R Programming Course Notes

Xing Su

Contents
Overview and History of R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Coding Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Workspace and Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

R Console and Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

R Objects and Data Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Vectors and Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Matrices and Data Frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Missing Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Sequence of Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

10

Subsetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

10

Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

10

Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

11

Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

11

Partial Matching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

11

Logic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

12

Understanding Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

12

Split-Apply-Combine Funtions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

split() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

apply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

lapply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

sapply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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vapply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

14

tapply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

14

mapply() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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aggregate() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

15

Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

16

Simulation Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

16

Generate Numbers for a Linear Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

17

Dates and Times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

18

Base Graphics

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

18

Reading Tabular Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Larger Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Textual Data Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

19

Interfaces to the Outside World . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

20

Control Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

21

if - else . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

21

for . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

21

while . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

22

repeat and break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

22

next and return . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

22

Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

23

Scoping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

24

Scoping Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

24

Lexical vs Dynamic Scoping Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

25

Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

26

Debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

27

R Profiler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

28

Overview and History of R

R = dialect of the S language

S was developed by John Chambers @ Bell Labs

initiated in 1976 as internal tool, originally FORTRAN libraries
1988 rewritten in C (version 3 of language)
1998 version 4 (what we use today)

History of S
Bell labs insightful Lucent Alcatel-Lucent
in 1998, S won the Association for computing machinerys software system award
History of R

1991
1993
1995
1996
1997
2000

created in New Zealand by Ross Ihaka & RobertGentleman

first announcement of R to public
Martin Machler convinces founders to use GNU General Public license to make R free
public mailing list created R-help and R-devel
R Core Group formed
R v1.0.0 released

R Features

Syntax similar to S, semantics similar to S, runs on any platforms, frequent releasees

lean software, functionalities in modular packages, sophisticated graphics capabilities
useful for interactive work, powerful programming language
active user community and FREE (4 freedoms)

freedom
freedom
freedom
freedom

to
to
to
to

run the program

study how the program works and adapt it
redistribute copies
improve the program

R Drawbacks

40 year-old technology
little built-in support for dynamic/3D graphics
functionality based on consumer demand
objects generally stored in physical memory (limited by hardware)

Design of the R system

2 conceptual parts: base R from CRAN vs. everything else
functionality divided into different packages
base R contains core functionality and fundamental functions
other utility packages included in the base install: util, stats, datasets, . . .
Recommended packages: bootclass, KernSmooth, etc
5000+ packages available

Coding Standards

Always use text files/editor

Indent code (4 space minimum)
limit the width of code (80 columns)
limit the length of individual functions

Workspace and Files

getwd() = return current working directory

setwd() = set current working directory
?function = brings up help for that function
dir.create("path/foldername", recursive = TRUE) = create directories/subdirectories
unlink(directory, recursive = TRUE) = delete directory and subdirectories
ls() = list all objects in the local workspace
list.files(recursive = TRUE) = list all, including subdirectories
args(function) = returns arguments for the function
file.create("name") = create file

.exists("name") = return true/false exists in working directory

.info("name") = return file info
.info("name")$property = returns value for the specific attribute
.rename("name1", "name2") = rename file
.copy("name1", "name2") = copy file
.path("name1") = return path of file

R Console and Evaluation

<- = assignment operator

# = comment
expression is evaluated after hitting enter and result is returned
autoprinting occurs when you call a variable
print(x) = explicitly printing

[1] at the beginning of the output = which element of the vector is being shown

R Objects and Data Structures

5 basic/atomic classes of objects:
1.
2.
3.
4.
5.

character
numeric
integer
complex
logical

Numbers

numbers generally treated as numeric objects (double precision real numbers - decimals)
Integer objects can be created by adding L to the end of a number(ex. 1L)
Inf = infinity, can be used in calculations
NaN = not a number/undefined
sqrt(value) = square root of value

