R-programming

http://www.r-project.org/
http://cran.r-project.org/
Hung Chen
 Outline
• Introduction: – Grouping, loops and conditional
– Historical development execution
– S, Splus – Function
– Capability • Reading and writing data from
– Statistical Analysis files
• References • Modeling
– Regression
• Calculator
– ANOVA
• Data Type
• Data Analysis on Association
• Resources
– Lottery
• Simulation and Statistical
– Geyser
Tables
– Probability distributions
• Smoothing
• Programming
 R, S and S-plus
• S: an interactive environment for data analysis developed at Bell
Laboratories since 1976
– 1988 - S2: RA Becker, JM Chambers, A Wilks
– 1992 - S3: JM Chambers, TJ Hastie
– 1998 - S4: JM Chambers

• Exclusively licensed by AT&T/Lucent to Insightful Corporation,

Seattle WA. Product name: “S-plus”.
• Implementation languages C, Fortran.
• See:
http://cm.bell-labs.com/cm/ms/departments/sia/S/history.html
• R: initially written by Ross Ihaka and Robert Gentleman at Dep.
of Statistics of U of Auckland, New Zealand during 1990s.
• Since 1997: international “R-core” team of ca. 15 people with
access to common CVS archive.
 Introduction
•R is “GNU S” — A language and environment for data manipula-
tion, calculation and graphical display.
– R is similar to the award-winning S system, which was developed at Bell
Laboratories by John Chambers et al.
– a suite of operators for calculations on arrays, in particular matrices,
– a large, coherent, integrated collection of intermediate tools for interactive data
analysis,
– graphical facilities for data analysis and display either directly at the computer
or on hardcopy
– a well developed programming language which includes conditionals, loops,
user defined recursive functions and input and output facilities.
•The core of R is an interpreted computer language.
– It allows branching and looping as well as modular programming using
functions.
– Most of the user-visible functions in R are written in R, calling upon a smaller
set of internal primitives.
– It is possible for the user to interface to procedures written in C, C++ or
FORTRAN languages for efficiency, and also to write additional primitives.
 What R does and does not
o data handling and storage: o is not a database, but
numeric, textual connects to DBMSs
o matrix algebra o has no graphical user
interfaces, but connects to
o hash tables and regular
Java, TclTk
expressions
o language interpreter can be
o high-level data analytic and
very slow, but allows to call
statistical functions
own C/C++ code
o classes (“OO”)
o no spreadsheet view of data,
o graphics but connects to
o programming language: Excel/MsOffice
loops, branching, o no professional /
subroutines commercial support
 R and statistics
o Packaging: a crucial infrastructure to efficiently produce, load
and keep consistent software libraries from (many) different
sources / authors
o Statistics: most packages deal with statistics and data analysis
o State of the art: many statistical researchers provide their
methods as R packages
 Data Analysis and Presentation
• The R distribution contains functionality for large number of
statistical procedures.
– linear and generalized linear models
– nonlinear regression models
– time series analysis
– classical parametric and nonparametric tests
– clustering
– smoothing
• R also has a large set of functions which provide a flexible
graphical environment for creating various kinds of data
presentations.
 References
• For R,
– The basic reference is The New S Language: A Programming Environment
for Data Analysis and Graphics by Richard A. Becker, John M. Chambers
and Allan R. Wilks (the “Blue Book”) .
– The new features of the 1991 release of S (S version 3) are covered in
Statistical Models in S edited by John M. Chambers and Trevor J. Hastie (the
“White Book”).
– Classical and modern statistical techniques have been implemented.
• Some of these are built into the base R environment.
• Many are supplied as packages. There are about 8 packages supplied with R
(called “standard” packages) and many more are available through the cran
family of Internet sites (via http://cran.r-project.org).
• All the R functions have been documented in the form of help
pages in an “output independent” form which can be used to create
versions for HTML, LATEX, text etc.
– The document “An Introduction to R” provides a more user-friendly starting
point.
– An “R Language Definition” manual
– More specialized manuals on data import/export and extending R.
 R as a calculator
> log2(32)

