

51
can be used.

myPath <- file.path("C://Project1")

file.exists(myPath)

## [1] FALSE

 Set myPath to be current directory

myPath <- file.path(getwd())

It is better to expand a path using le.path() rather than paste() as le.path() will expand the path with
delimiting characters appropriate to the operating system in use (eg / unix, \, windows etc)

myfile <- file.path(myPath, "Women.txt")

Use le.exists() to test if a file can be found. This is very useful. For example, use this to test if a file
exists, and if TRUE read the file or you could ask the R to warn or stop a script if the file does not exist

if (!file.exists(myfile)) {
print(paste(myfile, "cannot be found"))
} else {
Women <- read.table(myfile, sep = "\t", header = TRUE)
Women[1:2, ]
}

## height weight age

## 1 58 115 33
## 2 59 117 34

52
3.8 Exercise 3
1. Use read.table() to read the space separated text file WomenStats.txt directly from the website "http:
//bcb.dfci.harvard.edu/˜aedin/courses/R/WomenStats.txt", Call this data.frame
women.

2. Change the rownames to be the letters of the alphabet eg ”A”, ”B” ”C” ”D” etc

3. Write out this file as a tab delimited file using write.table()

4. Read this into R using read.table(). What parameters need modifying to read the data as a tab-
delimited file?

53
3.9 Sampling and Creating simulated data
1. seq and rep. we have already seen the function seq and rep which generate a sequence or repeat
elements.

2. Create data from a specific distribution

Often we want to sample data from a specific distribution, also sometimes called simulating data.
This data is usually used to test some algorithm or function that someone has written. Since the data
is simulated, you know where it came from and so what the answer should be from your algorithm or
function. Simulated data lets you double-check your work.
Each distribution has 4 functions associated with it:
For example, rnorm( ), dnorm( ), pnorm( ), and qnorm( ) give random normals, the normal density
(sometimes called the differential distribution function), the normal cumulative distribution function
(CDF), and the inverse of the normal CDF (also called the quantile function), respectively.
Almost all of the other distributions have similar sets of four functions. The ’r’ versions are rbeta,
rbinom, rcauchy, rchisq, rexp, rf, rgamma, rgeom, rhyper, rlogis, rlnorm, rmultinom, rnbinom, rnorm,
rpois, rsignrank, rt, runif, rweibull, and rwilcox (there is no rtukey because generally only ptukey and
qtukey are needed).
For example, generate 5 observations from a normal distribution with mean 0 and stdev 1, or 10
observation with a mean of 20 and a stdev of 2

rnorm(5, 0, 1)

## [1] -0.2986 -0.3762 0.7070 0.1605 0.7018

rnorm(10, 6, 2)

## [1] 7.530 7.741 5.947 4.622 8.804 8.149 10.949 3.339 6.213
## [10] 6.554

For most of the classical distributions, these simple function provide probability distribution functions
(p), density functions (d), quantile functions (q), and random number generation (r). Beyond this
basic functionality, many CRAN packages provide additional useful distributions. In particular, mul-
tivariate distributions as well as copulas are available in contributed packages. See http://cran.
r-project.org/web/views/Distributions.html and http://cran.r-project.
org/doc/manuals/R-intro.html#Probability-distributions for more informa-
tion.

3. Sample from existing data

The second type of simulation you may wish to perform is to bootstrap or permute existing data. In
bootstrapping one generally follows the same basic steps

(a) Resample a given data set a specified number of times

(b) Calculate a specific statistic from each sample

(c) Find the standard deviation of the distribution of that statistic

54
 The function sample() will resample a given data set with or without replacement

sample(1:10)

## [1] 3 8 9 7 2 6 4 10 1 5

sample(1:10, replace = TRUE)

## [1] 1 1 8 6 4 8 1 6 10 10

You can also add weights to bias selection or probability of selecting of a certain subset. For example
bootstrap sample from the same sequence (1:10) with probabilities that favor the numbers 1-5

weights <- c(rep(0.25, 5), rep(0.05, 5))

print(weights)

## [1] 0.25 0.25 0.25 0.25 0.25 0.05 0.05 0.05 0.05 0.05

sample(10, replace = T, prob = weights)

## [1] 5 2 10 5 1 3 5 4 9 2

3.10 Exercise 4
1. Create the vector which contains the first 20 letters of the alphabet and the sequence of number 0:200
in increments of 10 (hint use seq()).

2. Use sample() to randomize the order of the vector.

3. Use the function cat() to write this vector to a file called ”myVec.txt”.

4. Use scan() to read the first 10 items in the file, what value do you give to the parameter ’what’.
Compare running scan() with different data types; eg: what=”text”, what=123 and what=TRUE

55
Chapter 4

Introduction to programming and writing

Functions in R

4.1 Why do we want to write functions?

We have a general knowledge of function use, so how do we write our own functions. In other words, we
want to create objects of mode function.
1. Why do we want to write functions?
2. Definition of a function: assignment of the form

myFunction <- function(arg1, arg2, ...) expression

expression is an R expression using arguments arg1, arg2 to calculate a value. Function returns the
value of the expression
3. Call to a function within R

myFunction(expr1, expr2, ...)

4. Lets write a short function, a function to calculate the means of a vector.

myMean <- function(y1) {

mean <- sum(y1)/length(y1)
return(mean)
}

Now Lets test out function

testVec <- rnorm(50, 20, 4)

mean(testVec)

## [1] 19.72

myMean(testVec)

## [1] 19.72

56
 5. A more complex example
Example of a function ’twosam’: takes as arguments two vectors ’y1’ and ’y2’, calculates the 2-sample
t-test statistic (assuming equal variance), and returns the t-statistic

twosam <- function(y1, y2) {

n1 <- length(y1)
n2 <- length(y2)
yb1 <- mean(y1)
yb2 <- mean(y2)
s1 <- var(y1)
s2 <- var(y2)
s <- ((n1 - 1) * s1 + (n2 - 1) * s2)/(n1 + n2 - 2)
tst <- (yb1 - yb2)/sqrt(s * (1/n1 + 1/n2))
return(tst)
}

4.2 Conditional statements (if, ifelse, switch)

1. if statement

if (condition) expr1 else expr2

condition must evaluate to a single logical value, ie either TRUE or FALSE.

x <- 9
if (x > 0) sqrt(x) else sqrt(-x)

## [1] 3

Vectorized version of the if/else construct: ifelse(condition, expr1, expr2) function which returns a
vector with elements expr1 if condition is true, otherwise it returns expr2.

ifelse(x >= 0, sqrt(x), sqrt(-x))

## [1] 3

The switch function, a generalization of the if statement

spread <- function(x, type) {

switch(type, sd = sd(x), mad = mad(x), IQR = IQR(x)/1.349)
}
samp <- rnorm(50)
spread(samp, 2)

## [1] 1.043

57
spread(samp, "IQR")

## [1] 0.9385

Why IQR(x)/1.349 ? In a normal distribution 50% of the data (between 0.25 and 0.75 quartiles). So the distance between
the two quartiles IQR(x) = quantile(x,0.75) − quantile(x,0.25). For a normal distribution IQR is qnorm(0.75) - qnorm(0.25)
≈ 1.349. Therefore IQR/1.349 is an estimator of the standard deviation of a normal distribution.

4.2.1 Repetitive execution: For and While loops

(a) for loops

for (i in expr1) expr2

where i is the loop variable, expr1 is usually a sequence of numbers, and expr2 is an ex-
pression.

for (i in 1:5) print(i2)

## [1] 1
## [1] 4
## [1] 9
## [1] 16
## [1] 25

(b) while loops

while (condition) expr continues till the condition becomes false. Used often in iterative calcu-
lations

x <- 1
y <- 16
while (x2 < y) {
cat(x, "squared is ", x2, "\n")  print x and sq(x)
x <- x + 1
}

## 1 squared is 1
## 2 squared is 4
## 3 squared is 9

A word of caution, it is easy to write a while() loop that doesn’t terminate, in which case your
script may go into a never-ending cycle. Therefore if possible, write a for() loop in preference
to a while() loop.

58
4.3 Viewing Code of functions from R packages

Its often useful to view the code of R functions. To see the code, type the name of that code without
parenthesis. Take a look closer at a built-in function IQR. We see it is simply taking the difference
(diff() of the 25

help(IQR)

## starting httpd help server ...

## done

IQR

## function (x, na.rm = FALSE, type = 7)

## diff(quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE,
## type = type))
## <bytecode: 0x0000000002ee6778>
## <environment: namespace:stats>

args(IQR)

## function (x, na.rm = FALSE, type = 7)

## NULL

body(IQR)

## diff(quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE,

## type = type))

xx <- sample(1:30, 10)

quantile(xx)

## 0% 25% 50% 75% 100%

## 3.0 9.5 13.5 17.5 25.0

IQR(xx)

## [1] 8

(Sometimes, functions don’t appear to be ”visible”. In this case, use methods or getAnywhere to view the
function. This is a bit more complex for S4 functions).

mean

## function (x, ...)

## UseMethod("mean")
## <bytecode: 0x00000000064e3038>
## <environment: namespace:base>

59
methods(mean)

## [1] mean.data.frame mean.Date mean.default mean.difftime

## [5] mean.POSIXct mean.POSIXlt

mean.default

## function (x, trim = 0, na.rm = FALSE, ...)

## {
## if (!is.numeric(x) && !is.complex(x) && !is.logical(x)) {
## warning("argument is not numeric or logical: returning NA")
## return(NA_real_)
## }
## if (na.rm)
## x <- x[!is.na(x)]
## if (!is.numeric(trim) || length(trim) != 1L)
## stop("trim must be numeric of length one")
## n <- length(x)
## if (trim > 0 && n) {
## if (is.complex(x))
## stop("trimmed means are not defined for complex data")
## if (any(is.na(x)))
## return(NA_real_)
## if (trim >= 0.5)
## return(stats::median(x, na.rm = FALSE))
## lo <- floor(n * trim) + 1
## hi <- n + 1 - lo
## x <- sort.int(x, partial = unique(c(lo, hi)))[lo:hi]
## }
## .Internal(mean(x))
## }
## <bytecode: 0x00000000064e3828>
## <environment: namespace:base>

Some function are ”Non visible” that means you can see the code. When you These are hidden in the
package namespace. use the function methods, non visible functions are marked by an asterisk.

?(t.test)
t.test

## function (x, ...)

## UseMethod("t.test")
## <bytecode: 0x0000000004e640d8>
## <environment: namespace:stats>

methods(t.test)

## [1] t.test.default* t.test.formula*

##
## Non-visible functions are asterisked

60
To view a hidden or non-visible function use ”PackageName:::function”

stats:::t.test.default

To reduce the output and save paper in the manual, we will just view the first 5 and last 10 lines of the
function.

head((stats:::t.test.default), 5)

##
## 1 function (x, y = NULL, alternative = c("two.sided", "less", "greater"),
## 2 mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95,
## 3 ...)
## 4 {
## 5 alternative <- match.arg(alternative)

print("truncated...")

## [1] "truncated..."

tail((stats:::t.test.default), 10)

##
## 102 names(mu) <- if (paired || !is.null(y))
## 103 "difference in means"
## 104 else "mean"
## 105 attr(cint, "conf.level") <- conf.level
## 106 rval <- list(statistic = tstat, parameter = df, p.value = pval,
## 107 conf.int = cint, estimate = estimate, null.value = mu,
## 108 alternative = alternative, method = method, data.name = dname)
## 109 class(rval) <- "htest"
## 110 return(rval)
## 111 }

There are some functions that you will not be able to see using these commands. These are most
likely written in object orientated R (called S4). Much of Bioconductor’s functions are written in S4.
However a full discussion of S4 functions is beyond the scope of this course.

4.4 The Apply Functions

Iterative ”For loops” in R may sometimes be memory intensive, and functions such as apply, sweep
or aggregate should be should instead.

(a) apply
appply() applies a function over the rows or columns of a matrix. The syntax is

61
 apply(X, MARGIN, FUN, ARGs)

where X: array, matrix or data.frame; MARGIN: 1 for rows, 2 for columns, c(1,2) for both;
FUN: one or more functions; ARGs: possible arguments for function

For example, lets go back to the example dataset women which we loaded from the web.

summary(women)

## height weight age

## Min. :58.0 Min. :115 Min. :30.0
## 1st Qu.:61.5 1st Qu.:124 1st Qu.:32.0
## Median :65.0 Median :135 Median :34.0
## Mean :65.0 Mean :137 Mean :33.9
## 3rd Qu.:68.5 3rd Qu.:148 3rd Qu.:35.5
## Max. :72.0 Max. :164 Max. :39.0

colMeans(women)

## height weight age

## 65.00 136.73 33.93

apply(women, 2, mean)

## height weight age

## 65.00 136.73 33.93

testEq <- all(rowMeans(women) == apply(women, 1, mean))

print(testEq)

## [1] TRUE

if (testEq) print("rowMeans is equivalent to apply(df, 1,

mean)")

## [1] "rowMeans is equivalent to apply(df, 1, mean)"

Create a function using apply

colSd <- function(df) apply(df, 2, sd)

colSd(women)

## height weight age

## 4.472 15.499 2.576

62
(b) tapply
tapply() is a member of the very important apply() functions. It is applied to ”ragged” arrays,
that is array categories of variable lengths. Grouping is defined by vector.

The syntax is:

tapply(vector, factor, FUN)

Example:

ageSplit <- ifelse(womenage < 35, "under35", "over35")

print(ageSplit)

## [1] "under35" "under35" "over35" "under35" "under35" "under35"

## [7] "under35" "over35" "over35" "under35" "under35" "over35"
## [13] "under35" "under35" "over35"

tapply(womenweigh, ageSplit, length)

## over35 under35
## 5 10

tapply(womenweigh, ageSplit, summary)

## $over35
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 120 135 139 142 150 164
##
## $under35
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 115 124 130 134 145 159
##

(c) lapply and sapply

lapply() and sapply() are applied to lists. lapply() returns a list (of the same length as input).
sapply() is a user-friendly version of lapply by default returning a vector or matrix if appropri-
ate.
tapply will

myList <- list(ToothGrowth = TG, WomenAge = womenage, beta =

exp(-3:3),
logicalVec = c(TRUE, FALSE, FALSE, TRUE))
 compute the list mean for each list element
res1 <- lapply(myList, length)

63
 print(res1)
print(paste("Class of res1:", class(res1)))

res2 <- sapply(myList, length)

print(res2)
print(paste("Class of res2:", class(res2)))

(d) for more apply functions see the library plyr

4.5 Exercise 5

(a) Write a for loop printing the consecutive powers of 2, from 0 to 10

(b) Write a while loop printing the consecutive powers of 2, less than 1000

64
4.5.1 Efcient For Loop in R (Use apply)

sapply and lapply will repeat a function over a list

myList <- list(WomenMat = women, WomenAge = womenage, beta =

exp(-3:3),
logicalVec = c(TRUE, FALSE, FALSE, TRUE))
 compute the list mean for each list element
res1 <- lapply(myList, length)
print(res1)
print(paste("Class of res1:", class(res1)))

res2 <- sapply(myList, length)

print(res2)
print(paste("Class of res2:", class(res2)))

Note apply is much more computational efficient that a for loop. But if you can use built in functions
like rowMeans or colMeans these are quicker still

myMA <- matrix(rnorm(1e+06), 1e+05, 10, dimnames = list(1:1e+05,

paste("C", 1:10, sep = "")))

results <- NULL

system.time(for (i in seq(along = myMA[, 1])) results <- c(results,
mean(myMA[i, ])))

## user system elapsed

## 27.55 14.55 42.46

results <- numeric(length(myMA[, 1]))

system.time(for (i in seq(along = myMA[, 1])) results[i] <-
mean(myMA[i,
]))

## user system elapsed

## 2.33 0.00 2.33

system.time(myMAmean <- apply(myMA, 1, mean))

## user system elapsed

## 2.04 0.00 2.05

system.time(myMAmean <- rowMeans(myMA))

65
## user system elapsed
## 0 0 0

system.time(myMAsd <- apply(myMA, 1, sd))

## user system elapsed

## 3.94 0.01 3.96

system.time(myMAsd <- sqrt((rowSums((myMA -

rowMeans(myMA))2))/(length(myMA[1,
]) - 1)))

## user system elapsed

## 0.03 0.00 0.03

66
4.6 Functions for parsing text
There are many functions with R for parsing text. We will cover a few here.
• To search for text within an R vector, use grep. It uses the same regular expression patterns as perl is
you set perl=TRUE

grep("A", LETTERS)

## [1] 1

grep("A", LETTERS, value = TRUE)

## [1] "A"

• To substitute characters within a string use sub

sub("B", "A", LETTERS)

## [1] "A" "A" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P"
## [17] "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z"

• To split a character string use strsplit

a <- date()
strsplit(a, " ")

## [[1]]
## [1] "Tue" "Jun" "19" "15:01:08" "2012"
##

strsplit(a, "J")

## [[1]]
## [1] "Tue " "un 19 15:01:08 2012"
##

b <- strsplit(a, "11")

class(b)

## [1] "list"

b <- unlist(b)
class(b)

## [1] "character"

67
 • For special characters you need to precede them with a double back slash

a <- "aedin@jimmy.harvard.edu"
strsplit(a, "\\.")

## [[1]]
## [1] "aedin@jimmy" "harvard" "edu"
##

4.7 missing values

a <- c(1:10, NA, NA)

a <- c(1:10, NA, NA)
summary(a)

## Min. 1st Qu. Median Mean 3rd Qu. Max. NAs

## 1.00 3.25 5.50 5.50 7.75 10.00 2

mean(a)

## [1] NA

mean(a, na.rm = TRUE)

## [1] 5.5

68
4.8 Exercise 6: Parsing Real Data - World Population Data from Wikipedia
We demonstrated how to get data tables a URL. This means we can retrieve data from most any table on
the web. The function readHTMLTable is very flexible for this. Please retrieve the table entited ”Estimated
world population at various dates (in millions)” (Table 13) from
http://en.wikipedia.org/wiki/World_population.

require(XML)

## Loading required package: XML

worldPop <- readHTMLTable("http://en.wikipedia.org/wiki/Worldpopulation")

names(worldPop)

## [1] "NULL"
## [2] "toc"
## [3] "NULL"
## [4] "World population milestones (USCB estimates)"
## [5] "The 10 countries with the largest total population:"
## [6] "10 most densely populated countries (with population above 1 million)"
## [7] "Countries ranking highly in terms of both total population (more than 15 million p
## [8] "NULL"
## [9] "UN (medium variant 2010 revision) and US Census Bureau (December 2010) estimates
## [10] "UN 2008 estimates and medium variant projections (in millions)[98]"
## [11] "World historical and predicted populations (in millions)[102][103]"
## [12] "World historical and predicted populations by percentage distribution [102][103]"
## [13] "Estimated world population at various dates (in millions)"
## [14] "Starting at 500 million"
## [15] "Starting at 375 million"
## [16] "NULL"
## [17] "NULL"
## [18] "NULL"
## [19] "NULL"

worldPop <- worldPop[[13]]  Just look at Table 13

1. First tidy the data. The data are factors, its easier to edit data that are characater. Apply as.character
to each column

2. Remove rows with dates before 1750. Remove the additional header in row 32.

3. Remove colum 9 notes

4. Use the sub to remove the comma in the data values

5. convert the data to numeric

6. In what year did the population of Europe, Africa and Asia exceed 500 million?

7. Bonus: Plot the population growthof the World, Africa or Europe since 1750. Given this plot, would
you guess that the the population of the World, Africa or Europe would be more likely to double again
before the end of 21st century?