Variables
variable <- value = assignment of a value to a variable name
Vectors and Lists
atomic vector = contains one data type, most basic object
vector <- c(value1, value2, ...) = creates a vector with specified values
vector1*vector2 = element by element multiplication (rather than matrix multiplication)
if the vectors are of different lengths, shorter vector will be recycled until the longer runs out
computation on vectors/between vectors (+, -, ==, /, etc.) are done element by element by
default
%*% = force matrix multiplication between vectors/matrices
vector("class", n) = creates empty vector of length n and specified class
vector("numeric", 3) = creates 0 0 0
c() = concatenate
T, F = shorthand for TRUE and FALSE
1+0i = complex numbers
explicit coercion
as.numeric(x), as.logical(x), as.character(x), as.complex(x) = convert object from one
class to another
nonsensible coercion will result in NA (ex. as.numeric(c("a", "b"))
as.list(data.frame) = converts a data.frame object into a list object
as.character(list) = converts list into a character vector
implicit coercion
matrix/vector can only contain one data type, so when attempting to create matrix/vector with
different classes, forced coercion occurs to make every element to same class
least common denominator is the approach used (basically everything is converted to a class
that all values can take, numbers characters) and no errors generated
coercion occurs to make every element to same class (implicit)
x <- c(NA, 2, "D") will create a vector of character class
list() = special vector wit different classes of elements
5

 list = vector of objects of different classes

elements of list use [[]], elements of other vectors use []
logical vectors = contain values TRUE, FALSE, and NA, values are generated as result of logical conditions
comparing two objects/values
paste(characterVector, collapse = " ") = join together elements of the vector and separating
with the collapse parameter
paste(vec1, vec2, sep = " ") = join together different vectors and separating with the sep parameter
Note: vector recycling applies here too
LETTERS, letters= predefined vectors for all 26 upper and lower letters
unique(values) = returns vector with all duplicates removed
Matrices and Data Frames
matrix can contain only 1 type of data
data.frame can contain multiple
matrix(values, nrow = n, ncol = m) = creates a n by m matrix
constructed COLUMN WISE the elements are placed into the matrix from top to bottom
for each column, and by column from left to right
matrices can also be created by adding the dimension attribute to vector
dim(m) <- c(2, 5)
matrices can also be created by binding columns and rows
rbind(x, y), cbind(x, y) = combine rows/columns; can be used on vectors or matrices
* and / = element by element computation between two matrices
%*% = matrix multiplication
dim(obj) = dimensions of an object (returns NULL if a vector)
dim(obj) <- c(4, 5) = assign dim attribute to an object
if object is a vector, R converts the vector to a n by m matrix (i.e. 4 rows by 5 column from
the example command)
Note: if n by m is larger than length of vector, then an error is returned
example
# initiate a vector
x <-c(NA, 1, "cx", NA, 2, "dsa")
class(x)
## [1] "character"
x
## [1] NA

"1"

"cx"

NA

"2"

"dsa"

# convert to matrix
dim(x) <- c(3, 2)
class(x)
## [1] "matrix"

x
##
[,1]
## [1,] NA
## [2,] "1"
## [3,] "cx"

[,2]
NA
"2"
"dsa"

data.frame(var = 1:4, var2 = c(....)) = creates a data frame

nrow(), ncol() = returns row and column numbers
data.frame(vector, matrix) = takes any number of arguments and returns a single object of
class data.frame composed of original objects
as.data.frame(obj) = converts object to data frame
data frames store tabular data
special type of list where every list has the same length (can be of different type)
data frames are usually created through read.table() and read.csv()
data.matrix() = converts a matrix to data frame
colMeans(matrix) or rowMeans(matrix) = returns means of the columns/rows of a matrix/dataframe
in a vector
as.numeric(rownames(df)) = returns row indices for rows of a data frame with unnamed rows
attributes
objects can have attributes: names, dimnames, row.names, dim (matrices, arrays), class, length,
or any user-defined ones
attributes(obj), class(obj) = return attributes/class for an R object
attr(object, "attribute") <- "value" = creates/assigns a value to a new/existing attribute
for the object
names attribute
all objects can have names
names(x) = returns names (NULL if no name exists)
names(x) <- c("a", ...) = can be used to assign names to vectors
list(a = 1, b = 2, ...) = a, b are names
dimnames(matrix) <- list(c("a", "b"), c("c" , "d")) = assign names to matrices
use list of two vectors: row, column in that order
colnames(data.frame) = return column names (can be used to set column names as well, similar
to dim())
row.names = names of rows in the data frame (attribute)
Arrays
multi-dimensional collection of data with k dimensions
matrix = 2 dimensional array
array(data, dim, dimnames)
data = data to be stored in array
dim = dimensions of the array
dim = c(2, 2, 5) = 3 dimensional array creates 5 2x2 array
dimnames = add names to the dimensions
input must be a list
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 every element of the list must correspond in length to the dimensions of the array
dimnames(x) <- list(c("a", "b"), c("c", "d"), c("e", "f", "g", "h", "i"))
set the names for row, column, and third dimension respectively (2 x 2 x 5 in this case)
dim() function can be used to create arrays from vectors or matrices
x <- rnorm(20); dim(x) <- c(2, 2, 5) = converts a 20 element vector to a 2x2x5 array
Factors

factors are used to represent categorical data (integer vector where each value has a label)
2 types: unordered vs ordered
treated specially by lm(), glm()
Factors easier to understand because they self describe (vs. 1 and 2)
factor(c("a", "b"), levels = c("1", "2")) = creates factor
levels() argument can be used to specify baseline levels vs other levels
Note:without explicit specification, R uses alphabetical order
table(factorVar) = how many of each are in the factor