1.0
[1] 5

0.5
sin(seq(0, 2 * pi, length = 100))
> sqrt(2)
[1] 1.414214

0.0
-0.5
> seq(0, 5, length=6)
[1] 0 1 2 3 4 5 -1.0

0 20 40 60 80 100

Index

> plot(sin(seq(0, 2*pi, length=100)))

 Object orientation

primitive (or: atomic) data types in R are:

• numeric (integer, double, complex)

• character
• logical
• function
out of these, vectors, arrays, lists can be built.
 variables
> a = 49
> sqrt(a) numeric
[1] 7

> a = "The dog ate my homework"

> sub("dog","cat",a) character
[1] "The cat ate my homework“ string

> a = (1+1==3)
>a logical
[1] FALSE
 vectors, matrices and arrays
• vector: an ordered collection of data of the same type
> a = c(1,2,3)
> a*2
[1] 2 4 6

• Example: the mean spot intensities of all 15488 spots on a chip:

a vector of 15488 numbers

• In R, a single number is the special case of a vector with 1

element.
• Other vector types: character strings, logical
 vectors, matrices and arrays

• matrix: a rectangular table of data of the same type

• example: the expression values for 10000 genes for 30 tissue

biopsies: a matrix with 10000 rows and 30 columns.

• array: 3-,4-,..dimensional matrix

• example: the red and green foreground and background values
for 20000 spots on 120 chips: a 4 x 20000 x 120 (3D) array.
 Lists
• vector: an ordered collection of data of the same type.
> a = c(7,5,1)
> a[2]
[1] 5

• list: an ordered collection of data of arbitrary types.

> doe = list(name="john",age=28,married=F)
> doe$name
[1] "john“
> doe$age
[1] 28
• Typically, vector elements are accessed by their index (an integer),
list elements by their name (a character string). But both types
support both access methods.
 Data frames
data frame: is supposed to represent the typical data table that
researchers come up with – like a spreadsheet.

It is a rectangular table with rows and columns; data within each

column has the same type (e.g. number, text, logical), but
different columns may have different types.

Example:
>a
localisation tumorsize progress
XX348 proximal 6.3 FALSE
XX234 distal 8.0 TRUE
XX987 proximal 10.0 FALSE
 Factors
A character string can contain arbitrary text. Sometimes it is useful to use a limited
vocabulary, with a small number of allowed words. A factor is a variable that can only
take such a limited number of values, which are called levels.
>a
[1] Kolon(Rektum) Magen Magen
[4] Magen Magen Retroperitoneal
[7] Magen Magen(retrogastral) Magen
Levels: Kolon(Rektum) Magen Magen(retrogastral) Retroperitoneal
> class(a)
[1] "factor"
> as.character(a)
[1] "Kolon(Rektum)" "Magen" "Magen"
[4] "Magen" "Magen" "Retroperitoneal"
[7] "Magen" "Magen(retrogastral)" "Magen"
> as.integer(a)
[1] 1 2 2 2 2 4 2 3 2
> as.integer(as.character(a))
[1] NA NA NA NA NA NA NA NA NA NA NA NA
Warning message: NAs introduced by coercion
 Subsetting
Individual elements of a vector, matrix, array or data frame are
accessed with “[ ]” by specifying their index, or their name
>a
localisation tumorsize progress
XX348 proximal 6.3 0
XX234 distal 8.0 1
XX987 proximal 10.0 0
> a[3, 2]
[1] 10
> a["XX987", "tumorsize"]
[1] 10
> a["XX987",]
localisation tumorsize progress
XX987 proximal 10 0
>a
localisation tumorsize progress
XX348 proximal 6.3 0 Subsetting
XX234 distal 8.0 1
XX987 proximal 10.0 0
> a[c(1,3),]
localisation tumorsize progress subset rows by a
XX348 proximal 6.3 0 vector of indices
XX987 proximal 10.0 0
> a[c(T,F,T),]
localisation tumorsize progress subset rows by a
XX348 proximal 6.3 0 logical vector
XX987 proximal 10.0 0
> a$localisation
[1] "proximal" "distal" "proximal"
> a$localisation=="proximal" subset a column
[1] TRUE FALSE TRUE
> a[ a$localisation=="proximal", ] comparison resulting in
localisation tumorsize progress logical vector
XX348 proximal 6.3 0
XX987 proximal 10.0 0 subset the selected
rows
 Resources
• A package specification allows the production of loadable modules
for specific purposes, and several contributed packages are made
available through the CRAN sites.
• CRAN and R homepage:
– http://www.r-project.org/
It is R’s central homepage, giving information on the R project and
everything related to it.
– http://cran.r-project.org/
It acts as the download area,carrying the software itself, extension packages,
PDF manuals.
• Getting help with functions and features
– help(solve)
– ?solve
– For a feature specified by special characters, the argument must be enclosed in
double or single quotes, making it a “character string”: help("[[")
 Getting help
Details about a specific command whose name you know (input
arguments, options, algorithm, results):