69
4.8.1 Writing functions: More on arguments
We are equipped now with all basic tools we need for writing functions. We include a few tips on arguments
to functions.

1. Function arguments: Default values In many cases arguments have default values. For example the
qnorm(x, mean = 0, sd = 1,lower.tail = TRUE, log.p = FALSE ) has default values for the mean,
standard deviation, cdf calculation and probabilities on the original scale.

prob <- c(0.5, 0.9, 0.95, 0.975, 0.99)

args(qnorm)
qnorm(prob)
qnorm(prob, 2)
qnorm(prob, mean = 2, sd = 1)

2. Function arguments: order is important

• The argument sequence may begin in the unnamed, positional form, and specify named argu-
ments after the positional arguments

• If arguments to functions are given in the form name=object form, they may be given in any
order

• The argument sequence may be given in the unnamed, positional form

• For example the following statements are equivalent

prob <- c(0.5, 0.9, 0.95, 0.975, 0.99)

args(qnorm)
qnorm(p = prob, mean = 0, sd = 1, lower.tail = TRUE, log.p =
FALSE)
qnorm(prob, 0, 1, log = FALSE, low = TRUE)
qnorm(prob, 0, 1, TRUE, FALSE)

3. Functions: A few points

• Sometimes you may see the parameter ”...”, this is normally when functions call other functions
and arguments are passed from one function to another.

• If commands are stored in an external R script file, say L2.R they can be executed at any time
in R

source(paste(myPath, "L2.R",sep=))

• Once a function is defined, can call it from other functions

• The built-in functions supplied with R are a valuable resource for learning about R programming

70
4.9 Writing functions: more technical discussion -Scoping
1. Scoping
Symbols in the body of a function can be divided into three classes:

• Formal parameters (appear in the argument list of the function)

• Local variables (values are determined by the evaluation of expressions in the body of the
functions)

• Free variables (neither of the above)

In this example: x - formal parameter, y - local variable, z - free variable.

Example:

fn <- function(x) {
y <- 2 * x
print(x)
print(y)
print(z)
}

z <- 2
x <- 4
fn(x = 2)

## [1] 2
## [1] 4
## [1] 2

2. Lexical scope.
Example: function called cube.

cube <- function(n) {

sq <- function() n * n
n * sq()
}
cube(2)

## [1] 8

n <- 4
cube(2)

## [1] 8

71
4.10 Options for Running memory or CPU intensive jobs in R
4.10.1 Distributed computing in R
There are two ways to split or distribute a big job. The simplest it to send jobs to different processors on the
same machine (assuming it has multiple cores, which most new machines do). The second option is to split
or parallelize a job across many machines or a cluster of machines. For both of these, see the Bioconductor
package parallel which builds upon the older R packages snow and multicore
To install parallel use the Bioconductor package installer, BiocInstaller

library(BiocInstaller)
biocLite("parallel")

The package parallel has many functions which work like apply to distribute a computation. For example
use mclapply just like lapply to split a job over 4 cores.

library(parallel)
system.time(mclapply(1:4, function(i) mc.cores <- 4))

mclapply is a parallelized version of lapply, and will not work on windows (as far as I know) but on
Windows you can use functions parLapply, clusterApply and clusterApplyLB all in the parallel package.
The packages has several functions for different types of apply loops including parLapply, parSapply,
and parApply which are parallel versions of lapply, sapply and apply respectively.

library(parallel)
cl <- makeCluster(3)
parLapply(cl, 1:3, sqrt)
stopCluster(cl)

For more help on this package, see the vignette

vignette("parallel", package = "parallel")

There are several other packages for distributed computing see the reviews of R packages on CRAN task
views http://cran.r-project.org/web/views/HighPerformanceComputing.html. I
have received recommendations on R packages biglm, ff and bigmemory.

4.10.2 Running R in the Cloud

One quick-start approaching to running R in the Cloud is to register for an Amazon cloud account and then
simply direct your web browser at the Bioconductor RCloud instance
http://www.bioconductor.org/help/bioconductor-cloud-ami/.
It will open a RStudio interface and it has the same look and feel as the desktop version, making the
transition pretty seamless.
If you wish to set up your own instance, Louis Alsett at Trinity College Dublin provides an RStu-
dio Server Amazon Machine Image (AMI) which can install to your Cloud account see http://www.
louisaslett.com/RStudio_AMI/.
For more information about distributed computing on the Cloud based including using Hadoop (which
I think is used by Revolution Analytics) see the recent book ”parallel R” by Q Ethan McCallum http:
//www.amazon.com/Parallel-R-Q-Ethan-McCallum/dp/1449309925

72
4.11 Efcient R coding
4.11.1 What is an R script
A R script is simply a text file, with R commands. There are two ways to call these R commands, start R
and using the R function source, or at the command line using R CMD BATCH

4.11.2 What a script should look like ;-)


 Author: Mr Bob Parr
 Date: 2011-01-20
 Version: 1.0
 License: GPL (>= 3)

 Description: survival analysis function


 This function censors the survival data at a specific point in

 time. This is is useful if you used datasets having different
 follow-up periods.

 Arguments:
 -----------
 surv.time: vector of times to event occurrence [numeric]
 surv.event: vector of indicators for event occurrence [0/1]
 time.cens: point in time at which the survival data must
 be censored [integer]. Defaults value is 0

 Output: [list of two items]
 --------------------------
 surv.time.cens: vector of censored times to event occurrence [numeric]
 surv.event.cens: vector of censored indicators for event occurrence [0/1]

censor.time <- function(surv.time, surv.event, time.cens=0) {

stc <- surv.time
sec <- surv.event
cc.ix <- complete.cases(stc, sec)
if(time.cens != 0) {
stc[cc.ix][surv.time[cc.ix] > time.cens] <- time.cens
sec[cc.ix][surv.time[cc.ix] > time.cens] <- 0
}
return(list("surv.time.cens"=stc, "surv.event.cens"=sec))
}

You can save this script in a file named censortime.R in your working directory. If you want to
define this function in your workspace, just type source("censortime.R").
Of course, an R script may contain more than functions, it may also contain any analytical pipeline.
Here is another example:


 Author: Mr Bob Parr

73
 Date: 2011-01-20
 Version: 1.0
 License: GPL (>= 3)

 Description: Script fitting a Cox model on the colon data
 and writing the coefficients in a txt file


 load library
library(survival)

 load colon dataset

data(colon)

 Fit the cox model

coxm <- coxph(Surv(time, status) ˜ rx, data=colon)

 save summary in a txt file in the working directory

write.table(t(coxmcoefficients), sep="\t", file="coxcoefficientscolon.txt",
row.names=FALSE)

Save this script in a file named coxColon.R in your working directory. you can run it from your R
session using the command source(”coxColon.R”) or you can run it in batch mode from a command line
(e.g., shell console) using the command R CMD BATCH coxColon.

4.11.3 Coding Recommendations

These are the coding recommendations from the Bioconductor project, and whilst you do not have to do
these, it is handy to adopt good working practice when you learn a new language.

1. Indentation

• Use 4 spaces for indenting. No tabs.

• No lines longer than 80 characters. No linking long lines of code using ”;”

2. Variable Names

• Use camelCaps: initial lowercase, then alternate case between words.

3. Function Names

• Use camelCaps: initial lower case, then alternate case between words.

• In general avoid ’.’, as in some.func

Whilst beyond the scope of this class, R packages are written to either S3 or S4 standards. In
the S3 class system, some(x) where x is class func will dispatch to this function. Use a ’.’ if the
intention is to dispatch using S3 semantics.

4. Use of space

74
 • Always use space after a comma. This: a, b, c. Not: a,b,c.

• No space around ”=” when using named arguments to functions. This: somefunc(a=1, b=2),
not: somefunc(a = 1, b = 2).

• Space around all binary operators: a == b.

5. Comments

• Use ”##” to start comments.

• Comments should be indented along with the code they comment.

6. Misc

• Use "<-" not ”=” for assignment.

7. For Efficient R Programming, see slides and exercises from Martin

http://www.bioconductor.org/help/course-materials/2010/BioC2010/

8. R packages which tidy your code There is a package called formatR https://github.com/
yihui/formatR/wiki/ which will format all R script in a folder, indenting loops, convert the =
to -> etc. See its wiki pages above if you are interesting in testing it.

4.11.4 Debugging R Code

Use the cat() and print() functions to print values in scripts as you go. I also use the traceback to find out
what went wrong when a function doesn’t work A full list of functions for debugging R code is beyond
the scope of this lecture, but see the following useful tips from Duncan Murdoch http://www.stats.
uwo.ca/faculty/murdoch/software/debuggingR/

4.11.5 End-User Messages

• message() communicates diagnostic messages (e.g., progress during lengthy computations) during
code evaluation.

• warning() communicates unusual situations handled by your code.

• stop() indicates an error condition.

• cat() or print() are used only when displaying an object to the user, e.g., in a show method.

4.11.6 system.time
If you wish to check the efficient of your code to see how long it is taking to run, use the function system.time
which gives the compute time for a function

df <- matrix(rnorm(5e+06), ncol = 20000)

system.time(apply(df, 1, mean))

75
## user system elapsed
## 0.18 0.03 0.22

system.time(rowMeans(df))

## user system elapsed

## 0.01 0.00 0.01

system.time()

4.11.7 Etiquette when emailing the R mailing list

When all else failed, ask an expert. The R mailing list is a wonderful resource with a very help bunch of
experts who will be more than willing to help. But before you email, please do check if someone has asked
the same question before or if there is a simple answer to your problem in the R manual or frequently asked
questions (FAQ) documentation. The easiest way to do this is to search on http://www.rseek.org
If you still need to ask an expert on the mailing list

• Do Send in example code

• Include information about your operating system and version of R. The easiest way to do this is
using sessionInfo() for example, see this recent post on the mailing list https://stat.ethz.
ch/pipermail/r-sig-mixed-models/2010q3/004467.html

Writing R packages
Once you have written all your functions in one or several R files, you can use the function package.skeleton
to generate the necessary directories and empty help pages for your package.

package.skeleton(name = "myFirstRPackage")

For coding recommendations see http://google-styleguide.googlecode.com/svn/trunk/

google-r-style.html or http://wiki.fhcrc.org/bioc/Coding_Standards

Hint: all the packages on CRAN and BioConductor are open source, so you can easily download the
source of any package to take a closer look at it. It may be extremely insightful to see how experienced R
developers implemented their own packages.

76
Using SVN
RStudio v0.96 contains an easy interface to subversion (either GIT or SVN), but here is a detailed guide to
using svn
http://tortoisesvn.net/docs/release/TortoiseSVN_en/tsvn-repository.html#
tsvn-repository-create-tortoisesvn
Step 1. Create local SVN repository

1. Open the windows explorer

2. Create a new folder and name it e.g. SVNRepository

3. Right-click on the newly created folder and select TortoiseSVN Create Repository here....

4. A repository is then created inside the new folder. Don’t edit those files yourself!!!. If you get any
errors make sure that the folder is empty and not write protected.

5. For Local Access to the Repository you now just need the path to that folder. Just remember that
Subversion expects all repository paths in the form file:///C:/SVNRepository/. Note the use of forward
slashes throughout.

6. So far this is an empty repository, even though Subversion has created several directories and files!
We need to fill it with our project files and connect it with our working project directory

Step 2: Initial import.

1. Somewhere in your hard drive create a directory (e.g. tmp) with the following three subdirectories:

C:\tmp\new\branches
C:\tmp\new\tags
C:\tmp\new\trunk

2. Backup and Tidy your exisiting scripts and project files (C:\Projects\MyProject). (ie delete
unecessary files)

3. Copy the contents of \MyProject into the trunk subdirectory (C:\tmp\new\trunk).

4. Import the ’new’ directory into the repository (Right-click/TortoiseSVN/Import). Select URL as
file:///C:/SVNRepository/Myproject (forward slashes!)

5. To see it works, right mouse click start TortoiseSVN/Repo-browser... see your Imported
files.. Happy days. Now you have an SVN with all your files

Step 3. Using SVN

1. Now we have created the SVN, the trick is to use it!!! Start by checking out your data. Create a new
scripts directory (or go back to your old one and delete its contents). And right mouse click and select
”SVN Checkout”

2. To use the SVN Sending (checking in) your changes to the repository: Right-click on selected files
then ”SVN Commit”

3. To add new files to the repository. This is a two step process: , first Right-click on selected files then
”TortoiseSVN/Add” Then Right-click on selected files then ”SVN Commit”

77
4. If you wish to delete files (remember the SVN will always have a history of them) use ”Tortois-
eSVN/Delete”

5. Happy Subversioning!

78
Chapter 5

Introduction to graphics in R

To start let’s look at the basic plots that can be produced in R using the demo() function

demo(graphics)

On start up, R initiates a graphics device driver which opens a special graphics window for the display
of interactive graphics. If a new graphics window needs to be opened either win.graph() or windows()
command can be issued.
Once the device driver is running, R plotting commands can be used to produce a variety of graphical
displays and to create entirely new kinds of display.

5.1 The R function plot()

The plot() function is one of the most frequently used plotting functions in R.
IMPORTANT: This is a generic function, that is the type of plot produced is dependent on the class of
the first argument.

• Plot of Vector(s)

1. One vector x (plots the vector against the index vector)

x <- 1:10
plot(x)

79
 10
8
6
x
4
2

2 4 6 8 10
Index

2. Scatter plot of two vectors x and y

set.seed(13)
x <- -30:30
y <- 3 * x + 2 + rnorm(length(x), sd = 20)
plot(x, y)
100
50
y
0
−50

−30 −20 −10 0 10 20 30

x

• Plot of data.frame elements If the first argument to plot() is a data.frame, this can be as simply as
plot(x,y) providing 2 columns (variables in the data.frame).

80
Lets look at the data in the data.frame airquality which measured the 6 air quality in New York, on a
daily basis between May to September 1973. In total there are 154 observation (days).

airquality[1:2, ]

## Ozone Solar.R Wind Temp Month Day

## 1 41 190 7.4 67 5 1
## 2 36 118 8.0 72 5 2

plot(airquality)  all variables plotted against each other

pairs()

0 100 250 60 70 80 90 0 10 20 30

100
Ozone

50
0
250

Solar.R
100
0

20
15
Wind

10
5
60 70 80 90

Temp
9
8

Month
7
6
5
30
20

Day
10
0

0 50 100 5 10 15 20 5 6 7 8 9

Note most plotting commands always start a new plot, erasing the current plot if necessary. We’ll

81
discuss how to change the layout of plots so you can put multiple plots on the same page a bit later.
But a simple way to put multiple plots in the same window is by splitting the display using mfrow
Note if you give plot a vector and factor plot(factor, vector) or plot(vector factor) it will produce a
boxplot.

par(mfrow = c(1, 2))

attach(airquality)
plot(Ozone, Temp, main = "plot(Ozone, Temp)")
plot(airqualityOzone ˜ factor(airqualityMonth), col = 2:6,
sub = "plot(airqualityOzone˜ factor(airqualityMonth)", ylab =
"Ozone",
xlab = "month")

plot(Ozone, Temp)

150
90

100
80

Ozone
Temp
70

50
60

0 50 100 150 5 6 7 8 9
Ozone month
plot(airquality$Ozone~factor(airquality$Mo

detach(airquality)

82
5.2 Exercise 7
Using the ToothGrowth data we read earlier. Please draw the following plot

35
35
30

30
25

25
Tooth Length

Tooth Length
20

20
15

15
10

10

5
5

OJ 0.5

OJ 1

OJ 2

VC 0.5

VC 1

VC 2
OJ VC
Treatment Treatment and Dose

83
5.2.1 Arguments to plot
axes=FALSE Suppresses generation of axes-useful for adding your own custom axes with the axis()
function. The default, axes=TRUE, means include axes.

type= The type= argument controls the type of plot produced, as follows:

type=”p” Plot individual points (the default)

type=”l” Plot lines

type=”b” Plot points connected by lines (both)

type=”o” Plot points overlaid by lines

type=”h” Plot vertical lines from points to the zero axis (high-density)

type=”n” No plotting at all. However axes are still drawn (by default) and the coordinate system is set up
according to the data. Ideal for creating plots with subsequent low-level graphics functions.

xlab=string

ylab=string Axis labels for the x and y axes. Use these arguments to change the default labels, usually the
names of the objects used in the call to the high-level plotting function.

main=string Figure title, placed at the top of the plot in a large font.

sub=string Sub-title, placed just below the x-axis in a smaller font.