Missing Values
NaN or NA = missing values
NaN = undefined mathematical operations
NA = any value not available or missing in the statistical sense
any operations with NA results in NA
NA can have different classes potentially (integer, character, etc)
Note: NaN is an NA value, but NA is not NaN
is.na(), is.nan() = use to test if each element of the vector is NA and NaN
Note: cannot compare NA (with ==) as it is not a value but a placeholder for a quantity that is
not available
sum(my_na) = sum of a logical vector (TRUE = 1 and FALSE = 0) is effectively the number of TRUEs
Removing NA Values
is.na() = creates logical vector where T is where value exists, F is NA
subsetting with the above result can return only the non NA elements
complete.cases(obj1, obj2) = creates logical vector where TRUE is where both values exist,
and FALSE is where any is NA
can be used on data frames as well
complete.cases(data.frame) = creates logical vectors indicating which observation/row is
good
data.frame[logicalVector, ] = returns all observations with complete data
Imputing Missing Values = replacing missing values with estimates (can be averages from all other
data with the similar conditions)

Sequence of Numbers
1:20 = creates a sequence of numbers from first number to second number
works in descending order as well
increment = 1
?':' = enclose help for operators
seq(1, 20, by=0.5) = sequence 1 to 20 by increment of .5
length=30 argument can be used to specify number of values generated
length(variable) = length of vector/sequence
seq_along(vector) or seq(along.with = vector) = create vector that is same length as another
vector
rep(0, times = 40) = creates a vector with 40 zeroes
rep(c(1, 2), times = 10) = repeats combination of numbers 10 times
rep(c(1, 2), each = 10) = repeats first value 10 times followed by second value 10 times

Subsetting
R uses one based index starts counting at 1
x[0] returns numeric(0), not error
x[3000] returns NA (not out of bounds/error)
[] = always returns object of same class, can select more than one element of an object (ex. [1:2])
[[]] = can extract one element from list or data frame, returned object not necessarily list/dataframe
$ = can extract elements from list/dataframe that have names associated with it, not necessarily same
class
Vectors
x[1:10] = first 10 elements of vector x
x[is.na(x)] = returns all NA elements
x[!is.na(x)] = returns all non NA elements
x > 0 = would return logical vector comparing all elements to 0 (TRUE/FALSE for all values except
for NA and NA for NA elements (NA a placeholder)

x[x>"a"] = selects all elements bigger than a (lexicographical order in place)

x[logicalIndex] = select all elements where logical index = TRUE
x[-c(2, 10)] = returns everything but the second and tenth element
vect <- c(a = 1, b = 2, c = 3) = names values of a vector with corresponding names
names(vect) = returns element names for object
names(vet) <- c("a", "b", "c") = assign/change names of vector

identical(obj1, obj2) = returns TRUE if two objects are exactly equal

all.equal(obj1, obj2) = returns TRUE if two objects are near equal

10

Lists
x <- list(foo = 1:4, bar = 0.6)
x[1] or x["foo"] = returns the list object foo
x[[2]] or x[["bar"]] or x$bar = returns the content of the second element from the list (in this case
vector without name attribute)
Note: $ cant extract multiple elements
x[c(1, 3)] = extract multiple elements of list
x[[name]] = extract using variable, where as $ must match name of element
x[[c(1, 3)]] or x[[1]][[3]] = extracted nested elements of list third element of the first object
extracted from the list
Matrices
x[1, 2] = extract the (row, column) element
x[,2] or x[1,] = extract the entire column/row
x[ , 11:17] = subset the x data.frame with all rows, but only 11 to 17 columns
when an element from the matrix is retrieved, a vector is returned
behavior can be turned off (force return a matrix) by adding drop = FALSE
x[1, 2, drop = F]
Partial Matching
works with [[]] and $
$ automatically partial matches the name (x$a)
[[]] can partial match by adding exact = FALSE
x[["a", exact = false]]