>? t.test
or
>help(t.test)
Getting help

o HTML search engine

o Search for topics

with regular
expressions:
“help.search”
 Probability distributions
• Cumulative distribution function P(X ≤ x): ‘p’ for the CDF
• Probability density function: ‘d’ for the density,,
• Quantile function (given q, the smallest x such that P(X ≤ x) > q):
‘q’ for the quantile
• simulate from the distribution: ‘r
Distribution R name additional arguments
beta beta shape1, shape2, ncp
binomial binom size, prob
Cauchy cauchy location, scale
chi-squared chisq df, ncp
exponential exp rate
F f df1, df1, ncp
gamma gamma shape, scale
geometric geom prob
hypergeometric hyper m, n, k
log-normal lnorm meanlog, sdlog
logistic logis; negative binomial nbinom; normal norm; Poisson pois; Student’s t
t ; uniform unif; Weibull weibull; Wilcoxon wilcox
 Grouping, loops and conditional execution
• Grouped expressions
– R is an expression language in the sense that its only command type is a
function or expression which returns a result.
– Commands may be grouped together in braces, {expr 1, . . ., expr m}, in
which case the value of the group is the result of the last expression in the
group evaluated.
• Control statements
– if statements
– The language has available a conditional construction of the form
if (expr 1) expr 2 else expr 3
where expr 1 must evaluate to a logical value and the result of the entire
expression is then evident.
– a vectorized version of the if/else construct, the ifelse function. This has the
form ifelse(condition, a, b)
 Repetitive execution
• for loops, repeat and while
– for (name in expr 1) expr 2
where name is the loop variable. expr 1 is a vector expression,
(often a sequence like 1:20), and expr 2 is often a grouped
expression with its sub-expressions written in terms of the
dummy name. expr 2 is repeatedly evaluated as name ranges
through the values in the vector result of expr 1.
• Other looping facilities include the
– repeat expr statement and the
– while (condition) expr statement.
– The break statement can be used to terminate any loop, possibly
abnormally. This is the only way to terminate repeat loops.
– The next statement can be used to discontinue one particular
cycle and skip to the “next”.
 Branching

if (logical expression) {
statements
} else {
alternative statements
}

else branch is optional

 Loops
• When the same or similar tasks need to be performed multiple
times; for all elements of a list; for all columns of an array; etc.
• Monte Carlo Simulation
• Cross-Validation (delete one and etc)

for(i in 1:10) {
print(i*i)
}

i=1
while(i<=10) {
print(i*i)
i=i+sqrt(i)
}
 lapply, sapply, apply
• When the same or similar tasks need to be performed multiple
times for all elements of a list or for all columns of an array.
• May be easier and faster than “for” loops
• lapply(li, function )
• To each element of the list li, the function function is applied.
• The result is a list whose elements are the individual function
results.
> li = list("klaus","martin","georg")
> lapply(li, toupper)
> [[1]]
> [1] "KLAUS"
> [[2]]
> [1] "MARTIN"
> [[3]]
> [1] "GEORG"
 lapply, sapply, apply
sapply( li, fct )
Like apply, but tries to simplify the result, by converting it into a
vector or array of appropriate size

> li = list("klaus","martin","georg")
> sapply(li, toupper)
[1] "KLAUS" "MARTIN" "GEORG"