Some Examples of Plotting using different plot types and axes

xp <- 1:100/100
yp <- 3 * xp2 - 2 * xp + rnorm(100, sd = 0.2)

par(mfrow = c(3, 2))

for (i in c("l", "b", "o", "h")) plot(xp, yp, type = i, main =
paste("Plot type:",
i))

plot(xp, yp, type = "o", xlab = "index", ylab = "values",

main = "R simple plot")
plot(xp, yp, type = "l", axes = FALSE)
axis(1)
axis(2, at = c(-0.6, 0, 0.6, 1.2), col = "blue")
axis(3, at = c(0, 0.25, 0.5, 0.75, 1), col = "red")
axis(4, col = "violet", col.axis = "dark violet", lwd = 2)

84
 Plot type: l Plot type: b

1.5

1.5
1.0

1.0
0.5

0.5
yp

yp
0.0

0.0
−0.5

−0.5
0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
xp xp
Plot type: o Plot type: h
1.5

1.5
1.0

1.0
0.5

0.5
yp

yp
0.0

0.0
−0.5

−0.5
0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
xp 0.00 0.25
xp
0.50 0.75 1.00
R simple plot
1.5

1.2
1.0

0.6
0.5
values

yp
0.0

0.0
−0.5

−0.6

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
index xp

5.2.2 Other useful basic graphics functions

• boxplot(x) a boxplot show the distribution of a vector. It is very useful to example the distribution of
different variables.

boxplot(airquality)

85
 300
250
200
150
100
50
0

Ozone Solar.R Wind Temp Month Day

Note if you give plot a vector and factor plot(factor, vector) or plot(vector factor) it will produce a
boxplot.

par(mfrow = c(2, 2))

boxplot(airqualityOzone ˜ airqualityMonth, col = 2:6, xlab =
"month",
ylab = "ozone", sub =
"boxplot(airqualityOzone˜ airqualityMonth")
title("Equivalent plots")
plot(factor(airqualityMonth), airqualityOzone, col = 2:6,
xlab = "month", ylab = "ozone", sub =
"plot(factor(airqualityMonth), airqualityOzone")
plot(airqualityOzone ˜ factor(airqualityMonth), col = 2:6,
sub = "plot(airqualityOzone˜ factor(airqualityMonth)")

86
 Equivalent plots

150

150
100

100
ozone

ozone
50

50
0

0
5 6 7 8 9 5 6 7 8 9
month month
boxplot(airquality$Ozone~airquality$Month plot(factor(airquality$Month), airquality$Ozone
150
airquality$Ozone
100
50
0

5 6 7 8 9
factor(airquality$Month)
plot(airquality$Ozone~factor(airquality$Month)

• barplot Plot a bar plot of the mean ozone quality by month. First use tapply to calculate the mean of
ozone by month

OzMonthMean <- tapply(airqualityOzone, factor(airqualityMonth),

mean, na.rm = TRUE)
par(mfrow = c(1, 2))
barplot(OzMonthMean, col = 2:6, main = "Mean Ozone by month")

87
 Mean Ozone by month

50
40
30
20
10
0

5 6 7 8 9

• pie chart

pie(OzMonthMean, col = rainbow(5))

7
5

• hist(x)- histogram of a numeric vector x with a few important optional arguments: nclass= for the
number of classes, and breaks= for the breakpoints

88
 xt <- rt(100, 3)
hist(xt)

Histogram of xt
40
30
Frequency
20
10
0

−8 −6 −4 −2 0 2 4 6
xt

plot(density(xt))

density.default(x = xt)
0.30
0.25
0.20
Density
0.15
0.10
0.05
0.00

−5 0 5
N = 100 Bandwidth = 0.4973

• 3D scatterplot

89
require(scatterplot3d)

## Loading required package: scatterplot3d

data(trees)
trees[1:2, ]

## Girth Height Volume

## 1 8.3 70 10.3
## 2 8.6 65 10.3

s3d <- scatterplot3d(trees, type = "h", highlight.3d = TRUE,

angle = 55, scale.y = 0.7, pch = 16, main = "Example of
scatterplot3d plot: Tree Data")

 Now adding some points to the scatterplot3d

s3dpoints3d(seq(10, 20, 2), seq(85, 60, -5), seq(60, 10,
-10), col = "blue", type = "h", pch = 16)

 Now adding a regression plane to the scatterplot3d

attach(trees)
my.lm <- lm(Volume ˜ Girth + Height)
s3dplane3d(my.lm)

90
 Example of scatterplot3d plot: Tree Data

80
70
60
50
Volume

40

Height
90
85
30

80
75
20

70
65
60
10

8 10 12 14 16 18 20 22

Girth

detach(trees)

• Rvenn - draw a venn diagram. Input is a list. It will draw a venn diagram showing the intersect
between 2-6 vectors in a list.

require(gplots)
sample(LETTERS, 10)

## [1] "Z" "R" "M" "U" "Q" "E" "L" "S" "J" "D"

tt <- lapply(1:3, function(x) sample(LETTERS, 10))

names(tt) <- c("Lucy", "Sally", "Kate")
tt

91
## $Lucy
## [1] "Q" "P" "Z" "M" "J" "T" "F" "O" "A" "D"
##
## $Sally
## [1] "B" "Z" "V" "K" "D" "F" "Y" "Q" "M" "S"
##
## $Kate
## [1] "Y" "P" "H" "N" "Q" "J" "V" "I" "O" "G"
##

venn(tt)

Kate

3 2

2 3
Lucy Sally
4

Plot 4 intersections

tt <- lapply(1:4, function(x) sample(LETTERS, 10))

names(tt) <- paste("List", 1:4)
venn(tt)

92
 List 2 List 3
List 1 2 3 List 4
3 1 1

3 3
0 1

2
0 1
2 0
0

Color plots

require(venneuler)

## Loading required package: venneuler

IntersectMatrix <- function(tt) {

allElements <- unique(unlist(tt))
outMat <- sapply(1:length(tt), function(i) allElements in
tt[[i]])
rownames(outMat) <- allElements
colnames(outMat) <- names(tt)
return(outMat)
}
xx <- IntersectMatrix(tt)
print(xx[1:4, ])

## List 1 List 2 List 3 List 4

## H TRUE FALSE FALSE FALSE
## G TRUE TRUE TRUE TRUE
## J TRUE FALSE TRUE TRUE
## B TRUE FALSE FALSE FALSE

plot(venneuler(xx))

93
 List 1

3
List 4
List 2

It will even plot 5 intersections

tt <- lapply(1:5, function(x) sample(LETTERS, 10))

names(tt) <- sapply(tt, function(x) paste(sort(x), collapse = ""))
venn(tt)

94
 CDGKMOSUVX

1
CDJMNPWXYZ
CFGHIKPQVY 1 1
1 1 1
0
1
1
1
2 1
0 1

1 0 1
1
0
0
0
1
1 1 0
0
0 1
0

0
3

ADEINOTVYZ CDHJKMOUYZ

95
5.3 Editing the default plot with low-level plotting commands
Sometimes the standard plot functions don’t produce exactly the kind of plot you desire. In this case, low-
level plotting commands can be used to add edit or extra information (such as points, lines or text) to the
current plot. Some of the more useful low-level plotting functions are:

points(x, y)

lines(x, y) Adds points or connected lines to the current plot.

text(x, y, labels, ...) Add text to a plot at points given by x, y. Normally labels is an integer or character
vector in which case labels[i] is plotted at point (x[i], y[i]). The default is 1:length(x). Note: This
function is often used in the sequence
The graphics parameter type=”n” suppresses the points but sets up the axes, and the text() function
supplies special characters, as specified by the character vector names for the points.

abline(a, b) Adds a line of slope b and intercept a to the current plot.

abline(h=y) Adds a horizontal line

abline(v=x) Adds a vertical line

polygon(x, y, ...) Draws a polygon defined by the ordered vertices in (x, y) and (optionally) shade it in with
hatch lines, or fill it if the graphics device allows the filling of figures.

legend(x, y, legend, ...) Adds a legend to the current plot at the specified position. Plotting characters, line
styles, colors etc., are identified with the labels in the character vector legend. At least one other
argument v (a vector the same length as legend) with the corresponding values of the plotting unit
must also be given, as follows:
legend( , fill=v) Colors for filled boxes
legend( , col=v) Colors in which points or lines will be drawn
legend( , lty=v) Line styles
legend( , lwd=v) Line widths
legend( , pch=v) Plotting characters

title(main, sub) Adds a title main to the top of the current plot in a large font and (optionally) a sub-title
sub at the bottom in a smaller font.

axis(side, ...) Adds an axis to the current plot on the side given by the first argument (1 to 4, counting
clockwise from the bottom.) Other arguments control the positioning of the axis within or beside
the plot, and tick positions and labels. Useful for adding custom axes after calling plot() with the
axes=FALSE argument.

To add Greek characters, either specify font type 5 (see below) or use the function expression

plot(x, cos(x), main = expression(paste("A random eqn ", bar(x)) ==

sum(frac(alpha[i] + beta[z], n))), sub = "This is the
subtitle")

96
 A random eqn x = ∑

1.0
n

0.5
cos(x)
0.0
−0.5
−1.0

−30 −20 −10 0 10 20 30

x
This is the subtitle

Example using points lines and legend

attach(cars)
plot(cars, type = "n", xlab = "Speed [mph]", ylab = "Distance [ft]")
points(speed[speed < 15], dist[speed < 15], pch = "s", col = "blue")
points(speed[speed >= 15], dist[speed >= 15], pch = "f", col = "green")
lines(lowess(cars), col = "red")
legend(5, 120, pch = c("s", "f"), col = c("blue", "green"),
legend = c("Slow", "Fast"))
title("Breaking distance of old cars")

97
 Breaking distance of old cars

120
f
s Slow
f Fast
100 f
f f
s
80

f
Distance [ft]

f f
f f
s
60

f f f f
f f
s f f
f f f
40

s s s f
s s f f f
s s s s f
s s f
20

s s s s
s s
s s
0

5 10 15 20 25
Speed [mph]

detach(2)

To add formulae or Greek characters to a plot

par(mfrow = c(2, 1))

 Mean and Median Plot
x <- rexp(100, rate = 0.5)
hist(x, main = "Mean and Median of a Skewed Distribution")
abline(v = mean(x), col = 2, lty = 2, lwd = 2)
abline(v = median(x), col = 3, lty = 3, lwd = 2)
ex1 <- expression(bar(x) == sum(over(x[i], n), i == 1, n),
hat(x) == median(x[i], i == 1, n))
legend(4.1, 30, ex1, col = 2:3, lty = 2:3, lwd = 2)

x <- seq(-pi, pi, len = 65)

plot(x, sin(x), type = "l", col = "blue", xlab = expression(phi),
ylab = expression(f(phi)))
lines(x, cos(x), col = "magenta", lty = 2)
abline(h = -1:1, v = pi/2 * (-6:6), col = "gray90")
ex2 <- expression(plain(sin) * phi, paste("cos", phi))
legend(-3, 0.9, ex2, lty = 1:2, col = c("blue", "magenta"),
adj = c(0, 0.6))

98
 Mean and Median of a Skewed Distribution

40
30
xi
Frequency

n
x=∑
i=1 n
20

x^ = median(xi, i = 1, n)
10
0

0 2 4 6 8 10
x
1.0

sinφ
cosφ
0.5
f(φ )
0.0
−0.5
−1.0

−3 −2 −1 0 1 2 3
φ

5.4 Default parameters - par

When creating graphics, particularly for presentation or publication purposes, R’s defaults do not always
produce exactly that which is required. You can, however, customize almost every aspect of the display
using graphics parameters. R maintains a list of a large number of graphics parameters which control things
such as line style, colors, figure arrangement and text justification among many others. Every graphics
parameter has a name (such as ’col’, which controls colors,) and a value (a color number, for example.)
Graphics parameters can be set in two ways: either permanently, affecting all graphics functions which
access the current device; or temporarily, affecting only a single graphics function call.
The par() function is used to access and modify the list of graphics parameters for the current graphics

99
device. See help on par() for more details.
To see a sample of point type available in R, type

example(pch)

5.4.1 Interactive plots in R Studio - Effect of changing par

In RStudio the manipulate function accepts a plotting expression and a set of controls (e.g. slider, picker,
or checkbox) which are used to dynamically change values within the expression. When a value is changed
using its corresponding control the expression is automatically re-executed and the plot is redrawn.

library(manipulate)
manipulate(plot(1:x), x = slider(1, 100))
manipulate(plot(cars, xlim = c(0, x.max), type = type, ann = label,
col = col, pch = pch, cex = cex), x.max = slider(10, 25, step = 5,
initial = 25), type = picker(Points = "p", Line = "l", Step = "s"),
label = checkbox(TRUE, "Draw Labels"), col = picker(red = "red",
green = "green", yellow = "yellow"), pch = picker(1 = 1, 2 = 2,
3 = 3, 4 = 4, 5 = 5, 6 = 6, 7 = 7, 8 = 8, 9 = 9,
10 = 10, 11 = 11, 12 = 12, 13 = 13, 14 = 14, 15 = 15,
16 = 16, 17 = 17, 18 = 18, 19 = 19, 20 = 20, 21 = 21,
22 = 22, 23 = 23, 24 = 24), cex = picker(1 = 1, 2 = 2,
3 = 3, 4 = 4, 5 = 5, 6 = 6, 7 = 7, 8 = 8, 9 = 9,
10 = 10))

100
 type = p, col=red, pch=19, cex=1 type = p, col=blue, pch=21, cex=0.5

120

120
100

100
80

80
dist

dist
60

60
40

40
20

20
0

0
5 10 15 20 25 5 10 15 20 25
speed speed

type = p, col=green, pch=17, cex=2 type = line, col=orange

120

120
100

100
80

80
dist

dist
60

60
40

40
20

20
0

5 10 15 20 25 5 10 15 20 25
speed speed

101
5.4.2 R Colors
Thus far, we have frequently used numbers in plot to refer to a simple set of colors. There are 8 colors where
0:8 are white, black, red, green, blue, cyan, magenta, yellow and grey. If you provide a number greater than
8, the colors are recycled. Therefore for plots where other or greater numbers of colors are required, we
need to access a larger palette of colors.

plot(1:12, col = 1:12, main = "Default 9 Colors", ylab = "",

xlab = "", pch = 19, cex = 3)
text(1:12, c(1:12) + 0.75, c(1:8, 1:4))
Default 9 Colors
12

3
2
10

1
8
8

7
6
6

5
4
4

3
2
2

2 4 6 8 10 12

R has a large list of over 650 colors that R knows about. This list is held in the vector colors(). Have a
look at this list, and maybe search for a set you are interested in.

colors()[1:10]

## [1] "white" "aliceblue" "antiquewhite" "antiquewhite1"

## [5] "antiquewhite2" "antiquewhite3" "antiquewhite4" "aquamarine"
## [9] "aquamarine1" "aquamarine2"

length(colors())

## [1] 657

grep("yellow", colors(), value = TRUE)

## [1] "greenyellow" "lightgoldenrodyellow"

## [3] "lightyellow" "lightyellow1"

102
## [5] "lightyellow2" "lightyellow3"
## [7] "lightyellow4" "yellow"
## [9] "yellow1" "yellow2"
## [11] "yellow3" "yellow4"
## [13] "yellowgreen"

R are has defined palettes of colors, which provide complementing or contrasting color sets. For example
look at the color palette rainbow.

example(rainbow)

For a more complete listing of colors, along with the RGB numbers for each colors, the follow script
generates a several page pdf document which maybe a useful reference document for you.

source("http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.R")

A very useful RColorBrewer http://colorbrewer.org. This package will generate a ramp

color to provide color plattes that are sequential, diverging, and qualitative ramped, for example:

• Sequential palettes are suited to ordered data that progress from low to high. Lightness steps dominate
the look of these schemes, with light colors for low data values to dark colors for high data values.

• Diverging palettes put equal emphasis on mid-range critical values and extremes at both ends of the
data range. The critical class or break in the middle of the legend is emphasized with light colors and
low and high extremes are emphasized with dark colors that have contrasting hues.

• Qualitative palettes do not imply magnitude differences between legend classes, and hues are used to
create the primary visual differences between classes. Qualitative schemes are best suited to repre-
senting nominal or categorical data.

To see more about RColorBrewer run the example

library(RColorBrewer)
example(brewer.pal)

I use RColorBrewer to produce nicer colors in clustering heatmaps. For example if we look at the US
state fact and figure information in the package state, which contains a matrix called state.x77 containing
information on 50 US states (50 rows) on population, income, Illiteracy, life expectancy, murder, high school
graduation, number of days with frost, and area (8 columns). The default clustering of this uses a rather ugly
red-yellow color scheme which I changed to a red/brown-blue.

library(RColorBrewer)
hmcol <- colorRampPalette(brewer.pal(10, "RdBu"))(500)
heatmap(t(state.x77), col = hmcol, scale = "row")

103
 Alaska
Texas
Montana
California
Colorado
Wyoming
Oregon
New Mexico
Nevada
Arizona
West Virginia
Maine
South Carolina
Rhode Island
Delaware
Massachusetts
New Jersey
Hawaii
Connecticut
Maryland

104
Vermont
New Hampshire
North Dakota
Washington
Oklahoma
Missouri
South Dakota
Nebraska
Minnesota
Kansas
Utah
Idaho
New York
Ohio
Pennsylvania
Indiana
Virginia
Kentucky
Tennessee
Arkansas
Alabama
North Carolina
Louisiana
Mississippi
Georgia
Iowa
Wisconsin
Florida
Michigan
Illinois
Area

Frost
Murder
Income

Life Exp

Illiteracy
HS Grad
Population
5.5 Interacting with graphics
R also provides functions which allow users to extract or add information to a plot using a mouse via
locator() and verb+identify() functions respectively.
Identify members in a hierarchical cluster analysis of distances between European cities

hca <- hclust(eurodist)

plot(hca, main = "Distance between European Cities")
Distance between European Cities
4000
3000
2000
Height
1000

Stockholm
Athens
Rome
Gibraltar
Lisbon
Madrid
0

Barcelona
Marseilles
Copenhagen
Hamburg

Cherbourg
Munich
Vienna
Milan

Paris
Calais
Cologne
Brussels
Hook of Holland
Geneva
Lyons

eurodist
hclust (*, "complete")

(x <- identify(hca))
x

105
plot(1:20, rt(20, 1))
text(locator(1), "outlier", adj = 0)

Waits for the user to select locations on the current plot using the left mouse button.

attach(women)
plot(height, weight)
identify(height, weight, women)
detach(2)

Allow the user to highlight any of the points (identify(x,y,label)) defined by x and y (using
the left mouse button) by plotting the corresponding component of labels nearby (or the index number of
the point if labels is absent).
Right mouse click, to ”stop”.

106
5.5.1 Exercise 8 - Plotting
Using the women dataset

1. Set the plot layout to be a 2 x 2 grid (ie 2 rows, 2 columns)

2. Draw weight on the Y axis and height on the X axis.

3. Switch the orientation, Draw weight on the X axis and height on the Y axis.

4. Drawing a new plot, set the pch (point type) to be a solid circle, and color them red. Add a title ”study
of Women” to the plot

5. Drawing another plot, set the pch (point type) to be a solid square, Change the X axis label to be
”Weight of Women” and make the point size (using the parameter cex) larger to 1.5

107
5.6 Saving plots
5.6.1 Rstudio
In RStudio, there is a simple interface to export plots. Click on the ”Export” button in the plot window.

5.6.2 Devices
R can generate graphics (of varying levels of quality) on almost any type of display or printing device.
Before this can begin, however, R needs to be informed what type of device it is dealing with. This is done
by starting a device driver. The purpose of a device driver is to convert graphical instructions from R (”draw
a line,” for example) into a form that the particular device can understand. Device drivers are started by
calling a device driver function. There is one such function for every device driver: type help(Devices) for a
list of them all.
The most useful formats for saving R graphics:

postscript() For printing on PostScript printers, or creating PostScript graphics files.

pdf() Produces a PDF file, which can also be included into PDF files.

jpeg() Produces a bitmap JPEG file, best used for image plots.