11

Logic

<, >= = less than, greater or equal to

== = exact equality
!= = inequality
A | B = union
A & B = intersection
! = negation
& or | evaluates every instance/element in vector
&& or || evaluate only first element
Note: All AND operators are evaluated before OR operators

isTRUE(condition) = returns TRUE or FALSE of the condition

xor(arg1, arg2) = exclusive OR, one argument must equal TRUE one must equal FALSE
which(condition) = find the indicies of elements that satisfy the condition (TRUE)
any(condition) = TRUE if one or more of the elements in logical vector is TRUE
all(condition) = TRUE if all of the elements in logical vector is TRUE

Understanding Data
use class(), dim(), nrow(), ncol(), names() to understand dataset
object.size(data.frame) = returns how much space the dataset is occupying in memory
head(data.frame, 10), tail(data.frame, 10) = returns first/last 10 rows of data; default = 6
summary() = provides different output for each variable, depending on class,
for numerical variables, displays min max, mean median, etx.
for categorical (factor) variables, displays number of times each value occurs
table(data.frame$variable) = table of all values of the variable, and how many observations there
are for each
Note: mean for variables that only have values 1 and 0 = proportion of success
str(data.frame) = structure of data, provides data class, num of observations vs variables, and name
of class of each variable and preview of its contents
compactly display the internal structure of an R object
Whats in this object
well-suited to compactly display the contents of lists
view(data.frame) = opens and view the content of the data frame

12

Split-Apply-Combine Funtions
loop functions = convenient ways of implementing the Split-Apply-Combine strategy for data analysis
split()
takes a vector/objects and splits it into group b a factor or list of factors
split(x, f, drop = FALSE)
x = vector/list/data frame
f = factor/list of factors
drop = whether empty factor levels should be dropped
interactions(gl(2, 5), gl(5, 2)) = 1.1, 1.2, . . . 2.5
gl(n, m) = group level function
n = number of levels
m = number of repetitions
split function can do this by passing in list(f1, f2) in argument
split(data, list(gl(2, 5), gl(5, 2))) = splits the data into 1.1, 1.2, . . . 2.5 levels
apply()

evaluate a function (often anonymous) over the margins of an array

often used to apply a function to the row/columns of a matrix
can be used to average array of matrices (general arrays)
apply(x, margin = 2, FUN, ...)

x = array
MARGIN = 2 (column), 1 (row)
FUN = function
... = other arguments that need to be passed to other functions

examples

apply(x, 1, sum) or apply(x, 1, mean) = find row sums/means

apply(x, 2, sum) or apply(x, 2, mean) = find column sums/means
apply(x, 1, quantile, props = c(0.25, 0.75)) = find 25% 75% percentile of each row
a <- array(rnorm(2*2*10), c(2, 2, 10)) = create 10 2x2 matrix
apply(a, c(1, 2), mean) = returns the means of 10

lapply()
loops over a list and evaluate a function on each element and always returns a list
Note: since input must be a list, it is possible that conversion may be needed
lapply(x, FUN, ...) = takes list/vector as input, applies a function to each element of the list,
returns a list of the same length
x = list (if not list, will be coerced into list through as.list, if not possible > error)
data.frame are treated as collections of lists and can be used here
FUN = function (without parentheses)
anonymous functions are acceptable here as well - (i.e function(x) x[,1])
13

 ... = other/additional arguments to be passed for FUN (i.e. min, max for runif())
example
lapply(data.frame, class) = the data.frame is a list of vectors, the class value for each vector
is returned in a list (name of function, class, is without parentheses)
lapply(values, function(elem), elem[2]) = example of an anonymous function
sapply()
performs same function as lapply() except it simplifies the result
if result is of length 1 in every element, sapply returns vector
if result is vectors of the same length (>1) for each element, sapply returns matrix
if not possible to simplify, sapply returns a list (same as lapply())
vapply()
safer version of sapply in that it allows to you specify the format for the result
vapply(flags, class, character(1)) = returns the class of values in the flags variable in the
form of character of length 1 (1 value)
tapply()
split data into groups, and apply the function to data within each subgroup
tapply(data, INDEX, FUN, ..., simplify = FALSE) = apply a function over subsets of a vector

data = vector
INDEX = factor/list of factors
FUN = function
... = arguments to be passed to function
simplify = whether to simplify the result

example
x <- c(rnorm(10), runif(10), rnorm(10, 1))
f <- gl(3, 10); tapply(x, f, mean) = returns the mean of each group (f level) of x data
mapply()
multivariate apply, applies a function in parallel over a set of arguments
mapply(FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE)