> fct = function(x) { return(c(x, x*x, x*x*x)) }

> sapply(1:5, fct)
[,1] [,2] [,3] [,4] [,5]
[1,] 1 2 3 4 5
[2,] 1 4 9 16 25
[3,] 1 8 27 64 125
 apply
apply( arr, margin, fct )
Apply the function fct along some dimensions of the array arr,
according to margin, and return a vector or array of the
appropriate size.
>x
[,1] [,2] [,3]
[1,] 5 7 0
[2,] 7 9 8
[3,] 4 6 7
[4,] 6 3 5
> apply(x, 1, sum)
[1] 12 24 17 14
> apply(x, 2, sum)
[1] 22 25 20
 functions and operators
Functions do things with data
“Input”: function arguments (0,1,2,…)
“Output”: function result (exactly one)

Example:
add = function(a,b)
{ result = a+b
return(result) }

Operators:
Short-cut writing for frequently used functions of one or two
arguments.
Examples: + - * / ! & | %%
 functions and operators
• Functions do things with data
• “Input”: function arguments (0,1,2,…)
• “Output”: function result (exactly one)
Exceptions to the rule:
• Functions may also use data that sits around in other places, not
just in their argument list: “scoping rules”*
• Functions may also do other things than returning a result. E.g.,
plot something on the screen: “side effects”

* Lexical scope and Statistical Computing.

R. Gentleman, R. Ihaka, Journal of Computational and
Graphical Statistics, 9(3), p. 491-508 (2000).
 Reading data from files
• The read.table() function
– To read an entire data frame directly, the external file will normally have a
special form.
– The first line of the file should have a name for each variable in the data
frame.
– Each additional line of the file has its first item a row label and the values for
each variable.
Price Floor Area Rooms Age Cent.heat
01 52.00 111.0 830 5 6.2 no
02 54.75 128.0 710 5 7.5 no
03 57.50 101.0 1000 5 4.2 no
04 57.50 131.0 690 6 8.8 no
05 59.75 93.0 900 5 1.9 yes
...
• numeric variables and nonnumeric variables (factors)
 Reading data from files
• HousePrice <- read.table("houses.data", header=TRUE)
Price Floor Area Rooms Age Cent.heat
52.00 111.0 830 5 6.2 no
54.75 128.0 710 5 7.5 no
57.50 101.0 1000 5 4.2 no
57.50 131.0 690 6 8.8 no
59.75 93.0 900 5 1.9 yes
...
• The data file is named ‘input.dat’.
– Suppose the data vectors are of equal length and are to be read in in parallel.
– Suppose that there are three vectors, the first of mode character and the remaining two
of mode numeric.
• The scan() function
– inp<- scan("input.dat", list("",0,0))
– To separate the data items into three separate vectors, use assignments like
label <- inp[[1]]; x <- inp[[2]]; y <- inp[[3]]
– inp <- scan("input.dat", list(id="", x=0, y=0)); inp$id; inp$x; inp$y
 Storing data
• Every R object can be stored into and restored from a file with
the commands “save” and “load”.
• This uses the XDR (external data representation) standard of
Sun Microsystems and others, and is portable between MS-
Windows, Unix, Mac.

> save(x, file=“x.Rdata”)

> load(“x.Rdata”)
 Importing and exporting data

There are many ways to get data into R and out of R.

Most programs (e.g. Excel), as well as humans, know how to deal

with rectangular tables in the form of tab-delimited text files.

> x = read.delim(“filename.txt”)
also: read.table, read.csv

> write.table(x, file=“x.txt”, sep=“\t”)

 Explore Association
• Data(stackloss)
–It is a data frame with 21 observations on 4 variables.
– [,1] `Air Flow' Flow of cooling air
– [,2] `Water Temp' Cooling Water Inlet Temperature
– [,3] `Acid Conc.' Concentration of acid [per 1000, minus 500]
– [,4] `stack.loss' Stack loss
–The data sets `stack.x', a matrix with the first three (independent)
variables of the data frame, and `stack.loss', the numeric vector
giving the fourth (dependent) variable, are provided as well.
• Scatterplots, scatterplot matrix:
–plot(stackloss$Ai,stackloss$W)
–plot(stackloss) data(stackloss)
–two quantitative variables.
• summary(lm.stack <- lm(stack.loss ~ stack.x))
• summary(lm.stack <- lm(stack.loss ~ stack.x))
 Explore Association
• Boxplot suitable for showing
a quantitative and a
qualitative variable.
• The variable test is not
quantitative but categorical.
– Such variables are also called
factors.