5.6.3 Difference between vector and pixel images

Note there is a big difference between saving files in jpeg or postscript files. Image files save in jpg, bmp,
gif etc are pixel image files, these are like photographs, where you can just select a line and change its color.
By contact vector graphic, such as postscript, or windows meta files can be imported into drawing packages
such as Adobe illustrator (or some even into PowerPoint), you can double click on an axes, and since its a
vector graphic you can change the color of the line easily.
Format * Type Description (name) Designed for
TIFF, TIF image Tagged Image File Format High resolution printing of images, even to
postscript printers
PNG image Portable network graphic High resolution bitmap image,Screen dis-
play, printing
BMP image bitmap image Screen display under Windows
GIF image Graphic Interchange Format Screen display especially online im-
ages/Web
JPEG, JPG image Joint Photographic Experts Group Screen display especially online im- *
ages/Web
EPS, PS vector (Encapsulated) postscript High resolution printing of illustrations,
Printing to PostScript printers/Imagesetters
PDF vector Portable Document File High resolution printing of illustra-
tions, Printing to PostScript/PDF print-
ers/Imagesetters
EMF, WMF ** vector (Enhanced) Windows Metafile Screen display under Windows printing to
non-PostScript printer
For more information on image file format see http://en.wikipedia.org/wiki/Image_file_formats
** EMF files are a vector like files that can be inserted into PowerPoint. To insert an EMF image in a PowerPoint slide, click on
Insert-Picture-From File and locate the file. Click OK. This will add the EMF file to your page. Right mouse click on the image to
”ungroup”, now you can select lines/points to change colors/widths etc.
When in doubt, I save files an postscript format (eps), as several journals request this format. EPS files
can be open directly in adobe illustrator or other vector editing graphics packages.

108
 In R, to save the current image to file. Either use the file menu File -> Save as. Or use the functions
dev2bitmap, dev.copy2eps or dev.copy(device, le), where device can be one of png, jpeg or pdf and file is
your filename. For example:

plot(1:10, col = "red", pch = 19)

dev.copy(png, file = "test.png")
dev.off()

plot(1:10, col = "red", pch = 19)

dev.copy(pdf, file = "test.pdf")
dev.off()

To find out more about the image formats that can be saved in R, see the help on ?Devices.
If you wish to write an image directly to a file, without ”seeing” the plot screen (called X11 or Quartz
depending on the operating system). Use the functions pdf(), postscript(), jpeg() with the syntax:

pdf(file = "myplot.pdf")
plot(1:10, col = "blue", xlab = "X axis", ylab = "Y axis")
dev.off()

Remember it is very important to type dev.off in order to properly save the file
To list the current graphics devices that are open use dev.cur. When you have finished with a device, be
sure to terminate the device driver by issuing the command dev.off().
If you have open a device to write to for example pdf or png, dev.off will ensures that the device finishes
cleanly; for example in the case of hardcopy devices this ensures that every page is completed and has been
sent to the printer or file.
Example:

myPath <- file.path("P:/Bio503/Plots")

pdf(file = paste(myPath, "nicePlot.pdf", sep = ""))
x <- seq(0, 2 * pi, length = 100)
y <- sin(3 * x) + cos(x) + rnorm(100, sd = 0.2)
plot(x, y)
dev.off()

5.7 Useful Graphics Resources

If you have plots saved in a non-vector format, we have found the web-site VectorMagic from Stanford
http://vectormagic.stanford.edu/ to be very useful. It will convert bmp or jpeg files to vector
format.
The free software ImageMagick http://www.imagemagick.org can be downloaded and is also
useful for converting between image format.

109
Chapter 6

Advanced Graphics

6.1 Advanced plotting using Trellis; ggplots2, Lattice

One of the strengths of R is the variety and quality of its graphics capabilities. Both Lattice and ggplots2
offer trellis (layered graphics) which are both prettier and much more flexible than basic R plotting. Between
these two packages, there is no clear winner, but like Lattice other say ggplots2 is more flexible. But it is
worth investigating these packages if you wish to generate nice R graphics.

6.1.1 ggplots2
qplot is the basic plotting function in the ggplot2 package and is a convenient wrapper for creating a number
of different types of plots using a consistent calling scheme. See http://had.co.nz/ggplot2/
book/qplot.pdf for the chapter in the ggplot2 book which describes the usage of qplot in detail.
A nice introductions to ggplots is written by its author Hadley Wickham and is available from http://
www.ceb-institute.org/bbs/wp-content/uploads/2011/09/handout_ggplot2.pdf.
The following examples are taking from that tutorial
Basic ”Quick Plot” aka qplot in ggplots2

require("ggplot2")

## Loading required package: ggplot2

data(mtcars)
head(mtcars)

## mpg cyl disp hp drat wt qsec vs am gear

## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4
## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4
## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4
## Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3
## Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3
## Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3
## carb
## Mazda RX4 4
## Mazda RX4 Wag 4
## Datsun 710 1

110
## Hornet 4 Drive 1
## Hornet Sportabout 2
## Valiant 1

levels(mtcarscyl)

## NULL

qplot(wt, mpg, data = mtcars, colour = cyl)

35

30

cyl
25 4
5
mpg

6
20 7
8

15

10
2 3 4 5
wt

qplot(wt, mpg, data = mtcars, colour = factor(cyl))

111
 35

30

25 factor(cyl)
4
mpg

6
20 8

15

10
2 3 4 5
wt

mtcars is a dataset from 1974 Motor Trend US magazine, and comprises fuel consumption and 10
aspects of automobile design and performance (eg miles/gallon, number of cylinders, displacement, gross
horsepower, weight, seconds to complete a quarter mile, etc) for 32 automobiles. In the above plot we see a
plot of weight x miles per gallon given the number of cylinders in the car.
In the above plot, we view cylinder by color, but it could also be by shape or size

qplot(wt, mpg, data = mtcars, shape = factor(cyl))

35

30

25 factor(cyl)
4
mpg

6
20 8

15

10
2 3 4 5
wt

112
qplot(wt, mpg, data = mtcars, size = factor(cyl), colour = factor(cyl))

35

30

25 factor(cyl)
4
mpg

6
20 8

15

10
2 3 4 5
wt

The function mfrow and layout don’t work with ggplots2, so here is a little script to make layout of
multiple plots using ggplots2 (acknowledgement to Stephen Turner). First assign each ggplot2 plots to an
object, and then use the arrange function to display two or more.

arrange <- function(..., nrow = NULL, ncol = NULL, as.table = FALSE) {

vp.layout <- function(x, y) viewport(layout.pos.row = x,
layout.pos.col = y)
dots <- list(...)
n <- length(dots)
if (is.null(nrow)  is.null(ncol)) {
nrow <- floor(n/2)
ncol <- ceiling(n/nrow)
}
if (is.null(nrow)) {
nrow <- ceiling(n/ncol)
}
if (is.null(ncol)) {
ncol <- ceiling(n/nrow)
}
 NOTE see n2mfrow in grDevices for possible alternative

grid.newpage()
pushViewport(viewport(layout = grid.layout(nrow, ncol)))

113
 ii.p <- 1
for (ii.row in seq(1, nrow)) {
ii.table.row <- ii.row
if (as.table) {
ii.table.row <- nrow - ii.table.row + 1
}
for (ii.col in seq(1, ncol)) {
ii.table <- ii.p
if (ii.p > n)
break
print(dots[[ii.table]], vp = vp.layout(ii.table.row,
ii.col))
ii.p <- ii.p + 1
}
}
}

p1 <- qplot(wt, mpg, data = mtcars, shape = factor(cyl))

p2 <- qplot(wt, mpg, data = mtcars, size = factor(cyl), colour =
factor(cyl))
 Arrange and display the plots into a 2x1 grid
arrange(p1, p2, nrow = 1)

35 35

30 30

25 factor(cyl) 25 factor(cyl)
4 4
mpg

mpg

6 6
20 8 20 8

15 15

10 10
2 3 4 5 2 3 4 5
wt wt

Using Facets to plot several plots

114
qplot(wt, mpg, data = mtcars, facets = cyl ˜ .)

35

30

25

4
20

15

10
35

30

25
mpg

6
20

15

10
35

30

25

8
20

15

10
2 3 4 5
wt

More complex Facets to view cross-tabulated categories. For example you would expect a strong inter-
action between cylinder and horsepower.

table(mtcarscyl, mtcarshp)

##
## 52 62 65 66 91 93 95 97 105 109 110 113 123 150 175 180 205 215
## 4 1 1 1 2 1 1 1 1 0 1 0 1 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 3 0 2 0 1 0 0 0
## 8 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 1 1

115
##
## 230 245 264 335
## 4 0 0 0 0
## 6 0 0 0 0
## 8 1 2 1 1

qplot(wt, mpg, data = mtcars, facets = cyl ˜ hp, xlab = "Weight",

ylab = "Miles per Gallon")

52 62 65 66 91 93 95 97 105 109 110 113 123 150 175 180 205 215 230 245 264 335
35

30

25

4
20

15

10
35

30
Miles per Gallon

25

6
20

15

10
35

30

25
8

20

15

10
2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345 2345
Weight

In the scatterplot examples above, we implicitly used a point geom, the default when you supply two
arguments to qplot(). qplots can produce several other plots, if a different geom is defined
(modified from ggplots2: Elegant Graphics for Data Analysis, Chapter 3)

116
 Plot Geom Other features
scatterplot point
bubblechart point size defined by variable
barchart bar
box-whisper boxplot
line line

When given a single vector, the default geom is Histogram. Defining geom as density will instead draw
a density (smoothed histogram)

p1 <- qplot(wt, data = mtcars)

p2 <- qplot(wt, data = mtcars, binwidth = 0.01)
p3 <- qplot(wt, data = mtcars, geom = "density")
p4 <- qplot(wt, data = mtcars, geom = "density", colour = factor(cyl))
 Arrange and display the plots into a 2x1 grid
arrange(p1, p2, p3, p4, nrow = 2, ncol = 2)

## stat_bin: binwidth defaulted to range/30. Use binwidth = x to

## adjust this.

117
 5 3.0

2.5
4

2.0
3
count

count
1.5
2
1.0

1
0.5

0 0.0
2 3 4 5 2 3 4 5
wt wt

0.5 1.0

0.4 0.8

factor(cyl)
0.3 0.6
density

density

4
6
0.2 0.4 8

0.1 0.2

0.0 0.0
2 3 4 5 2 3 4 5
wt wt

Geoms - point and smooth and coord_polar (Pie Charts)

p1 <- qplot(wt, mpg, data = mtcars, geom = "line")

p2 <- qplot(wt, mpg, data = mtcars, geom = c("point", "smooth"),
method = "lm")

px <- ggplot(mtcars, aes(x = factor(1), fill = factor(cyl))) +

geombar(width = 1)
 map a barchart to a polar coordinate system
p3 <- px + coordpolar()
p4 <- px + coordpolar(theta = "y")
arrange(p1, p2, p3, p4, nrow = 2, ncol = 2)

118
 35 35

30
30

25
25
mpg

mpg
20
20
15

15
10

10 5
2 3 4 5 2 3 4 5
wt wt

30 0
30
25
20 factor(cyl) 5 factor(cyl)
15 1
factor(1)

10 4 25 4
count

5
0
6 6
8 10 8
20
15

factor(1) count

6.1.2 lattice
Lattice plots allow the use of the layout on the page to reflect meaningful aspects of data structure. They
offer abilities similar to those in the S-PLUS trellis library.
The lattice package sits on top of the grid package. To use lattice graphics, both these packages must be
installed. Providing it is installed, the grid package will be loaded automatically when lattice is loaded.
Resources for lattice

• Book on Lattice http://lmdvr.r-forge.r-project.org/figures/figures.html

• See examples at http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/

display.examples.html

119
 • To get on help on lattice functions, use help just like you would do for any package help(package =
lattice)

6.1.3 Examples that Present Panels of Scatterplots using xyplot()

The basic function for drawing panels of scatterplots is xyplot(). We will use the data frame ’Chick-
Weight’ to demonstrate the use of xyplot(). The ’ChickWeight’ data frame has 578 rows and 4 columns
from an experiment on the effect of diet on early growth of chicks. This data frame contains the following
columns:

weight a numeric vector giving the body weight of the chick (gm).

Time a numeric vector giving the number of days since birth when the measurement was made.

Chick an ordered factor with levels ’18’ ¡ ... ¡ ’48’ giving a unique identifier for the chick. The ordering
of the levels groups chicks on the same diet together and orders them according to their final weight
(lightest to heaviest) within diet.

Diet a factor with levels 1,...,4 indicating which experimental diet the chick received.

Figure below shows the style of graph that one can get from xyplot().

6.1.4 Simple use of xyplot

The lattice function xyplot() is the most commonly used lattice function, and plots pairs of variables. Whilst
designed mainly for two continuous variates, factors can be supplied as well, in which case they will simply
be coerced to numeric.

library(lattice)
xyplot(weight ˜ Time | Diet, data = ChickWeight)  Simple use of
xyplot

120
 0 5 10 15 20

3 4

300

200

100
weight

1 2

300

200

100

0 5 10 15 20

Time

Here is the statement used to get a figure with the observations for the same Chick connected via lines.

xyplot(weight ˜ Time | Diet, data = ChickWeight, panel =

panel.superpose,
groups = Chick, type = "b")

121
 0 5 10 15 20

3 4

300

200

100
weight

1 2

300

200

100

0 5 10 15 20

Time

This function shows the defaults for the graphical display of Trellis displays
show.settings()
An incomplete list of lattice Functions
splom( ˜ data.frame) # Scatterplot matrix
bwplot(factor ˜ numeric , . .) # Box and whisker plot
dotplot(factor ˜ numeric , . .) # 1-dim. Display
stripplot(factor ˜ numeric , . .) # 1-dim. Display
barchart(character ˜ numeric,...)
histogram( ˜ numeric, ...) # Histogram
densityplot( ˜ numeric, ...) # Smoothed version of histogram
qqmath(numeric ˜ numeric, ...) # QQ plot
splom( ˜ dataframe, ...) # Scatterplot matrix
parallelplot( ˜ dataframe, ...) # Parallel coordinate plots
In each instance, conditioning variables can be added.
Examples:

x <- 1:10
y <- 1:10
g <- factor(1:10)
barchart(y ˜ g | 1)

122
 1
10

6
y

1 2 3 4 5 6 7 8 9 10

More examples:Lattice density histogram splom and more

angle <- seq(0, 2 * pi, length = 21)[-21]

xx <- cos(angle)
yy <- sin(angle)
gg <- factor(rep(1:2, each = 10))

bwplot(yy ˜ gg | 1)

123
 1
1.0

0.5
yy

0.0

−0.5

−1.0

1 2

densityplot(˜ yy | 1)

0.4

0.3
Density

0.2

0.1

0.0

−2 −1 0 1 2

yy

124
histogram(˜ yy | 1)

1
25

20
Percent of Total

15

10

−1.0 −0.5 0.0 0.5 1.0

yy

qqmath(˜ yy | 1)

1
1.0

0.5
yy

0.0

−0.5

−1.0

−2 −1 0 1 2

qnorm

125
xyplot(xx ˜ yy | 1)

1
1.0

0.5
xx

0.0

−0.5

−1.0

−1.0 −0.5 0.0 0.5 1.0

yy

splom(˜ data.frame(x = xx[1:10], y = yy[1:10]) | 1, pscales = 0)

Scatter Plot Matrix

126
parallelplot(˜ data.frame(x = xx[1:10], y = yy[1:10]) | 1)

1
y

Min Max

More than two variables

aaa <- seq(0, pi, length = 10)

xxx <- rep(aaa, 10)
yyy <- rep(aaa, each = 10)
zzz <- sin(xxx) + sin(yyy)

levelplot(zzz ˜ xxx + yyy | 1, colorkey = FALSE)

127
 1
3.0

2.5

2.0
yyy

1.5

1.0

0.5

0.0

0.0 0.5 1.0 1.5 2.0 2.5 3.0

xxx

contourplot(zzz ˜ xxx + yyy | 1, labels = FALSE, cuts = 8)

1
3.0

2.5

2.0
yyy

1.5

1.0

0.5

0.0

0.0 0.5 1.0 1.5 2.0 2.5 3.0

xxx

128
cloud(zzz ˜ xxx + yyy | 1, zlab = NULL, zoom = 0.9, par.settings =
list(box.3d = list(lwd = 0.01)))

yyy
xxx

wireframe(zzz ˜ xxx + yyy | 1, zlab = NULL, zoom = 0.9, drape = TRUE,

par.settings = list(box.3d = list(lwd = 0.01)), colorkey = FALSE)

yyy
xxx

129
 Note whilst, lattice plots are highly customizable. Note: the base graphics settings; in particular, par()
settings usually have no effect on lattice plots. Use trellis.par.get() and trellis.par.set() to change default plot
parameters.

130
6.2 GoogleVis and GoogleMaps visualization
There are multiple visualization tools available within the googleVis library. These include the Hans Rosling
type bubble plots. See http://code.google.com/apis/visualization/documentation/
gallery/motionchart.html
See http://blog.revolutionanalytics.com/graphics/ for some exampels of R code

 install.packages(googleVis)
library(googleVis)

## Loading required package: RJSONIO

## Welcome to googleVis version 0.2.16
##
## Please read the Google API Terms of Use before you use the package:
## http://code.google.com/apis/terms/index.html
##
## Type ?googleVis to access the overall documentation and
## vignette(googleVis) for the package vignette. You can execute a
## demo of the package via: demo(googleVis)
##
## More information is available on the googleVis project web-site:
## http://code.google.com/p/google-motion-charts-with-r/
##
## Contact: <rvisualisation@gmail.com>
##
## To suppress the this message use:
## suppressPackageStartupMessages(library(googleVis))

M <- gvisMotionChart(Fruits, "Fruit", "Year")

plot(M)
cat(Mhtmlchart, file = "tmp.html")

GoogleVis also provide nice support for Maps and spatial visualization of trends.

 Pretty plots competition

library(googleVis)
help(package = "googleVis")

 looking at all loaded datasets

data(state)
states <- as.data.frame(state.x77)
stateslocation <- rownames(states)
attach(states)

## The following object(s) are masked from package:googleVis:

##
## Population

states.Inc <- gvisGeoMap(states, locationvar = "location",

131
 Figure 6.1: This is actually an interactive animated html file

numvar = "Income", options = list(region = "US", dataMode =

"regions",
colors = "[0xBEBEBE, 0x00008B]"))
 note this is per capita income by state from 1974

plot(states.Inc)

states.Illit <- gvisGeoMap(states, locationvar = "location",

numvar = "Illiteracy", options = list(region = "US", dataMode =
"regions",
colors = "[0xBEBEBE, 0x8B0000]"))
plot(states.Illit)

merge <- gvisMerge(states.Inc, states.Illit, horizontal = FALSE)

merge.plot <- plot(merge)
detach(states)

For alternative approaches to spatial or info Maps see http://ryouready.wordpress.com/

2009/11/16/infomaps-using-r-visualizing-german-unemployment-rates-by-color-on-a-ma
Also see the packages RgoogleMaps which provide a comfortable R interface to query the Google server
for static maps, and to also use the map as a background image to overlay plots within R.
Another packages is osmar (OpenStreetMap and R) which package provides infrastructure to access
OpenStreetMap data.