FUN = function
... = arguments to apply over
MoreArgs = list of other arguments to FUN
SIMPLIFY = whether the result should be simplified

example
mapply(rep, 1:4, 4:1)

14

##
##
##
##
##
##
##
##
##
##
##

[[1]]
[1] 1 1 1 1
[[2]]
[1] 2 2 2
[[3]]
[1] 3 3
[[4]]
[1] 4

aggregate()
aggregate computes summary statistics of data subsets (similar to multiple tapply at the same time)
aggregate(list(name = dataToCompute), list(name = factorVar1,name = factorVar2),
function, na.rm = TRUE)

dataToCompute = this is what the function will be applied on

factorVar1, factorVar1 = factor variables to split the data by
Note: order matters here in terms of how to break down the data
function = what is applied to the subsets of data, can be sum/mean/median/etc
na.rm = TRUE removes NA values

15

Simulation
sample(values, n, replace = FALSE) = generate random samples
values = values to sample from
n = number of values generated
replace = with or without replacement
sample(1:6, 4, replace = TRUE, prob=c(.2, .2...)) = choose four values from the range
specified with replacing (same numbers can show up twice), with probabilities specified
sample(vector) = can be used to permute/rearrange elements of a vector
sample(c(y, z), 100) = select 100 random elements from combination of values y and z
sample(10) = select positive integer sample of size 10 without repeat

Each probability distribution functions usually have 4 functions associated with them:

r***
d***
p***
q***

function
function
function
function

(for
(for
(for
(for

random) random number generation (ex. rnorm)

density) calculate density (ex. dunif)
probability) cumulative distribution (ex. ppois)
quantile) quantile function (ex. qbinom)

If is the cumulative distribution function for a standard Normal distribution, then pnorm(q) = (q)
and qnorm(p) = 1 (q).
set.seed() = sets seed for randon number generator to ensure that the same data/analysis can be
reproduced
Simulation Examples
rbinom(1, size = 100, prob = 0.7) = returns a binomial random variable that represents the
number of successes in a give number of independent trials
1 = corresponds number of observations
size = 100 = corresponds with the number of independent trials that culminate to each resultant
observation
prob = 0.7 = probability of success
rnorm(n, mean = m, sd = s) = generate n random samples from the standard normal distribution
(mean = 0, std deviation = 1 by default)

rnorm(1000) = 1000 draws from the standard normal distribution

n = number of observation generated
mean = m = specified mean of distribution
sd = s = specified standard deviation of distribution

dnorm(x, mean = 0, sd = 1, log = FALSE)

log = evaluate on log scale
pnorm(q, mean = 0, sd = 1, lower.tail = TRUE, log.p = FALSE)
lower.tail = left side, FALSE = right
qnorm(p, mean = 0, sd = 1, lower.tail = TRUE, log.p = FALSE)
lower.tail = left side, FALSE = right
rpois(n, lambda) = generate random samples from the poisson distrbution
n = number of observations generated
lambda = parameter for the poisson distribution or rate

16

 rpois(n, r) = generating Poisson Data

n = number of values
r = rate
ppois(n, r) = cumulative distribution
ppois(2, 2) = P r(x <= 2)
replicate(n, rpois()) = repeat operation n times
Generate Numbers for a Linear Model
Linear model
y = 0 + 1 x +  where  N (0, 22 ), x N (0, 12 ), 0 = 0.5, 1 = 2
set.seed(20)
x <- rnorm(100)
# normal
x <- rbinom(100, 1, 0.5) # binomial
e <- rnorm(100, 0, 2)
y <- 0.5 + 2* x + e
Poisson model
Y P oisson()log() = 0 + 1 x where 0 = 0.5, 1 = 2
x <- rnorm(100)
log.mu <- 0.5 + 0.3* x
y <- rpois(100, exp(log.mu))

17

Dates and Times

Date = date class, stored as number of days since 1970-01-01

POSIXct = time class, stored as number of seconds since 1970-01-01
POSIXlt = time class, stored as list of sec min hours
Sys.Date() = todays date
unclass(obj) = returns what obj looks like internally
Sys.time() = current time in POSIXct class
t2 <- as.POSIXlt(Sys.time()) = time in POSIXlt class
t2$min = return min of time (only works for POSIXlt class)

weekdays(date), months(date), quarters(date) = returns weekdays, months, and quarters of

time/date inputed
strptime(string, "%B %d, %Y %H:%M") = convert string into time format using the format specified
difftime(time1, time2, units = 'days') = difference in times by the specified unit

Base Graphics
data(set) = load data
plot(data) = R plots the data as best as it can

x = variable, x axis
y = variable
xlab, ylab = corresponding labels
main, sub = title, subtitle
col = 2 or col = "red" = color
pch = 2 = different symbols for points
xlim,ylim(v1, v2) = restrict range of plot

boxplot(x ~ y, data = d) = creates boxplot for x vs y variables using the data.frame provided
hist(x, breaks) = plots histogram of the data
break = 100 = split data into 100 bins

18

Reading Tabular Data

read.table(), read.csv() = most common, read text files (rows, col) return data frame
readLines() = read lines of text, returns character vector
source(file) = read R code
dget() = read R code files (R objects that have been reparsed)
load(), unserialize() = read binary objects
writing data
write.table(), writeLines(), dump(), put(), save(), serialize()

read.table() arguments:

file = name of file/connection

header = indicator if file contains header
sep = string indicating how columns are separated
colClasses = character vector indicating what each column is in terms of class
nrows = number of rows in dataset
comment.char = char indicating beginning of comment
skip = number of lines to skip in the beginning
stringsAsFactors = defaults to TRUE, should characters be coded as Factor

read.table can be used without any other argument to create data.frame

telling R what type of variables are in each column is helpful for larger datasets (efficiency)
read.csv() = read.table except default sep is comma (read.table default is sep = " " and
header = TRUE)
Larger Tables
Note: help page for read.table important
need to know how much RAM is required calculating memory requirements
numRow x numCol x 8 bytes/numeric value = size required in bites
double the above results and convert into GB = amount of memory recommended
set comment.char = "" to save time if there are no comments in the file
specifying colClasses can make reading data much faster
nrow = n = number of rows to read in (can help with memory usage)
initial <- read.table("file", rows = 100) = read first 100 lines
classes <- sapply(initial, class) = determine what classes the columns are
tabAll <- read.table("file", colClasses = classes) = load in the entire file with determined classes
Textual Data Formats
dump and dput preserve metadata
text formats are editable, not space efficient, and work better with version control system (they can
only track changes in text files)
dput(obj, file = "file.R") = creates R code to store all data and meta data in file.R (ex. data,
class, names, row.names)
dget("file.R") = loads the file/R code and reconstructs the R object
dput can only be used on one object, where as dump can be used on multiple objects
dump(c("obj1", "obj2"), file= "file2.R") = stores two objects
source("file2.R") = loads the objects
19

Interfaces to the Outside World

url() = function can read from webpages

file() = read uncompressed files
gzfile(), bzfile() = read compressed files (gzip, bzip2)
file(description = "", open = "") = file syntax, creates connection

description = description of file

open = r -readonly, w - writing, a - appending, rb/wb/ab - reading/writing/appending binary
close() = closes connection
readLines() = can be used to read lines after connection has been established

download.file(fileURL, destfile = "fileName", method = "curl")

fileURL = url of the file that needs to be downloaded
destfile = "fileName" = specifies where the file is to be saved
dir/fileName = directories can be referenced here
method = "curl" = necessary for downloading files from https:// links on Macs
method = "auto" = should work on all other machines

20

Control Structures
Common structures are

if, else = testing a condition

for = execute a loop a fixed number of times
while = execute a loop while a condition is true
repeat = execute an infinite loop
break = break the execution of a loop
next = skip an interation of a loop
return = exit a function

Note: Control structures are primarily useful for writing programs; for command-line interactive work,
the apply functions are more useful
if - else

# basic structure
if(<condition>) {
## do something
} else {
## do something else
}
# if tree
if(<condition1>) {
## do something
} else if(<condition2>) {
## do something different
} else {
## do something different
}
y <- if(x>3){10} else {0} = slightly different implementation than normal, focus on assigning value
for