132
 Figure 6.2: This is actually an interactive html file, if you hover over a state you see its information

6.3 Graph theory and Network visualization using R packages network and
igraph

 install.packages(network)
library(network)

## network: Classes for Relational Data Version 1.7-1 created on March

## 1, 2012. copyright (c) 2005, Carter T. Butts, University of
## California-Irvine Mark S. Handcock, University of Washington David
## R. Hunter, Penn State University Martina Morris, University of
## Washington For citation information, type citation("network").
## Type help("network-package") to get started.

m <- matrix(rbinom(100, 1, 1.5/9), 10)

diag(m) <- 0

133
g <- network(m)
 Plot the graph
plot(g)

 Load Padgetts marriage data

data(flo)
nflo <- network(flo)
 Display the network, indicating degree and flagging the Medicis
plot(nflo, vertex.cex = apply(flo, 2, sum) + 1, usearrows = FALSE,
vertex.sides = 3 + apply(flo, 2, sum), vertex.col = 2 +
(network.vertex.names(nflo) ==

134
 "Medici"))

using the package igraph

 install.packages(igraph)
library(igraph)

## Attaching package: igraph

## The following object(s) are masked from package:network:
##
## %c%, %s%, add.edges, add.vertices, delete.edges, delete.vertices,
## get.edge.attribute, get.edges, get.vertex.attribute, is.bipartite,

135
## is.directed, list.edge.attributes, list.vertex.attributes,
## set.edge.attribute, set.vertex.attribute

adj.mat <- matrix(sample(c(0, 1), 9, replace = TRUE), nr = 3)

g <- graph.adjacency(adj.mat)
plot(g)

136
6.4 Tag Clouds, Literature Mining
The following script will create tag cloud given a list of PubMed abstract identifiers.

 -------------------------------------------------------- Given a
 list of PMIDs get their annotation Aedin, Dec 2011 To Run given
 pmids2tagcloud a list of pmids eg pmids=c(10521349, 10582678,
 11004666, 11108479, 11108479, 11114790, 11156382, 11156382,
 11156382, 11165872) pmids2tagcloud(pmids)
 ---------------------------------------------------------
getPMIDAnnot <- function(pmidlist) {
require(annotate)
require(XML)
print("Using annotate and XML to get info on each PMID")
pubmedRes <- xmlRoot(pubmed(pmidlist))
numAbst <- length(xmlChildren(pubmedRes))
absts <- list()
for (i in 1:numAbst) {
absts[[i]] <- buildPubMedAbst(pubmedRes[[i]])
}

 unlist(lapply(absts, function(x) authors(x)[1]))

 Write Output to PMIDInfo

PMIDInfo <- data.frame(matrix(NA, nrow = length(pmidlist)))
PMIDInfoFirstAuthor <- unlist(lapply(absts, function(x)
authors(x)[1]))
PMIDInfoJournal <- unlist(lapply(absts, function(x)
journal(x)[1]))
PMIDInfopubDate <- unlist(lapply(absts, function(x)
pubDate(x)[1]))
PMIDInfoarticleTitle <- unlist(lapply(absts, function(x)
articleTitle(x)[1]))
PMIDInfoabstText <- unlist(lapply(absts, function(x)
abstText(x)[1]))
PMIDInfoPubMedID <- unlist(lapply(absts, function(x) pmid(x)[1]))
rownames(PMIDInfo) <- PMIDInfoPubMedID
PMIDInfo <- PMIDInfo[, -1]

 Res<-cbind(outMat, Total= apply(outMat, 1, sum), PMIDInfo[,c(5,

 1,3,4,2)]) RespubDate<-unlist(strsplit(RespubDate,  ))[seq(2,
 length(RespubDate)*2, 2)] names(Res)[10] =Year print(Res)

 print(PMIDInfo[1:2,])
return(PMIDInfo)
}

137
pmids2tagcloud <- function(pmids, addTitle = TRUE, colorPalette =
c("orange",
"cyan", "green4", "maroon", "slateblue")) {
require(tm)
require(wordcloud)
require(RColorBrewer)
print(paste("Using tm and wordcloud to create tag cloud from",
length(pmids),
"abstracts"))
pubmedAbsts <- getPMIDAnnot(as.character(unique(pmids)))
words <-
tolower(unlist(strsplit(as.character(pubmedAbstsabstText),
" ")))
 remove parentheses, comma, [semi-]colon, period, quotation marks
words <- words[-grep("[\\)\\(,;:\\.\\\\\"]", words)]
words <- words[-grep("\\d+", words)]
words <- words[!words in stopwords()]
wt <- table(words)

 Use R Color Brewer Colors

pal <- brewer.pal(9, "BuGn")
pal <- pal[-(1:4)]

wordcloud(names(wt), as.vector(wt), colors = colorPalette)

if (addTitle)
title(main = paste("TagCloud generated from", length(pmids),
"PubMed Abstracts"), sub = paste("PMIDS:", paste(pmids,
collapse = " "),
sep = ""), cex.sub = 0.5, col.main = "green4", col.sub =
"gray")
}

pmids <- c(10521349, 10582678, 11004666, 11108479, 11108479,

11114790, 11156382, 11156382, 11156382, 11165872)
pmids2tagcloud(pmids)

## [1] "Using tm and wordcloud to create tag cloud from 10 abstracts"

## [1] "Using annotate and XML to get info on each PMID"

138
 TagCloud generated from 10 PubMed Abstracts

approach tumor cancer

cell molecular samples
determine breast

cdna expression
tissue specific measured
provide
class phenotypic pulmonary
c−jun consists cellular dna
signaling set microdissection vivo development

mcf+sod
grade revealed array
data results antisense
human sets found ap−1 blots mnsod
up−regulated normal et rat
profile classes

leukemia
classification
gadd153 analysis using
microarray mnsod−induced
acute diffuse target
genes capture
laser

cells
gene

PMIDS:10521349 10582678 11004666 11108479 11108479 11114790 11156382 11156382 11156382 11165872

6.5 Other visualization resources

Note whilst we have only looked at ”static” plotting, R can generate dynamic plots using R packages Jav-
aGD or ggobi and http://www.ggobi.org/. Dynamic plots can be interactively manipulated, rotated
or animated. see http://cran.r-project.org/src/contrib/Views/Graphics.html.
Other visualization resources that you may like to explore

1. Rggobi http://www.ggobi.org/rggobi/ 3D visualization of multidimensional data http:

//www.ggobi.org/rggobi/introduction.pdf

2. For a discussion on different graph packages see

139
 using Rgraphviz http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/
r/rgraphviz/ or see the many examples on the bioconuductor website
a recent discussion online about the topic: http://stats.stackexchange.com/questions/
6155/graph-theory-analysis-and-visualization
R cytoscape http://db.systemsbiology.net:8080/cytoscape/RCytoscape/vignette/
RCytoscape.html

3. Additional demos available in the graphics package: demo(image), demo(persp) and example(symbol).

The following web pages have many examples (and code) to produce different R plots. Browse through
the plots, see what you like and try some.

• Basic plotting examples from Paul Murrell book, R Graphics http://www.stat.auckland.

ac.nz/˜paul/RGraphics/rgraphics.html

• The homepage of the R package ggplot2 http://had.co.nz/ggplot2/. This package pro-

duces nice plots and can easily add color scale legend bars to plots

• rggobi and ggplot2 run workshops in R graphics. Their course website provides examples of ba-
sic and advanced plots, animated movies, lectures and R code to reproduce the plots at http:
//lookingatdata.com/

• The R Gallery wiki provides examples of R plots and code to reproduce these http://addictedtor.
free.fr/graphiques/. Here is one random sample from this website:

6.6 Summary on plotting

• Basic plotting:

– plot(), pairs(), histogram, pie etc

– Low-level plotting: points(), lines(), abline()

low-level other: text(), legend(), title()

• Manipulating the plotting window

– Temporary changes to just one command: “  ” argument to plot() function

– To view or change default plot settings: par(). This will change the settings for all subsequent
plot commands.

• Advanced plotting using ggplots2 library.

140
Chapter 7

Statistical Analysis, linear models and

survival analysis in R

7.1 This section

1. Basic statistics such as t-test, χ2 ,. . .

2. Intro to linear models in R

3. Model formulae and model options

4. Output and extraction from fitted models

5. model.matrix, contrasts

6. Models considered:

• Linear regression: lm()

• Logistic regression: glm(), Poisson regression: glm()

• Survival analysis: Surv(), coxph() in the survival and functions in the package survcomp

7. Advanced model options are covered in detail in the recommended text of Venables and Ripley.

• Generalized Linear Mixed-Effects Models lmer, lme

• Generalized additive models gam()

• Non-Linear models nls, nlme

• Other useful packages lme4, gmodels

• The arm package contains R functions for Bayesian inference using lm, glm, mer and polr
objects. The bayesm is aims at markefting and micro economics fields but includes functions
for Bayes Regression and Hierarchical Linear Models.

• The R package doBy is useful for groupwise computations of summary statistics. Facilities
for groupwise computations of summary statistics and other facilities for working with grouped
data (similar to what can be achieved by proc means or proc summary of the sas system).

141
• See http://cran.r-project.org/src/contrib/Views/ for lists of more R pack-
ages.

142
7.2 Basic Statistics
7.2.1 Continuous Data: t test
The t.test performs a one or two sample t test. To see the arguments of t.test, look at the help documentation
?t.test
Arguments include alternative which is one of ”two.sided”, ”less” or ”greater”, and var.equal which is
a logical (FALSE or TRUE) to indicate unequal or equal variance (default is unequal). The input to t.test is
one vector (one sample t test), two vectors or a formula (two sample t test). A formula is given by y ∼ x,
where the tilde ’∼’ operator specifies ”described by”
One sample t test:

data(ChickWeight)
ChickWeight[1:2, ]

## weight Time Chick Diet

## 1 42 0 1 1
## 2 51 2 1 1

t.test(ChickWeight[, 1], mu = 100)

##
## One Sample t-test
##
## data: ChickWeight[, 1]
## t = 7.38, df = 577, p-value = 5.529e-13
## alternative hypothesis: true mean is not equal to 100
## 95 percent confidence interval:
## 116.0 127.6
## sample estimates:
## mean of x
## 121.8
##

Two sample t test. Note these are equivalent

t.test(ChickWeightweight[ChickWeightDiet == "1"],
ChickWeightweight[ChickWeightDiet ==
"2"])

##
## Welch Two Sample t-test
##
## data: ChickWeight$weight[ChickWeight$Diet == "1"] and ChickWeight$weight[ChickW
## t = -2.638, df = 201.4, p-value = 0.008995
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -34.900 -5.042
## sample estimates:

143
## mean of x mean of y
## 102.6 122.6
##

t.test(weight ˜ Diet, data = ChickWeight, subset = Diet in

c("1", "2"))

##
## Welch Two Sample t-test
##
## data: weight by Diet
## t = -2.638, df = 201.4, p-value = 0.008995
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -34.900 -5.042
## sample estimates:
## mean in group 1 mean in group 2
## 102.6 122.6
##

For a pairwise comparisons or multiple testing use:

pairwise.t.test(ChickWeightweight, ChickWeightDiet, p.adjust.method =

"bonferroni")

##
## Pairwise comparisons using t tests with pooled SD
##
## data: ChickWeight$weight and ChickWeight$Diet
##
## 1 2 3
## 2 0.06838 - -
## 3 2.5e-06 0.14077 -
## 4 0.00026 0.95977 1.00000
##
## P value adjustment method: bonferroni

7.2.2 adjusting for multiple testing

The p.adjust can be used to correct p-values for multiple testing. Adjustment methods include the Bonferroni
correction in which the p-values are multiplied by the number of comparisons. Less conservative corrections
are also included by Holm (1979) (”holm”), Hochberg (1988) (”hochberg”), Hommel (1988) (”hommel”),
Benjamini and Hochberg (1995) (”BH” or its alias ”fdr”), and Benjamini and Yekutieli (2001) (”BY”)

x <- rnorm(50, mean = c(rep(0, 25), rep(3, 25)))

p <- 2 * pnorm(sort(-abs(x)))

144
pVal <- round(p, 3)
Bonferroni <- round(p.adjust(p, "bonferroni"), 3)

 FDR and BH are equivalent

FDR <- round(p.adjust(p, "fdr"), 3)

BH <- round(p.adjust(p, "BH"), 3)

res <- cbind(none = pVal, Bonferroni = Bonferroni, FDR = FDR,

BH = BH)
res <- res[order(res[, "Bonferroni"]), ]
print(res[1:20, ])

## none Bonferroni FDR BH

## [1,] 0.000 0.001 0.001 0.001
## [2,] 0.000 0.003 0.001 0.001
## [3,] 0.000 0.008 0.002 0.002
## [4,] 0.000 0.010 0.002 0.002
## [5,] 0.000 0.010 0.002 0.002
## [6,] 0.000 0.021 0.003 0.003
## [7,] 0.000 0.023 0.003 0.003
## [8,] 0.001 0.040 0.005 0.005
## [9,] 0.001 0.042 0.005 0.005
## [10,] 0.001 0.056 0.006 0.006
## [11,] 0.001 0.065 0.006 0.006
## [12,] 0.002 0.096 0.008 0.008
## [13,] 0.003 0.143 0.011 0.011
## [14,] 0.003 0.163 0.011 0.011
## [15,] 0.003 0.165 0.011 0.011
## [16,] 0.004 0.187 0.011 0.011
## [17,] 0.004 0.197 0.011 0.011
## [18,] 0.004 0.204 0.011 0.011
## [19,] 0.010 0.505 0.027 0.027
## [20,] 0.016 0.784 0.039 0.039

7.2.3 Continuous Data: One- and two-way analysis of variance

To run a one-way analysis of variance, use lm. To use lm, the input is a vector and a factor. Note here that
Diet is a factor. The function lm provides limited information. Use summary to provide a short summary of
the distribution of each of the variables. Extract the analysis of variance with anova.

lmDiet <- lm(weight ˜ Diet, data = ChickWeight)

lmDiet

##
## Call:

145
## lm(formula = weight ˜ Diet, data = ChickWeight)
##
## Coefficients:
## (Intercept) Diet2 Diet3 Diet4
## 102.6 20.0 40.3 32.6
##

summary(lmDiet)

##
## Call:
## lm(formula = weight ˜ Diet, data = ChickWeight)
##
## Residuals:
## Min 1Q Median 3Q Max
## -104.0 -53.6 -13.6 40.4 230.1
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 102.65 4.67 21.96 < 2e-16 ***
## Diet2 19.97 7.87 2.54 0.011 *
## Diet3 40.30 7.87 5.12 4.1e-07 ***
## Diet4 32.62 7.91 4.12 4.3e-05 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## Residual standard error: 69.3 on 574 degrees of freedom
## Multiple R-squared: 0.0535,Adjusted R-squared: 0.0485
## F-statistic: 10.8 on 3 and 574 DF, p-value: 6.43e-07
##

anova(lmDiet)

## Analysis of Variance Table

##
## Response: weight
## Df Sum Sq Mean Sq F value Pr(>F)
## Diet 3 155863 51954 10.8 6.4e-07 ***
## Residuals 574 2758693 4806
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

In some statistical packages, the sum of the squares are labeled ”between groups” and ”within groups”.
Since lm and anova tables are used for a wide range of statistical models, the output from R is different. The
Between groups sum of the squares is labeled by the name of the factor groupings (Diet). The within sum of
the squares is labeled Residuals. The aov function is a wrapper which calls lm, but express the results these
in the traditional language of the analysis of variance rather than that of linear models.

146
 For examples of different analysis of variance (using aov) at http://personality-project.
org/r/r.anova.html

aov(weight ˜ Diet, data = ChickWeight)

## Call:
## aov(formula = weight ˜ Diet, data = ChickWeight)
##
## Terms:
## Diet Residuals
## Sum of Squares 155863 2758693
## Deg. of Freedom 3 574
##
## Residual standard error: 69.33
## Estimated effects may be unbalanced

For a two-way analysis of variance, provide a second factor to lm

lmDiet <- lm(weight ˜ Diet + Time, data = ChickWeight)

summary(lmDiet)

##
## Call:
## lm(formula = weight ˜ Diet + Time, data = ChickWeight)
##
## Residuals:
## Min 1Q Median 3Q Max
## -136.8 -17.1 -2.6 15.0 141.8
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 10.924 3.361 3.25 0.0012 **
## Diet2 16.166 4.086 3.96 8.6e-05 ***
## Diet3 36.499 4.086 8.93 < 2e-16 ***
## Diet4 30.233 4.107 7.36 6.4e-13 ***
## Time 8.750 0.222 39.45 < 2e-16 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## Residual standard error: 36 on 573 degrees of freedom
## Multiple R-squared: 0.745,Adjusted R-squared: 0.744
## F-statistic: 419 on 4 and 573 DF, p-value: <2e-16
##

anova(lmDiet)

## Analysis of Variance Table

##

147
## Response: weight
## Df Sum Sq Mean Sq F value Pr(>F)
## Diet 3 155863 51954 40.1 <2e-16 ***
## Time 1 2016357 2016357 1556.4 <2e-16 ***
## Residuals 573 742336 1296
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

7.2.4 Discrete Data: Contingency Table

A contingency table (also referred to as cross tabulation or cross tab) is often used to record and analyze
the relation between two or more discrete/categorical variables. It displays the (multivariate) frequency
distribution of the variables in a matrix format. Test for association between such categorical variables are
very common in research. Given two factors of at least 2 (usually unordered) levels, you can use the package
vcd to compute several association statistics for a contingency table.
The simplest
√ measure of association between two categorical variables is the φ coefficient defined by
χ2
φ= N
n (Oi −Ei )2
with N is the total number of observation and χ2 = i=1 Ei

where

χ2 = Pearson’s cumulative test statistic

Oi = an observed frequency;

Ei = an expected (theoretical) frequency, asserted by the null hypothesis;

n = the number of cells in the table.