# basic structure
for(i in 1:10) {
# print(i)
}
# nested for loops
x <- matrix(1:6, 2, 3)
for(i in seq_len(nrow(x))) {
for(j in seq_len(ncol(x))) {
# print(x[i, j])
}
}
for(letter in x) = loop through letter in character vector
21

 seq_along(vector) = create a number sequence from 1 to length of the vector

seq_len(length) = create a number sequence that starts at 1 and ends at length specified
while
count <- 0
while(count < 10) {
# print(count)
count <- count + 1
}
conditions can be combined with logical operators
repeat and break
repeat initiates an infinite loop
not commonly used in statistical applications but they do have their uses
The only way to exit a repeat loop is to call break
x0 <- 1
tol <- 1e-8
repeat {
x1 <- computeEstimate()
if(abs(x1 - x0) < tol) {
break
} else {
x0 <- x1 # requires algorithm to converge
}
}
Note: The above loop is a bit dangerous because theres no guarantee it will stop
Better to set a hard limit on the number of iterations (e.g. using a for loop) and then report
whether convergence was achieved or not.
next and return
next = (no parentheses) skips an element, to continue to the next iteration
return = signals that a function should exit and return a given value
for(i in 1:100) {
if(i <= 20) {
## Skip the first 20 iterations
next
}
## Do something here
}

22

Functions
name <- function(arg1, arg2, ...){ }

inputs can be specified with default values by arg1 = 10

it is possible to define an argument to NULL
returns last expression of function
many functions have na.rm, can be set to TRUE to remove NA values from calculation

structure
f <- function(<arguments>) {
## Do something interesting
}
function are first class object and can be treated like other objects (pass into other functions)
functions can be nested, so that you can define a function inside of another function
function have named arguments (i.e. x = mydata) which can be used to specifiy default values
sd(x = mydata) (matching by name)
formal arguments = arguments included in the functional definition
formals() = returns all formal arguments
not all functional call specifies all arguments, some can be missing and may have default values
args() = return all arguments you can specify
multiple arguments inputted in random orders (R performs positional matching) not recommended
argument matching order: exact partial positional

partial = instead of typing data = x, use d = x

Lazy Evaluation
R will evaluate as needed, so everything executes until an error occurs
f <- function (a, b) {a2}
if b is not used in the function, calling f(5) will not produce an error
... argument
used to extend other functions by representing the rest of the arguments
generic functions use ... to pass extra arguments (i.e. mean = 1, sd = 2)
necessary when the number of arguments passed can not be known in advance
functions that use ... = paste(), cat()
Note: arguments coming after ... must be explicitly matched and cannot be partially matched

23

Scoping
scoping rules determine how a value is associated with a free variable in a function
free variables = variables not explicitly defined in the function (not arguments, or local variables variable defined in the function)
R uses lexical/static scoping
common alternative = dynamic scoping
lexical scoping = values of free vars are searched in the environment in which the function is
defined
environment = collection of symbol/value pairs (x = 3.14)
each package has its own environment
only environment without parent environment is the empty environment
closure/function closure = function + associated environment
search order for free variable
1.
2.
3.
4.
5.

environment where the function is defined

parent environment
. . . (repeat if multiple parent environments)
top level environment: global environment (worspace) or namespace package
empty environment produce error

when a function/variable is called, R searches through the following list to match the first result
1.
2.
3.
4.
5.
6.
7.
8.
9.

.GlobalEnv
package:stats
package:graphics
package:grDeviced
package:utils
package:datasets
package:methods
Autoloads
package:base

order matters
.GlobalEnv = everything defined in the current workspace
any package that gets loaded with library() gets put in position 2 of the above search list
namespaces are separate for functions and non-functions
possible for object c and function c to coexist
Scoping Example
make.power <- function(n)
pow <- function(x) {
x^n
}
pow
}
cube <- make.power(3)
#
square <- make.power(2) #
cube(3)
#

defines a function with only n defined (x^3)

defines a function with only n defined (x^2)
defines x = 3

24

## [1] 27
square(3)

# defines x = 3

## [1] 9
# returns the free variables in the function
ls(environment(cube))
## [1] "n"

"pow"

# retrieves the value of n in the cube function

get("n", environment(cube))
## [1] 3
Lexical vs Dynamic Scoping Example
y <- 10
f <- function(x) {
y <- 2
y^2 + g(x)
}
g <- function(x) {
x*y
}
Lexical Scoping
1. f(3) calls g(x)
2. y isnt defined locally in g(x) searches in parent environment (working environment/global
workspace)
3. finds y y = 10
Dynamic Scoping
1. f(3) calls g(x)
2. y isnt defined locally in g(x) searches in calling environment (f function)
3. find y y <- 2
parent frame = refers to calling environment in R, environment from which the function was
called
Note: when the defining environment and calling environment is the same, lexical and dynamic scoping
produces the same result
Consequences of Lexical Scoping
all objects must be carried in memory
all functions carry pointer to their defining environment (memory address)

25

Optimization
optimization routines in R (optim, nlm, optimize) require you to pass a function whose argument is a
vector of parameters
Note: these functions minimize, so use the negative constructs to maximize a normal likelihood
constructor functions = functions to be fed into the optimization routines
example
# write constructor function
make.NegLogLik <- function(data, fixed=c(FALSE,FALSE)) {
params <- fixed
function(p) {
params[!fixed] <- p
mu <- params[1]
sigma <- params[2]
a <- -0.5*length(data)*log(2*pi*sigma^2)
b <- -0.5*sum((data-mu)^2) / (sigma^2)
-(a + b)
}
}
# initialize seed and print function
set.seed(1); normals <- rnorm(100, 1, 2)
nLL <- make.NegLogLik(normals); nLL
## function(p) {
##
params[!fixed] <- p
##
mu <- params[1]
##
sigma <- params[2]
##
a <- -0.5*length(data)*log(2*pi*sigma^2)
##
b <- -0.5*sum((data-mu)^2) / (sigma^2)
##
-(a + b)
##
}
## <environment: 0x7fda426462a8>
# Estimating Prameters
optim(c(mu = 0, sigma = 1), nLL)$par
##
mu
sigma
## 1.218239 1.787343
# Fixing sigma = 2
nLL <- make.NegLogLik(normals, c(FALSE, 2))
optimize(nLL, c(-1, 3))$minimum
## [1] 1.217775
# Fixing mu = 1
nLL <- make.NegLogLik(normals, c(1, FALSE))
optimize(nLL, c(1e-6, 10))$minimum
## [1] 1.800596

26

Debugging
message: generic notification/diagnostic message, execution continues
message() = generate message
warning: somethings wrong but not fatal, execution continues
warning() = generate warning
error: fatal problem occurred, execution stops
stop() = generate error
condition: generic concept for indicating something unexpected can occur
invisible() = suppresses auto printing
Note: random number generator must be controlled to reproduce problems (set.seed to pinpoint
problem)
traceback: prints out function call stack after error occurs
must be called right after error
debug: flags function for debug mode, allows to step through function one line at a time
debug(function) = enter debug mode
browser: suspends the execution of function wherever its placed
embedded in code and when the code is run, the browser comes up
trace: allows inserting debugging code into a function at specific places
recover: error handler, freezes at point of error
options(error = recover) = instead of console, brings up menu (similar to browser)

R Profiler
optimizing code cannot be done without performance analysis and profiling
# system.time example
system.time({
n <- 1000
r <- numeric(n)
for (i in 1:n) {
x <- rnorm(n)
r[i] <- mean(x)
}
})
##
##

user
0.148

system elapsed
0.004
0.173

system.time(expression)

takes R expression, returns amount of time needed to execute (assuming you know where)
computes time (in sec) gives time until error if error occurs
can wrap multiple lines of code with {}
returns object of class proc_time
user time = time computer experience
27

 elapsed time = time user experience

usually close for standard computation
elapse > user = CPU wait around other processes in the background (read webpage)
elapsed < user = multiple processor/core (use multi-threaded libraries)
Note: R doesnt multi-thread (performing multiple calculations at the same time) with basic
package
Basic Linear Algebra Standard [BLAS] libraries do, prediction, regression routines, matrix
i.e. vecLib/Accelerate, ATLAS, ACML, MKL
Rprof() = useful for complex code only
keeps track of functional call stack at regular intervals and tabulates how much time is spent in
each function
default sampling interval = 0.02 second
calling Rprof() generates Rprof.out file by default
Rprof("output.out") = specify the output file
Note: should NOT be used with system.time()
summaryRprof() = summarizes Rprof() output, 2 methods for normalizing data
loads the Rprof.out file by default, can specify output file summaryRprof("output.out")
by.total = divide time spent in each function by total run time
by.self = first subtracts out time spent in functions above in call stack, and calculates ratio to
total
$sample.interval = 0.02 interval
$sampling.time = 7.41 seconds, elapsed time
Note: generally user spends all time at top level function (i.e. lm()), but the function simply
calls helper functions to do work so it is not useful to know about the top level function times
Note: by.self = more useful as it focuses on each individual call/function
Note: R must be compiled with profiles support (generally the case)
good to break code into functions so profilers can give useful information about where time is spent
C/FORTRAN code is not profiled
Miscellaneous
unlist(rss) = converts a list object into data frame/vector
ls("package:elasticnet") = list methods in package

28