Another measure of association is the Cramer’s V statistic that is generalizable to rectangular contin-
gency table
√
χ2
V = N (k−1) ,
k being the number of rows or the number of columns, whichever is less.
See http://en.wikipedia.org/wiki/Contingency_table for more details about measure of
association in a contingency table.
In R, first create a contingency table and then use the function assocstats to computes the Pearson chi-
Squared test, the Likelihood Ratio, chi-Squared test, the phi coefficient, the contingency coefficient, and
Cramer’s V statistics.

 load library
library(vcd)

## Loading required package: colorspace

148
 load data
attach(Arthritis)

 check the variables of interest

is.factor(ArthritisTreatment)

## [1] TRUE

print(levels(ArthritisTreatment))

## [1] "Placebo" "Treated"

is.factor(ArthritisImproved)

## [1] TRUE

print(levels(ArthritisImproved))

## [1] "None" "Some" "Marked"

 build the contingency table

tab <- table(ArthritisTreatment, ArthritisImproved)
print(tab)

##
## None Some Marked
## Placebo 29 7 7
## Treated 13 7 21

 compute statistics
res <- assocstats(tab)
print(res)

## Xˆ2 df P(> Xˆ2)

## Likelihood Ratio 13.530 2 0.0011536
## Pearson 13.055 2 0.0014626
##
## Phi-Coefficient : 0.394
## Contingency Coeff.: 0.367
## Cramers V : 0.394

detach(Arthritis)

The structure of the res object can be printed using the str function

149
str(res)

## List of 5
## $ table : table int [1:2, 1:3] 29 13 7 7 7 21
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : chr [1:2] "Placebo" "Treated"
## .. ..$ : chr [1:3] "None" "Some" "Marked"
## $ chisq_tests: num [1:2, 1:3] 13.52981 13.05502 2 2 0.00115 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : chr [1:2] "Likelihood Ratio" "Pearson"
## .. ..$ : chr [1:3] "Xˆ2" "df" "P(> Xˆ2)"
## $ phi : num 0.394
## $ contingency: num 0.367
## $ cramer : num 0.394
## - attr(*, "class")= chr "assocstats"

You can easily access the various statistics from the res object

 Pearson chi squared test

print(reschisqtests[2, ])

## Xˆ2 df P(> Xˆ2)

## 13.055020 2.000000 0.001463

 Cramers V statistic
print(rescramer)

## [1] 0.3942

If you want to compute the agreement between two classifications or raters, you can estimate the κ
coefficient which can have the following typical values
Kappa value magnitude of agreement
<0 no
0 - 0.2 small
0.2 - 0.4 fair
0.4 - 0.6 moderate
0.6 - 0.8 substantial
0.8 - 1 almost perfect

 two random classification

set.seed(12345)
c1 <- sample(0:1, 100, replace = TRUE)
c2 <- sample(0:1, 100, replace = TRUE)
tab <- table(C1 = c1, C2 = c2)
Kappa(x = tab, weights = matrix(rep(1, 4), ncol = 2))

## value ASE

150
## Unweighted -0.04839 0.10073
## Weighted NaN 0.08598

In a practical situation, your Kappa coefficient needs to be over 0.6 to claim that your categorization is
valid. You may also want to report both the agreement (%)

agr <- sum(diag(tab))/sum(tab)

cat(sprintf("Agreement: .2g\n", agr))

## Agreement: 0.48%

7.2.5 Common statistical Tests in R

Here is a quick (incomplete) list of useful R functions for basic statistical comparisons:

• Continuous Data

– t.test

– pairwise.t.test: pairwise comparisons

– var.test: comparison of two variances.

– lm(y∼x): linear regression analysis

– lm(y∼f1): one-way analysis of variance

– lm(y∼f1+f2): two-way analysis of variance (ANOVA), f1 and f2 are factors.

– lm(y∼f1+x): analysis of co-variance

– lm(y∼x1+x2+x3): multiple regression analysis

– bartlett.test: Bartlett’s test of the null that the variances in each of the groups (samples) are the
same

• Non-Parametric

– wilcox.test: one- and two-sample Wilcoxon tests on vectors of data; the latter is also known as
Mann-Whitney test.

– kruskal.test: non-parametric one-way analysis of variance.

– friedman.test: non-parametric two-way analysis of variance.

• Correlation
cor, cor.test: correlation and Correlation tests. Cor.test methods include ”kendall” ”spearman” or
”pearson”.

• Discrete response data

151
 – chisq.test: chi-squared contingency table tests, sher.test exact test for small tables.

– binom.test: binomial test

– prop.test: prop.trend.test comparison of proportions.

– glm(y x1+x2+x3, binomial): logistic regression

* As a complete aside and to continue stories of Ireland’s mathematicians and statisticians, which I started with the story of
George Boole, the first professor of mathematics of University College Cork. The t statistic was introduced by William Sealy
Gosset to monitoring the quality of brewing in the Guinness brewery in Dublin, Ireland. Guinness’s has an innovative policy of
recruiting the best graduates from Oxford and Cambridge to apply biochemistry and statistics to Guinness’ industrial processes.
Gosset published the t test in Biometrika in 1908, but published using the pen name Student.

152
7.3 Model formulae and model options
• Most modeling done in a standard way

• Data set is usually a single data frame object

• Model is fitted using model tting function

• Form of the model specified by a formula

• Resulting tted model object can be interrogated, analyzed and modified

Basic output of the model fitting process is minimal. Details obtained via extractor functions.

153
7.3.1 Model formulae
We have already seen in several functions (boxplot, t.test, lm) that a simply function is defined by y ∼ x.
We will now discuss formulae in much more detail.

Define a template for statistical models

p
∑
yi = βj xij + i , i ∼ NID(0, σ 2 ), i = 1,    , n
j=0

In the matrix form this model is

y = Xβ + 
where y is the response vector, X is the model matrix or design matrix with columns x0 , x1 ,    , xp .
NOTATION:
y, x, x0, x1, x2, ... - numeric variables
A, B, C, ... - factors

Examples of model formula with numeric variables:

y ˜ x
y ˜ 1 + x - simple regression (first - implicit intercept,
second - explicit intercept)
----------------------------------------------------------------------
y ˜ 0 + x
y ˜ x - 1
y ˜ -1 + x - regression through the origin
----------------------------------------------------------------------
y ˜ x1 + x2 + x3 - multiple regression
----------------------------------------------------------------------
y ˜ x + I(xˆ2) - quadratic regression
----------------------------------------------------------------------
log(y) ˜ x1 + x2 - multiple regression of transformed variable
Examples of model formula with factors and numeric variables:
y ˜ A - single analysis of variance model
y ˜ A + x - single analysis of covariance model with
covariate x
----------------------------------------------------------------------
y ˜ A* B
y ˜ A + B + A:B - two-factor model with interaction
----------------------------------------------------------------------
y ˜ (A + B + C)ˆ2 - all two-factor interactions
----------------------------------------------------------------------
y ˜ A*B + Error(C) - two factor model with interaction and error
strata determined by C

154
 General form:

response ˜ op_1 term_1 + op_2 term_2 + ...

where

response - a vector or expression evaluating to a vector defining the

response variable
op_i - an operator, either + (inclusion of a term)
or - (exclusion of a term) in the model
term_i - either a vector or matrix expression,
or 1, a factor,
or a formula expression consisting of factors, vectors or
matrices connected by formula operators.

7.3.2 Example of linear regression

Will use data ’cats’ from the MASS library.

library(MASS)
help("cats")
str(cats)

## data.frame: 144 obs. of 3 variables:

## $ Sex: Factor w/ 2 levels "F","M": 1 1 1 1 1 1 1 1 1 1 ...
## $ Bwt: num 2 2 2 2.1 2.1 2.1 2.1 2.1 2.1 2.1 ...
## $ Hwt: num 7 7.4 9.5 7.2 7.3 7.6 8.1 8.2 8.3 8.5 ...

cats.lmB <- lm(Hwt ˜ Bwt, data = cats)

cats.lmS <- lm(Hwt ˜ Sex, data = cats)
cats.lmBS <- lm(Hwt ˜ Bwt + Sex, data = cats)
cats.lmBxS <- lm(Hwt ˜ Bwt * Sex, data = cats)
cats.lmB2 <- lm(Hwt ˜ Bwt + I(Bwt2), data = cats)

155
7.3.3 Contrasts, model.matrix
We need to understand how model formulae specify the columns of the model matrix.

1. Continuous variables (simplest): each variable provides a column of the model matrix (and the inter-
cept will provide a column of ones if included in the model).

2. k-level factor A
The answer differs for unordered and ordered factors.

• Unordered factors
k − 1 columns are generated for the indicators of the second, third, . . . , up to kth levels of the
factor. (Implicit parameterization is to contrast the response at each level with that at the first.)

• Ordered factors
k − 1 columns are the orthogonal polynomials on 1,    , k, omitting the constant term.

If the intercept is omitted in a model that contains a factor term, the first such term is encoded into k
columns giving the indicators for all the levels.
R default setting is:

options(contrasts = c("contr.treatment", "contr.poly"))

Contrasts can be defined using the contrasts or C function Example

contr.treatment(n = 3, base = 2)

## 1 3
## 1 1 0
## 2 0 0
## 3 0 1

contr.sum(n = 3)

## [,1] [,2]
## 1 1 0
## 2 0 1
## 3 -1 -1

156
7.4 Exercise 9

 What is the difference in output?

lm(Hwt ˜ Sex, data = cats)

##
## Call:
## lm(formula = Hwt ˜ Sex, data = cats)
##
## Coefficients:
## (Intercept) SexM
## 9.20 2.12
##

lm(Hwt ˜ Sex - 1, data = cats)

##
## Call:
## lm(formula = Hwt ˜ Sex - 1, data = cats)
##
## Coefficients:
## SexF SexM
## 9.2 11.3
##

model.matrix is useful to view the terms in the fitted model.

157
7.5 Output and extraction from tted models
As mentioned earlier, the printed output of the model fit is minimal. However, the value of a fitted model
object is stored in an object. Information about the fitted model can be displayed, extracted and plotted.
Extractor functions:

coef(obj) - regression coefficients

resid(obj) - residuals
fitted(obj) - fitted values
summary(obj) - analysis summary
predict(obj,newdata = ndat) - predict for new data
deviance(obj) - residual sum of squares
print(obj) - Print concise summary
plot(obj) - produce diagnostic plots
formula(obj) - extract the model formula
anova(obj1, obj2) - compare 2 models (one is a submodel with the outer model)
step(obj) - add, drop terms
update(obj, formula) - update a model with a new formula

Let’s go back to the cats example. Now, we can extract more information about the fits.

attach(cats)
cats.lmBS <- lm(Hwt ˜ Bwt + Sex, data = cats)
coef(cats.lmBS)

## (Intercept) Bwt SexM

## -0.4150 4.0758 -0.0821

fit.catsBS <- fitted(cats.lmBS)

cats.lmBxS <- lm(Hwt ˜ Bwt * Sex, data = cats)

fit.catsBxS <- fitted(cats.lmBxS)

Plot these 2 models.

plot(Bwt, Hwt)
lines(Bwt, fit.catsBS, col = "green", lwd = 2)  OR
 abline(cats.lmBS, col=green, lwd=2)
lines(Bwt[Sex == "F"], fit.catsBxS[Sex == "F"], col = "red")
lines(Bwt[Sex == "M"], fit.catsBxS[Sex == "M"], col = "blue")
legend(x = 2, y = 20, legend = c("LMBS", "lmBxS.female", "lmBxS.male"),
col = c("green", "red", "blue"), lwd = c(2, 1, 1))

158
 20
LMBS
lmBxS.female
lmBxS.male
18
16
14
Hwt
12
10
8
6

2.0 2.5 3.0 3.5

Bwt

Prediction of Hwt values

predict(cats.lmBxS, data.frame(Bwt = seq(2, 5, 1), Sex = "M"))

## 1 2 3 4
## 7.441 11.754 16.067 20.379

detach(cats)

Some more useful, but non-standard, ways of extracting information from a model.

df.residual(obj) - residual degrees of freedom

names(obj) - gives names of the components in obj

159
names(summary(obj)) - gives names of the components in summary(obj)

How to get the residual variance of the fit? There are at least 2 ways. The first is the direct calculation

var.catsB <- deviance(cats.lmB)/df.residual(cats.lmB)  direct

calculation
var.catsB <- summary(cats.lmB)sigma2

160
7.6 Exercise 10 :Multivariate linear regression
• Read the data contained in the file lungs.csv from the course website into R. Fit a multivariate
regression model (function lm) of pemax using all variables. Call the result lungFit.

• Which terms appear to be significant (summary)?

• What is the residual error of this model?

• Which are the most and least significant variables in this model?

161
7.6.1 Residual plots, diagnostics
Important part of modeling - checking the model assumptions. Some easy to check and interpret model
diagnostics

1. Fit to the data (predictions) vs. raw data (observations)

2. Histogram of the residuals

3. Scatterplot of the residuals vs. fitted values

4. QQ-plot of the residuals

attach(cats)
plot(Bwt, Hwt, main = "Model fit")
abline(cats.lmB, col = "green", lwd = 2)

Fit the model

hist(resid(cats.lmB), main = "Residual histogram")

Residual histogram

plot(fitted(cats.lmB), resid(cats.lmB), main = "Residuals vs. fitted

values")
lines(lowess(fitted(cats.lmB), resid(cats.lmB)), col = "red")
abline(h = 0)

Residuals vs. tted values

qqnorm(resid(cats.lmB))
qqline(resid(cats.lmB))
detach()

QQ-plot of residuals

162
 Model fit Residual histogram

40
18

30
Frequency
14
Hwt

20
10

10
8

0
6
2.0 2.5 3.0 3.5 −4 −2 0 2 4 6

Bwt resid(cats.lmB)

Residuals vs. fitted values Normal Q−Q Plot

4

4
Sample Quantiles
resid(cats.lmB)

2
0

0
−2

−2
8 10 12 14 −2 −1 0 1 2

fitted(cats.lmB) Theoretical Quantiles

Figure 7.1: Plots of the fitted Model,Residuals vs. fitted values and QQ-PLots of the residuals

Default plots available in plot of class lm

par(mfrow = c(2, 2))

plot(cats.lmB, which = 1:4, id.n = 5)

163
 6

4
144 144

3
4 135
135

Standardized residuals
71
71

2
2
Residuals

1
0

0
−1
−2

31

−2
140 31
−4

140

8 10 12 14 −2 −1 0 1 2
Fitted values Theoretical Quantiles
Scale−Location Cook's distance

0.35
144
144

0.30
135 140
1.5

31 71
Standardized residuals

0.25
Cook's distance
0.20
1.0

0.15

140
0.10
0.5

135
0.05

136
142
0.00
0.0

8 10 12 14 0 20 40 60 80 100 120 140

Fitted values Obs. number

7.6.2 ANOVA and updating models

Anova tables for a sequence of fitted models

anova(obj_1, obj_2) - compare two models where obj_1 and obj_2 are two regression

The sums of squares shown are the decrease in the residual sums of squares resulting from an inclusion
of that term in the model at that place in the sequence. Only for orthogonal experiments will the order of
inclusion be inconsequential.

164
anova(cats.lmB, cats.lmBS)

## Analysis of Variance Table

##
## Model 1: Hwt ˜ Bwt
## Model 2: Hwt ˜ Bwt + Sex
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 142 300
## 2 141 299 1 0.155 0.07 0.79

anova(cats.lmB, cats.lmBxS)

## Analysis of Variance Table

##
## Model 1: Hwt ˜ Bwt
## Model 2: Hwt ˜ Bwt * Sex
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 142 300
## 2 140 291 2 8.49 2.04 0.13

anova(cats.lmB, cats.lmBS, cats.lmBxS)

## Analysis of Variance Table

##
## Model 1: Hwt ˜ Bwt
## Model 2: Hwt ˜ Bwt + Sex
## Model 3: Hwt ˜ Bwt * Sex
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 142 300
## 2 141 299 1 0.15 0.07 0.785
## 3 140 291 1 8.33 4.01 0.047 *
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

The update() function allows a model to be fitted that differs from one previously fitted usually by just a
few additional or removed terms.
Syntax:
new.model <- update(old.model, new.formula)
Special name in the new formula - a period ’.’ - can be used to stand for “corresponding part of the old
model formula”.
Example:
Data set mtcars, fuel consumption and 10 aspects of automobile design and performance for 32 auto-
mobiles.

help("mtcars")
cars.lm <- lm(mpg ˜ hp + wt, data = mtcars)
cars.lm2 <- update(cars.lm, . ˜ . + disp)

165
 cars.lms <- update(cars.lm2, sqrt(.) ˜ .)

what does the following do?

 anova(cars.lm, cars.lm2, cars.lms)

anova(cars.lm, cars.lm2)

## Analysis of Variance Table

##
## Model 1: mpg ˜ hp + wt
## Model 2: mpg ˜ hp + wt + disp
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 29 195
## 2 28 195 1 0.0571 0.01 0.93

7.6.3 Model selection

There are functions in R automating the choice of terms in the statistical models. Adding, dropping and
performing stepwise selection in a sequence of models.

• Dropping terms: drop1() or dropterm() from the MASS library

• Adding terms: add1() or addterm() from the MASS library

• Stepwise selection: step() or stepAIC() from the MASS library

More details:

dropterm Fits all models that differ from the current model by dropping a single term, maintaining marginal-
ity.

dropterm(model.big, test=F) # for linear models

dropterm(model.big, test=Chisq) # for generalized linear models

addterm Fits all models that differ from the current model by adding a single term from those supplied,
maintaining marginality

addterm(model.small, scope=model.big, test=F) # for linear models

stepAIC Performs stepwise model selection by exact AIC

stepAIC(model.small,
scope=list(upper=model.big, lower= ˜1),
test=F) # for linear models

166
Example
Data set mtcars

# Fit regression model with all other covariates as predictors

cars.all <- lm(mpg ˜ ., data=mtcars)
# Drop terms
dropterm(cars.all, test = "F")

# Probably not appropriate analysis. Try

cars.some <- lm(mpg ˜ factor(cyl) + hp + wt + disp + qsec + factor(gear),
data=mtcars)
dropterm(cars.some, test = "F")

# Start with one variable

cars.sm <- update(cars.some, .˜ wt)
addterm(cars.sm, cars.some, test=F)

# Stepwise selection
cars.step <- stepAIC(cars.some, scope=list(lower = ˜ wt))

7.7 Cross-validation
Another approach, developed by the machine Learning community, is cross-validation. The idea is to
sequentially divide the dataset in training and test sets to fit and assess the performance of the model,
respectively. This approach enables to use all the observations both for training and testing the prediction
model.
Here is an example of a 10-fold cross-validation on the mtcars dataset where we compare the model
with one variable (wt) and all the variables to predict mpg. Once the root mean squared error (RMSE) is
computed for each fold, a paired Wilcoxon Rank Sum test is used to compare the performance of the small
and big models.

nfold <- 10
 nr is the number of observations
nr <- nrow(mtcars)
 nfold is the number of folds in the cross-validation
if (nfold > 1) k <- floor(nr/nfold) else {
k <- 1
nfold <- nr
}
smpl <- sample(nr)
mse.big <- mse.small <- NULL

for (i in 1:nfold) {
if (i == nfold)
s.ix <- smpl[c(((i - 1) * k + 1):nr)] else s.ix <- smpl[c(((i -
1) * k + 1):(i * k))]
 fit the model

167
 mm.big <- lm(mpg ˜ ., data = mtcars[-s.ix, , drop = FALSE])
mm.small <- lm(mpg ˜ wt, data = mtcars[-s.ix, , drop = FALSE])
 assess the performance of the model
pp.big <- predict(object = mm.big, newdata = mtcars[s.ix,
!is.element(colnames(mtcars),
"mpg")])
pp.small <- predict(object = mm.small, newdata = mtcars[s.ix,
!is.element(colnames(mtcars),
"mpg")])
 compute mean squared error (MSE)
mse.big <- c(mse.big, sqrt(mean((mtcars[s.ix, "mpg"] - pp.big)2)))
mse.small <- c(mse.small, sqrt(mean((mtcars[s.ix, "mpg"] -
pp.small)2)))
}
names(mse.big) <- names(mse.small) <- paste("fold", 1:nfold,
sep = ".")

 compare the performance of the big and small models using a

 Wilcoxon Rank Sum test
wilcox.test(mse.big, mse.small, paired = TRUE, alternative = "less")

##
## Wilcoxon signed rank test
##
## data: mse.big and mse.small
## V = 35, p-value = 0.7842
## alternative hypothesis: true location shift is less than 0
##

As can be seen, there is not enough evidence in the dataset to claim that the big prediction model
outperforms the small one (p-value > 005). You can easily change the number of folds in the cross-
validation by setting the variable nfold to another value, nf old = 1 for leave-one-out cross-validation.

168
7.8 Statistical models
Will talk today about 3 classes of statistical models: linear regression, generalized linear models (e.g. logis-
tic and Poisson regression), and survival models.

7.8.1 Linear Regression: Weighted Models, Missing Values

We have talked and went through examples of linear regression using the function lm(). Will expand here
on the options for the function lm()

lm(formula, data, subset, weights, na.action, ...)

subset - (optional) a subset of observations to be used in the fitting process

weights - (optional) weights to fit the model using weighted list squares method

na.action - what happens to data containing missing values ’NA’s;

na.omit - is the default; another option na.fail

attach(ChickWeight)
time.wgt <- tapply(weight, Time, var)
time.wgt.rep <- as.numeric(time.wgt[match(Time,
as.numeric(names(time.wgt)))])
detach(2)
Chick.anl <- data.frame(ChickWeight, time.wgt.rep = time.wgt.rep)
chick.lm.wgt <- lm(weight ˜ Time, data = Chick.anl, weight =
1/time.wgt.rep)
chick.lm.T0 <- lm(weight ˜ Time, data = Chick.anl, subset = (Time ==
0))

169
7.8.2 Generalized linear modeling
• One generalization of multiple linear regression.

• Response, y, predictor variables x1 , x2 ,    , xp

• The distribution of Y depends on the x’s through a single linear function, the ’linear predictor’

ν = β1 x1 + β 2 x2 +    + βp xp (7.1)

with xi having no influence on y if and only if βi = 0

• There may be an unknown ’scale’ (or ’variance’) parameter φ to estimate as well

• The mean, µ, is a smooth invertible function of the linear predictor

µ = m(ν), ν = m−1 (µ) = l(µ) (7.2)

and this inverse function, l(), is called the link function

• The deviance is a generalization of the residual sum of squares.

• The protocols are very similar to linear regression and the inferential logic is virtually identical.

The class of generalized linear models handled by facilities supplied in R includes gaussian, binomial,
poisson, inverse gaussian and gamma response distributions.
Families of distributions and links

Distribution Link
------------- -------------------------------
binomial logit, probit, log, cloglog
gaussian identity, log, inverse
Gamma identity, inverse, log
inverse.gaussian 1/muˆ2, identity, inverse, log
poisson identity, log, sqrt

The R function to fit a generalized linear model is glm() which uses the form

fitted.model <- glm(formula, family=family.generator, data=data.frame)

The only difference from lm() is the family.generator, which is the instrument by which the family is
described. It is the name of a function that generates a list of functions and expressions that together define
and control the model and estimation process.
We will concentrate on the binomial family with the logit link or as you probably know it ’logistic
regression’,.

Logistic regression
To fit a binomial model using glm() there are three possibilities for the response:

1. If the response is a vector it is assumed to hold binary data, and so must be a 0/1 vector.

2. If the response is a two-column matrix it is assumed that the first column holds the number of suc-
cesses for the trial and the second holds the number of failures.

170
 3. If the response is a factor, its first level is taken as failure (0) and all other levels as ’success’ (1).
Syntax:
glm(y ˜ x, family=binomial(link=logit), data = data.frame)
Link is optional, since the default link is logit. Necessary, if another link is desired, e.g. probit.
Example of logistic regression using data set esophagus
Data from a case-control study of (o)esophageal cancer in Ile-et-Vilaine, France containing records for 88
age/alcohol/tobacco combinations with the 3 covariates grouped into 6, 4 and 4 groups respectively.

summary(esoph)

## agegp alcgp tobgp ncases

## 25-34:15 0-39g/day:23 0-9g/day:24 Min. : 0.00
## 35-44:15 40-79 :23 10-19 :24 1st Qu.: 0.00
## 45-54:16 80-119 :21 20-29 :20 Median : 1.00
## 55-64:16 120+ :21 30+ :20 Mean : 2.27
## 65-74:15 3rd Qu.: 4.00
## 75+ :11 Max. :17.00
## ncontrols
## Min. : 1.0
## 1st Qu.: 3.0
## Median : 6.0
## Mean :11.1
## 3rd Qu.:14.0
## Max. :60.0

effects of alcohol and tobacco, age-adjusted

eso.age <- glm(cbind(ncases, ncontrols) ˜ agegp, data = esoph,

family = binomial())

eso.base <- glm(cbind(ncases, ncontrols) ˜ agegp + tobgp +

alcgp, data = esoph, family = binomial())

eso.base <- update(eso.age, . ˜ . + tobgp + alcgp)

eso.TA <- glm(cbind(ncases, ncontrols) ˜ agegp + tobgp * alcgp,

data = esoph, family = binomial())
eso.2way <- glm(cbind(ncases, ncontrols) ˜ (agegp + tobgp +
alcgp)2, data = esoph, family = binomial())

Stepwise model selection

eso.base <- glm(cbind(ncases, ncontrols) ˜ agegp + tobgp +

alcgp, data = esoph, family = binomial())
eso.stp <- stepAIC(eso.age, scope = list(upper = ˜ agegp +
tobgp + alcgp, lower = ˜ 1), test = "Chisq")

171
## Start: AIC=298.6
## cbind(ncases, ncontrols) ˜ agegp
##
## Df Deviance AIC LRT Pr(Chi)
## + alcgp 3 64.6 230 74.5 4.5e-16 ***
## + tobgp 3 120.0 286 19.1 0.00026 ***
## <none> 139.1 299
## - agegp 5 227.2 377 88.1 < 2e-16 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## Step: AIC=230.1
## cbind(ncases, ncontrols) ˜ agegp + alcgp
##
## Df Deviance AIC LRT Pr(Chi)
## + tobgp 3 54.0 226 10.6 0.014 *
## <none> 64.6 230
## - agegp 5 138.8 294 74.2 1.4e-14 ***
## - alcgp 3 139.1 299 74.5 4.5e-16 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## Step: AIC=225.4
## cbind(ncases, ncontrols) ˜ agegp + alcgp + tobgp
##
## Df Deviance AIC LRT Pr(Chi)
## <none> 54.0 226
## - tobgp 3 64.6 230 10.6 0.014 *
## - alcgp 3 120.0 286 66.1 3.0e-14 ***
## - agegp 5 131.5 293 77.5 2.8e-15 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

Prediction and residuals Plot the fitted values for ’age’ effect

attach(esoph)
eso.pred.age <- predict.glm(eso.base, data.frame(agegp = agegp,
tobgp = rep("30+", 88), alcgp = rep("40-79", 88)), type =
"response")
plot(eso.pred.age ˜ agegp, ylab = "Predicted Age", xlab = "Age group
(True age)")

172
 0.4
0.3
Predicted Age
0.2
0.1

25−34 35−44 45−54 55−64 65−74 75+

Age group (True age)

detach(esoph)

4 types of residuals can be requested for the glm() models: deviance, working, Pearson, response

opar <- par(mfrow = c(2, 2))

for (i in c("deviance", "working", "pearson", "response"))
plot(resid(eso.base,
type = i), ylab = i, pch = 19, col = "red")
mtext("Different types of residuals", line = -2, outer = T,
cex = 1.2)

173
 Different types of residuals

15
1

10
deviance

working
0

5
−1

0
0 20 40 60 80 0 20 40 60 80
Index Index
4

0.4
3

0.2
2

response
pearson
1

0.0
0

−0.2
−1

0 20 40 60 80 0 20 40 60 80
Index Index

par(opar)

7.8.3 Other packages

• Tibshirani and Hastie’s provide elastic net, lasso, ridge regression, adaptive lasso and the adaptive
elastic net regularized generalized linear models available in the package glmnet

• Other packages for machine learning are listed on http://cran.r-project.org/web/views/

MachineLearning.html

174
7.9 Survival modeling

Survival Analysis is a class of statistical methods for studying the occurrence and timing of events.
These methods are most often applied to the study of deaths but can also handle different kinds of
events, including the onset of disease and equipment failure for instance. For instance a disease
consists of a transition from an healthy state to a diseased state. Moreover, the timing of the event is
also considered for analysis.
Survival data have a common feature, namely censoring, that is difficult to handle with conventional
statistical methods. Consider the following example, which illustrates the problem of censoring. A
sample of breast cancer patients were followed during 10 years after diagnosis. The event of interest
was the appearance of a distant metastasis (a tumor initiated from the primary breast tumor cells and
that is located in another organ). The aim was to determine how the occurrence and timing of distant
metastasis appearance depended on several variables.

7.9.1 Censored Data

An observation on a random variable t is right-censored if all you know about t is that it is greater
than some value c. In survival analysis, t is typically the time of occurrence for some event, and cases
are right-censored because observation is terminated before the event occurs.
Random censoring occurs when observations are terminated for reasons that are not under the control
of the investigator. This situation can be illustrated in our example. Patients who are still free of
distant metastasis after 10 years are censored by a mechanism identical to that applied to the singly
right-censored data. But some patients may move away, and it may be impossible to contact them.
Some patients may die from another cause. Still other patients may refuse to participate after, say, 5
years. These kinds of censoring are depicted in Figure 7.2, where the symbol ”+” for the patients A
and C indicates that observation is censored at that point in time.

Figure 7.2: Randomly censored data.

The vast majority of the he functions we need to do survival analysis are in the package survival.
Check if the package survival is already loaded into your work space, if it isn’t load the library
survival

search()
library(survival)

## Loading required package: splines

We will work with the data set ’leukemia’ containing times of death or censoring in patients with
Acute Myelogenous Leukemia. The survival data are usually stored in a Surv object that is a one-
column matrix containing the survival times and events/censoring.

data(leukemia)
head(leukemia)

175
## time status x
## 1 9 1 Maintained
## 2 13 1 Maintained
## 3 13 0 Maintained
## 4 18 1 Maintained
## 5 23 1 Maintained
## 6 28 0 Maintained

?(Surv)
mysurv <- Surv(leukemiatime, leukemiastatus)
head(mysurv)

## [1] 9 13 13+ 18 23 28+

Several methods for survival analysis are implemented in R, mainly in the survival package:

Surv - creates a survival object used as a response variable in a model formula,

e.g. Surv(time, status)

survt - computes an estimate of a survival curve for censored data using the Kaplan-Meier method,
e.g. survt(Surv(time, status) group)

survdiff - Tests if there is a difference between two or more survival curves,

e.g. survdiff(Surv(time, status) group)

survreg - regression for a parametric survival model with special case, the accelerated failure models
that use a log transformation of the response.

coxph - fits a Cox proportional hazards regression model

7.9.2 Kaplan-Meier curve estimation

We can easily draw the survival curve of patients representing the proportion of patients who survived
over time. We provide the function survt with the following set of arguments:

survfit(formula, data, weights, subset, na.action,

newdata, individual=F, conf.int=.95, se.fit=T,
type=c("kaplan-meier","fleming-harrington", "fh2"),
error=c("greenwood","tsiatis"),
conf.type=c("log","log-log","plain","none"),
conf.lower=c("usual", "peto", "modified"))

# To see help on this function or a description of these arguments

?survfit

176
leuk.km <- survfit(Surv(time, status) ˜ x, data = leukemia)
plot(leuk.km, lty = 1, col = c("darkblue", "darkred"))
legend(100, 1, legend = c("Maintain", "Non-main"), lty = 1:2,
col = c("darkblue", "darkred"))
1.0

Maintain
Non−main
0.8
0.6
0.4
0.2
0.0

0 50 100 150

Compute confidence intervals and plot them

leuk.km2 <- survfit(Surv(time, status) ˜ x, data = leukemia,

conf.type = "log-log")
summary(leuk.km2)

## Call: survfit(formula = Surv(time, status) ˜ x, data = leukemia, conf.type =

##
## x=Maintained
## time n.risk n.event survival std.err lower 95% CI upper 95% CI
## 9 11 1 0.909 0.0867 0.5081 0.987
## 13 10 1 0.818 0.1163 0.4474 0.951
## 18 8 1 0.716 0.1397 0.3502 0.899
## 23 7 1 0.614 0.1526 0.2658 0.835
## 31 5 1 0.491 0.1642 0.1673 0.753
## 34 4 1 0.368 0.1627 0.0928 0.657
## 48 2 1 0.184 0.1535 0.0117 0.525

177
##
## x=Nonmaintained
## time n.risk n.event survival std.err lower 95% CI upper 95% CI
## 5 12 2 0.8333 0.1076 0.48171 0.956
## 8 10 2 0.6667 0.1361 0.33702 0.860
## 12 8 1 0.5833 0.1423 0.27014 0.801
## 23 6 1 0.4861 0.1481 0.19188 0.730
## 27 5 1 0.3889 0.1470 0.12627 0.650
## 30 4 1 0.2917 0.1387 0.07240 0.561
## 33 3 1 0.1944 0.1219 0.03120 0.461
## 43 2 1 0.0972 0.0919 0.00575 0.349
## 45 1 1 0.0000 NaN NA NA
##

plot(leuk.km2, mark.time = FALSE, conf.int = TRUE, lty = 1,

col = c("darkblue", "darkred"))
legend(100, 1, legend = c("Maintain", "Non-main"), lty = 1:2,
col = c("darkblue", "darkred"))

178
 1.0
Maintain
Non−main

0.8
0.6
0.4
0.2
0.0

0 50 100 150

Test for difference (log-rank test)

survdiff(Surv(time, status) ˜ x, data = leukemia)

## Call:
## survdiff(formula = Surv(time, status) ˜ x, data = leukemia)
##
## N Observed Expected (O-E)ˆ2/E (O-E)ˆ2/V
## x=Maintained 11 7 10.69 1.27 3.4
## x=Nonmaintained 12 11 7.31 1.86 3.4
##
## Chisq= 3.4 on 1 degrees of freedom, p= 0.0653

179
7.9.3 Cox proportional hazards model

The (semi-parametric) Cox regression model refers to the method first proposed in 1972 by the British
statistician Cox in his seminal paper “Regression Models and Life Tables”. It is difficult to exaggerate
the impact of this paper. In the 1992 Science Citation Index, it was cited over 800 times, making it the
most highly cited journal article in the entire literature of statistics. In fact, Garfield reported that its
cumulative citation count placed it among the top 100 papers in all branches of science.
This enormous popularity can be explained by the fact that, unlike the parametric methods, Cox’s
method does not require the selection of some particular probability distribution to represent survival
times. For this reason, the method is called semi-parametric. Cox made two significant innovations.
First, he proposed a model that is often referred to as the proportional hazards model. Second, he
proposed a new estimation method that was later named maximum partial likelihood. The term Cox
regression refers to the combination of the model and the estimation method
Here is an example of Cox regression estimating the benefit of maintaining chemotherapy of with
respect to the survival of the patients.

leuk.ph <- coxph(Surv(time, status) ˜ x, data = leukemia)

summary(leuk.ph)

## Call:
## coxph(formula = Surv(time, status) ˜ x, data = leukemia)
##
## n= 23, number of events= 18
##
## coef exp(coef) se(coef) z Pr(>|z|)
## xNonmaintained 0.916 2.498 0.512 1.79 0.074 .
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## xNonmaintained 2.5 0.4 0.916 6.81
##
## Concordance= 0.619 (se = 0.073 )
## Rsquare= 0.137 (max possible= 0.976 )
## Likelihood ratio test= 3.38 on 1 df, p=0.0658
## Wald test = 3.2 on 1 df, p=0.0737
## Score (logrank) test = 3.42 on 1 df, p=0.0645
##

 plot(leuk.km2, mark.time=F, lty=1:2) lines(survfit(leuk.ph),

 lty=1:2, lwd=2)

It is not trivial to estimate the relevance of a variable with survival. If this variable is categorical,
you can draw the survival curves and statistically compare them. If the variable under interest is
continuous you can arbitrarily discretize it (not advisable) or use many existing performance criteria
published so far for survival analysis: hazard ration (see coxph), D.index, concordance.index, time-

180
dependent ROC curve, Brier score,. . . The survcomp package contains functions to estimate these
criteria.

181
7.10 Exercise 11: Survival Anlaysis

– Use the colon dataset from the library survival

– draw the Kaplan-Meier survival curves for the three group of patients encode by ’rx’.

– Use different colors for the curves and plot the lines twice as thick as the default size (parameter
lwd).

– Which color encodes which group? Add a legend to the plot to make this clear.

– Generate a PDF output of the plot and put it in the website dropbox along with your code.

– Test if the different patient group have signicantly different outcome?

182
Chapter 8

Solutions to Exercises

8.1 Solution to Exercise 1

Women Data

myURL <-
"http://bcb.dfci.harvard.edu/˜ aedin/courses/Bioconductor/Women.txt"
women <- read.table(myURL, sep = "\t", header = TRUE)
?(colnames)
women

## height weight age

## 1 58 115 33
## 2 59 117 34
## 3 60 120 37
## 4 61 123 31
## 5 62 126 31
## 6 63 129 34
## 7 64 132 31
## 8 65 135 39
## 9 66 139 35
## 10 67 142 34
## 11 68 146 34
## 12 69 150 36
## 13 70 154 33
## 14 71 159 30
## 15 72 164 37

class(women)

## [1] "data.frame"

str(women)

183
## data.frame: 15 obs. of 3 variables:
## $ height: int 58 59 60 61 62 63 64 65 66 67 ...
## $ weight: int 115 117 120 123 126 129 132 135 139 142 ...
## $ age : int 33 34 37 31 31 34 31 39 35 34 ...

nrow(women)

## [1] 15

ncol(women)

## [1] 3

dim(women)

## [1] 15 3

summary(women)

## height weight age

## Min. :58.0 Min. :115 Min. :30.0
## 1st Qu.:61.5 1st Qu.:124 1st Qu.:32.0
## Median :65.0 Median :135 Median :34.0
## Mean :65.0 Mean :137 Mean :33.9
## 3rd Qu.:68.5 3rd Qu.:148 3rd Qu.:35.5
## Max. :72.0 Max. :164 Max. :39.0

colMeans(women)

## height weight age

## 65.00 136.73 33.93

colnames(women)

## [1] "height" "weight" "age"

?(colnames)
sum(womenweight < 120)

## [1] 2

women[order(womenweight), ]

184
## height weight age
## 1 58 115 33
## 2 59 117 34
## 3 60 120 37
## 4 61 123 31
## 5 62 126 31
## 6 63 129 34
## 7 64 132 31
## 8 65 135 39
## 9 66 139 35
## 10 67 142 34
## 11 68 146 34
## 12 69 150 36
## 13 70 154 33
## 14 71 159 30
## 15 72 164 37

mean(womenheight[womenweight > 124  womenweight < 150])

## [1] 65

rownames(women)[5] <- "Lucy"

8.2 Solution to Exercise 2

ToothGrowth data

TG <- read.table("ToothGrowth.txt", sep = "\t", header = TRUE)

TG2 <- read.csv("ToothGrowth.csv")
nrow(TG)

## [1] 60

nrow(TG2)

## [1] 60

mean(TGlen)

## [1] 18.81

sd(TGlen)

## [1] 7.649

185
mean(TG2len)

## [1] 18.81

sd(TG2len)

## [1] 7.649

anova(lm(len ˜ supp + dose, data = TG))

## Analysis of Variance Table

##
## Response: len
## Df Sum Sq Mean Sq F value Pr(>F)
## supp 1 205 205 11.4 0.0013 **
## dose 1 2224 2224 124.0 6.3e-16 ***
## Residuals 57 1023 18
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

8.3 Solution to Exercise 3

women <-
read.table("http://bcb.dfci.harvard.edu/˜ aedin/courses/R/WomenStats.txt",
sep = "\t", header = TRUE)
nrow(women)

## [1] 16

ncol(women)

## [1] 1

colnames(women)

## [1] "X.html."

summary(women)

## X.html.
## </div> :2
## </body> :1

186
## </head> :1
## </html> :1
## </td></tr></table> :1
## <body style=background-color:#fff>:1
## (Other) :9

rownames(women) <- LETTERS[1:nrow(women)]

write.table(women, "modifedWomen.txt", sep = "\t")
women2 <- read.table("modifedWomen.txt", sep = "\t", as.is = TRUE,
header = TRUE)

8.4 Solution to Exercise 4

myVec <- c(LETTERS[1:20], seq(0, 200, 10))

myVec

## [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J"
## [11] "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T"
## [21] "0" "10" "20" "30" "40" "50" "60" "70" "80" "90"
## [31] "100" "110" "120" "130" "140" "150" "160" "170" "180" "190"
## [41] "200"

myVec <- sample(myVec)

myVec

## [1] "T" "70" "80" "200" "160" "130" "Q" "M" "100" "120"
## [11] "180" "30" "S" "110" "50" "N" "I" "190" "C" "10"
## [21] "A" "F" "140" "P" "0" "20" "B" "G" "150" "J"
## [31] "40" "L" "60" "90" "H" "E" "170" "R" "K" "D"
## [41] "O"

cat(myVec, file = "myVec.txt")

scan("myVec.txt", n = 10, what = "text")

## [1] "T" "70" "80" "200" "160" "130" "Q" "M" "100" "120"

scan("myVec.txt", n = 10, what = 123)

## Error: scan() expected a real, got T

scan("myVec.txt", n = 10, what = TRUE)

## Error: scan() expected a logical, got 70

187
8.5 Solution to Exercise 5

for (i in 1:10) print(2i)

## [1] 2
## [1] 4
## [1] 8
## [1] 16
## [1] 32
## [1] 64
## [1] 128
## [1] 256
## [1] 512
## [1] 1024

x <- 1
while (2x < 1000) {
print(2x)
x <- x + 1
}

## [1] 2
## [1] 4
## [1] 8
## [1] 16
## [1] 32
## [1] 64
## [1] 128
## [1] 256
## [1] 512

8.6 Solution to Exercise 6

require(XML)
 Reads all the tables in the webpage into a list
worldPop <-
readHTMLTable("http://en.wikipedia.org/wiki/Worldpopulation")

 There are 19 tables

class(worldPop)

## [1] "list"

188
length(worldPop)

## [1] 19

 With the following names, so of the names are very long so we

 have trucated them using substr
substr(names(worldPop), 1, 60)

## [1] "NULL"
## [2] "toc"
## [3] "NULL"
## [4] "World population milestones (USCB estimates)"
## [5] "The 10 countries with the largest total population:"
## [6] "10 most densely populated countries (with population above 1"
## [7] "Countries ranking highly in terms of both total population ("
## [8] "NULL"
## [9] "UN (medium variant 2010 revision) and US Census Bureau (De"
## [10] "UN 2008 estimates and medium variant projections (in million"
## [11] "World historical and predicted populations (in millions)[102"
## [12] "World historical and predicted populations by percentage dis"
## [13] "Estimated world population at various dates (in millions)"
## [14] "Starting at 500 million"
## [15] "Starting at 375 million"
## [16] "NULL"
## [17] "NULL"
## [18] "NULL"
## [19] "NULL"

worldPop <- worldPop[[13]]  Just look at Table 13

To tidy up this tables, lets look at dates after 1750AD, so lets remove rows 1 to 14 as these have only
world population information. Also we will remove row 32 which is just column names

 Now lets check the structure of the table The data are factors,
 lets convert to characters as these are easier to edit
str(worldPop)

## data.frame: 32 obs. of 9 variables:

## $ Year : Factor w/ 32 levels "10,000 BC","1000",..: 27 1 30
## $ World : Factor w/ 32 levels "< 0.015","1",..: 1 2 14 22 29
## $ Africa : Factor w/ 19 levels "","1,022","106",..: 1 1 1 1 1
## $ Asia : Factor w/ 19 levels "","1,398","1,542",..: 1 1 1 1
## $ Europe : Factor w/ 19 levels "","163","203",..: 1 1 1 1 1 1
## $ Latin America[Note 1]: Factor w/ 19 levels "","16","167",..: 1 1 1 1 1 1
## $ Northern America : Factor w/ 19 levels "","172","187",..: 1 1 1 1 1 1

189
## $ Oceania : Factor w/ 17 levels "","12.8","14.3",..: 1 1 1 1 1
## $ Notes : Factor w/ 6 levels "","[104]","[105]",..: 2 1 1 3

 We need to convert them to numeric. But first lets get rid of

 the BC and < characters

worldPop <- apply(worldPop, 2, as.character)

str(worldPop)

## chr [1:32, 1:9] "70,000 BC" "10,000 BC" "9000 BC" ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:9] "Year" "World" "Africa" "Asia" ...

 Remove rows 1-14, 32

worldPop <- worldPop[-c(1:14, 32), ]

 Remove Notes Column

worldPop <- worldPop[, -9]

 Lets convert to numeric and remove the period

worldPop <- apply(worldPop, 2, function(x) as.numeric(sub(",",
"", x)))
worldPop <- as.data.frame(worldPop)

 Lets get rid of Note 1 To get rid of the square brakets we

 have to put \\ before them
colnames(worldPop) <- sub("\\[Note 1\\]", "", colnames(worldPop))
str(worldPop)

## data.frame: 17 obs. of 8 variables:

## $ Year : num 1750 1800 1850 1900 1950 ...
## $ World : num 791 978 1262 1650 2519 ...
## $ Africa : num 106 107 111 133 221 247 277 314 357 408 ...
## $ Asia : num 502 635 809 947 1398 ...
## $ Europe : num 163 203 276 408 547 575 601 634 656 675 ...
## $ Latin America : num 16 24 38 74 167 191 209 250 285 322 ...
## $ Northern America: num 2 7 26 82 172 187 204 219 232 243 ...
## $ Oceania : num 2 2 2 6 12.8 14.3 15.9 17.6 19.4 21.5 ...

 In what year did the population of Europe, Africa and Asia exceed
 500 million?
for (i in c("Europe", "Asia", "Africa")) {

190
 print(paste(i, min(worldPopYear[worldPop[, i] > 500]), sep = "
"))
}

## [1] "Europe 1950"

## [1] "Asia 1750"
## [1] "Africa 1985"

Now that the data are tidy, lets create the bonus plot

 Make a vector regions (exclude World and Year)

regions <- colnames(worldPop)[-c(1:2)]
regions

## [1] "Africa" "Asia" "Europe"

## [4] "Latin America" "Northern America" "Oceania"

 Create a empty Plot

plot(worldPopYear, worldPopAsia, xlab = "Year", ylab =
"Population (millions)",
col = "red", type = "n", ylim = c(200, 4000))

for (i in 1:length(regions)) {
region <- regions[i]
print(region)
lines(worldPopYear, worldPop[, region], col = i, type = "l")
}

## [1] "Africa"
## [1] "Asia"
## [1] "Europe"
## [1] "Latin America"
## [1] "Northern America"
## [1] "Oceania"

legend("topleft", regions, fil = 1:length(regions))

191
 4000
Africa
Asia
Europe
Latin America
Northern America
Oceania
3000
Population (millions)
2000
1000

1750 1800 1850 1900 1950 2000

Year

8.7 Solution to Exercise 7

TG <- read.table("ToothGrowth.txt", sep = "\t", header = TRUE)

summary(TG)

## len supp dose

## Min. : 4.2 OJ:30 Min. :0.50
## 1st Qu.:13.1 VC:30 1st Qu.:0.50
## Median :19.2 Median :1.00
## Mean :18.8 Mean :1.17
## 3rd Qu.:25.3 3rd Qu.:2.00

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## Max. :33.9 Max. :2.00

par(mfrow = c(1, 2))

boxplot(TGlen ˜ TGsupp, col = 2:4, las = 2, xlab = "Treatment",
ylab = "Tooth Length")
boxplot(TGlen ˜ paste(TGsupp, TGdose), col = rep(2:3, each = 3),
las = 2, xlab = "Treatment and Dose", ylab = "Tooth Length")

8.8 Solution to Exercise 8

par(mfrow = c(2, 2))

data(women)
attach(women)
plot(height, weight)
plot(weight, height)
plot(weight, height, pch = 19, col = "red", main = "Study of
Women")
plot(weight, height, xlab = "Weight of Women (lbs)", ylab = "height
of women (inches)",
pch = 15, col = "red", cex = 1.5)

193
 72
160

70
150

68
66
weight

height
140

64
130

62
60
120

58
58 60 62 64 66 68 70 72 120 130 140 150 160
height weight

Study of Women
72

72
70

70
height of women (inches)
68

68
66

66
height
64

64
62

62
60

60
58

58

120 130 140 150 160 120 130 140 150 160
weight Weight of Women (lbs)

194
8.9 Solution to Exercise 9

mod1 <- lm(Hwt ˜ Sex, data = cats)

model.matrix(mod1)[1:10, ]

## (Intercept) SexM
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 6 1 0
## 7 1 0
## 8 1 0
## 9 1 0
## 10 1 0

mod1 <- lm(Hwt ˜ Sex - 1, data = cats)

model.matrix(mod1)[1:10, ]

## SexF SexM
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 6 1 0
## 7 1 0
## 8 1 0
## 9 1 0
## 10 1 0

8.10 Solution to Exercise 10

data.lungs <- read.csv("lungs.csv", stringsAsFactors = FALSE)

head(data.lungs)

## age sex height weight bmp fev1 rv frc tlc pemax

## 1 7 0 109 13.1 68 32 258 183 137 95
## 2 7 1 112 12.9 65 19 449 245 134 85
## 3 8 0 124 14.1 64 22 441 268 147 100
## 4 8 1 125 16.2 67 41 234 146 124 85
## 5 8 0 127 21.5 93 52 202 131 104 95
## 6 9 0 130 17.5 68 44 308 155 118 80

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lungFit <- lm(pemax ˜ ., data = data.lungs)
summary(lungFit)

##
## Call:
## lm(formula = pemax ˜ ., data = data.lungs)
##
## Residuals:
## Min 1Q Median 3Q Max
## -37.34 -11.53 1.08 13.39 33.41
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 176.058 225.891 0.78 0.45
## age -2.542 4.802 -0.53 0.60
## sex -3.737 15.460 -0.24 0.81
## height -0.446 0.903 -0.49 0.63
## weight 2.993 2.008 1.49 0.16
## bmp -1.745 1.155 -1.51 0.15
## fev1 1.081 1.081 1.00 0.33
## rv 0.197 0.196 1.00 0.33
## frc -0.308 0.492 -0.63 0.54
## tlc 0.189 0.500 0.38 0.71
##
## Residual standard error: 25.5 on 15 degrees of freedom
## Multiple R-squared: 0.637,Adjusted R-squared: 0.42
## F-statistic: 2.93 on 9 and 15 DF, p-value: 0.032
##

resid(lungFit)

## 1 2 3 4 5 6 7 8
## 10.031 -3.414 13.386 -11.532 18.691 -31.552 -11.480 20.034
## 9 10 11 12 13 14 15 16
## -20.307 -13.182 15.646 10.748 -3.664 -33.118 10.460 33.405
## 17 18 19 20 21 22 23 24
## 21.034 -3.002 12.096 1.081 -37.338 11.864 -4.332 -34.233
## 25
## 28.677

 most significant
sort(summary(lungFit)coefficients[, 4], decreasing = FALSE)[1]

## bmp
## 0.1517

196
 least significant
sort(summary(lungFit)coefficients[, 4], decreasing = TRUE)[1]

## sex
## 0.8123

8.11 Solution to Exercise 11

library(survival)
head(colon)

## id study rx sex age obstruct perfor adhere nodes status

## 1 1 1 Lev+5FU 1 43 0 0 0 5 1
## 2 1 1 Lev+5FU 1 43 0 0 0 5 1
## 3 2 1 Lev+5FU 1 63 0 0 0 1 0
## 4 2 1 Lev+5FU 1 63 0 0 0 1 0
## 5 3 1 Obs 0 71 0 0 1 7 1
## 6 3 1 Obs 0 71 0 0 1 7 1
## differ extent surg node4 time etype
## 1 2 3 0 1 1521 2
## 2 2 3 0 1 968 1
## 3 2 3 0 0 3087 2
## 4 2 3 0 0 3087 1
## 5 2 2 0 1 963 2
## 6 2 2 0 1 542 1

colonFit <- survfit(Surv(time, status) ˜ rx, data = colon)

plot(colonFit)

197
 1.0
0.8
0.6
0.4
0.2
0.0

0 500 1000 1500 2000 2500 3000

plot(colonFit, col = 2:4, lwd = 2)

plot(colonFit, col = 2:4, lwd = 2)
legend("bottomleft", legend = levels(colonrx), fill = 2:4)

198
 1.0
0.8
0.6
0.4
0.2

Obs
Lev
0.0

Lev+5FU

0 500 1000 1500 2000 2500 3000

pdf(file = "Surv.pdf")
plot(colonFit, col = 2:4, lwd = 2)
legend("bottomleft", legend = levels(colonrx), fill = 2:4)
dev.off()

## pdf
## 2

survdiff(Surv(time, status) ˜ rx, data = colon)

## Call:

199
## survdiff(formula = Surv(time, status) ˜ rx, data = colon)
##
## N Observed Expected (O-E)ˆ2/E (O-E)ˆ2/V
## rx=Obs 630 345 299 7.01 10.40
## rx=Lev 620 333 295 4.93 7.26
## rx=Lev+5FU 608 242 326 21.61 33.54
##
## Chisq= 33.6 on 2 degrees of freedom, p= 4.99e-08

cp <- coxph(Surv(time, status) ˜ rx, data = colon)

summary(cp)

## Call:
## coxph(formula = Surv(time, status) ˜ rx, data = colon)
##
## n= 1858, number of events= 920
##
## coef exp(coef) se(coef) z Pr(>|z|)
## rxLev -0.0209 0.9793 0.0768 -0.27 0.79
## rxLev+5FU -0.4410 0.6434 0.0839 -5.26 1.5e-07 ***
## ---
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## rxLev 0.979 1.02 0.842 1.138
## rxLev+5FU 0.643 1.55 0.546 0.758
##
## Concordance= 0.545 (se = 0.009 )
## Rsquare= 0.019 (max possible= 0.999 )
## Likelihood ratio test= 35.2 on 2 df, p=2.23e-08
## Wald test = 33.1 on 2 df, p=6.45e-08
## Score (logrank) test = 33.6 on 2 df, p=4.99e-08
##

200
8.12 sessionInfo()

sessionInfo()

## R version 2.15.0 (2012-03-30)

## Platform: x86_64-pc-mingw32/x64 (64-bit)
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] splines grid stats graphics grDevices utils
## [7] datasets methods base
##
## other attached packages:
## [1] survival_2.36-14 vcd_1.2-13 colorspace_1.1-1
## [4] annotate_1.34.0 AnnotationDbi_1.18.1 Biobase_2.16.0
## [7] BiocGenerics_0.2.0 wordcloud_2.0 Rcpp_0.9.10
## [10] tm_0.5-7.1 igraph_0.5.5-4 network_1.7-1
## [13] googleVis_0.2.16 RJSONIO_0.98-1 lattice_0.20-6
## [16] ggplot2_0.9.1 RColorBrewer_1.0-5 venneuler_1.1-0
## [19] gplots_2.11.0 MASS_7.3-17 KernSmooth_2.23-7
## [22] caTools_1.12 bitops_1.0-4.1 gdata_2.10.6
## [25] gtools_2.6.2 scatterplot3d_0.3-33 XML_3.9-4.1
## [28] R2HTML_2.2 SAScii_0.2 stringr_0.6
## [31] XLConnect_0.1-9 XLConnectJars_0.1-4 rJava_0.9-3
## [34] knitr_0.6
##
## loaded via a namespace (and not attached):
## [1] codetools_0.2-8 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2
## [5] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 IRanges_1.14.3
## [9] labeling_0.1 memoise_0.1 munsell_0.3 parser_0.0-14
## [13] plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1 RSQLite_0.11.1
## [17] scales_0.2.1 slam_0.1-24 stats4_2.15.0 tools_2.15.0
## [21] xtable_1.7-0

201