Getting Started with R

Lecture 1

Arun Kaushik
Dept. of Statistics, BHU
Introduction R Console & Script Editor Documentation Other Features

Outline
1. Introduction
 What is R?
 Installing R
2. R Console and Script Editor
 R as a calculator
 Assigning objects and function calls
3. Documentation
4. Other Features
 Working Directory and Workspace
 Setting options

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What is R?
 R is a high-level computer language and environment for statistics and
graphics
 Performs a variety of simple and advanced statistical methods
 Produces high quality graphics
 R is a computer language so we can write new functions that extends R’s
uses
 R was initially written by Ross Ihaka and Robert Gentleman at the
Department of Statistics of the University of Auckland in Auckland, New
Zealand (hence the name).
 R is a free open source software maintained by several contributors.
Including an “R Core Team” of 17 programmers who are responsible for
modifying the R source code.
 The official R home page is

http://www.R-project.org

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Installing R
 The R system can be installed on, Windows, Mac or Linux.
 You will want to install the base system. To do so visit the R website and
follow the installation directions.
 In addition to the base system there are user contributed add-on packages.
 Packages are a collection of functions, examples and documentation that
usually focus on a specific task.
 The base system contains some packages. To install an additional package,
say gplots, be connected to the Internet and type
> install.packages("gplots")
You will be asked to select the mirror site nearest to you, after that
everything is automatic.
 Before using the contents of the package we need to load it,
> library(gplots)
 See the R website for a complete list of contributed packages

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R Console
 The R Console is where computations are performed
 An expression is inputed into the console and the expression is evaluated.
Depending on the expression, the system may respond by outputting results
to the console or creating a graph in a new window. Then another
expression is inputed and evaluated.
 An R session is this interaction between you and the system
 To get the last expression entered use the up arrow
 To get the value of the last evaluated expression type .Last.value
 Press Esc to stop evaluating the current expression

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Calculator
 Enter a math expression and the result is outputted to the console
Binary Operators + - ∗ / ˆ %%
Math Functions abs sqrt log exp log10 factorial
Trig Functions sin cos tan asin acos atan
Rounding round ceiling floor trunc signif zapsmall
Math Quantities Inf -Inf NaN pi exp(1) 1i
%% is for modular arithmetic
> 5 %% 4
[1] 1
> log(2)
[1] 0.6931472
> cos(pi)
[1] -1
> ceiling(3.2)
[1] 4
> 0/0
[1] NaN
> 1/Inf
[1] 0 6 of 18
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Objects and Functions

 What we normally do is create objects and then perform functions on those
objects (functions are also considered objects, more on this later).
 Assign an object a name "x" using either
x <- object (object -> x)
x = object
 Call a function by
function name(list of arguments separated by commas)
 Each function has a set of formal arguments some with default values; these
can be found in the function’s documentation.
 A function call can include any subset of the complete argument list.
 To specify a particular argument use the argument’s name.
 Arguments do not have to be named if they are entered in the same order as
the function’s formal argument list. However, to make your code easier to
understand it is usually a good idea to name your arguments.
 When specifying values for an argument use an =.
 R is CASE SENSITIVE.

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Example - Assigning Objects & Function Calls

 Suppose I want to find the mean of a set of numbers. I first assign the
vector of numbers a clever name x and then call the function mean().
> x = c(0,5,7,9,1,2,8)
> x
[1] 0 5 7 9 1 2 8
> mean(x)
[1] 4.571429
> X
Error: object ’X’ not found
 Now suppose I want to sort a vector y so that the numbers are descending.
By default R will sort ascending so I need to change the formal argument
decreasing to TRUE (the default value for decreasing is FALSE).
> y <- c(4,2,0,9,5,3,10)
> y
[1] 4 2 0 9 5 3 10
> sort(y)
[1] 0 2 3 4 5 9 10
> sort(y, decreasing=TRUE)
[1] 10 9 5 4 3 2 0
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Script Editor
 The script editor is used for writing programs in R.
 To start a new script, click File> New Script
 The easiest way to run code is keyboard shortcuts
 To run part of a program, highlight the lines you want and hit Ctrl+R
 To run an entire program, select all the code then run, Ctrl+A then Ctrl+R
 When you save a script file in R you need to include the .R extension, R
doesn’t automatically add the file type.
 You don’t need semi-colons at the end of each line. However, if you enter
more than one expression on the same line you will need semi-colons.
 You can wrap a long expression onto several lines, but you need to be
careful that R does not treat your unfinished code as a complete expression.
 To comment a line of code use a #. There is no block commenting in R.

Commenting Code
Comments are notes that help users understand portions of your code. They are
also useful reminders to yourself of what was done and why it was done.
Including meaningful comments in code is a major part of writing good
programs, this semester we will practice commenting our programs.
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Example - Sample Script

# Calculate the mean of x
x = c(0,5,7,9,1,2,8)
mean(x)

# How and how not to wrap expressions

long.variable.name <- 5
really.long.variable.name <- 7

# R views the first line as a complete expression. Thus the code is

# treated as two separate expressions instead of one long expression.
long.answer.name <- 500*factorial(long.variable.name)
+ sqrt(really.long.variable.name)

# Here the first line is not a complete expression (trailing + sign) so

# R continues reading lines of code until the expression is complete
long.answer.name <- 500*factorial(long.variable.name) +
sqrt(really.long.variable.name)

# Writing two expressions on the same line requires a ;

mean(x); var(x)
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Documentation
 R function documentation contains:
 A general description of the function
 A list and description of the function’s formal arguments and default settings
 Details about the function
 A list and description of values returned by the function
 References
 An executable example
Sometimes the documentation is very complete and other times it is vague.
It is more of a quick reference and not intended for instruction.
 Better educational resources are the R manuals, contributed manuals, and
FAQs available on the R website.
 There are also mailing lists. You can search archived posts or post new
questions. Posting is not for the faint of heart. If you post, be sure to have
a thoughtful question and read the posting guide.

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Documentation
 To look at the documentation for a specific function from a loaded
package,
?function name
help(function name)
 To look at the documentation of a symbol put quotations around the
symbol, i.e. ?”:”
 To search the documentation of all installed packages for key words,
??"key words"
help.search("key words")
A list of functions with the corresponding package is returned,
package::function name
 To run the example included with the documentation,
example(function name)
 There are also demos included with the base system and some packages.
To see a complete list of demos in the base system, demo(). To run a
particular demo, demo("topic").

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Example - Documentation
 Suppose we need help with the linear regression function. If we know the
name of the function, lm, but have a question about the syntax,
> ?lm
 On the other hand if we don’t know what function to use,
> help.search("regression")
 To execute the example include with lm,
> example(lm)

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Package Documentation
 To get an overview of an installed package and its contents,
help(package=package name)
 Some packages include a vignette, a file with additional documentation and
examples. To get a list of all vignettes from all installed packages,
vignette()
 To see a particular vignette,
vignette("topic")
 We don’t need to load the package to look at the contents or vignette, but
we do need to load the package to look at the documentation for a specific
function or to run a demo.

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Example - Package Documentation

 Suppose we are interested in making a flow chart. After browsing the list of
contributed packages on the R website we decide to use diagram.
 First download, install and load the package diagram
> install.packages("diagram")
> library(diagram)
 List of functions with brief descriptions in the diagram package
> help(package=diagram)
 View the vignette
> vignette("diagram")
 Look at the documentation for the function plotmat()
> ?plotmat

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Working Directory
 When we load/save datasets, load source files or save graphs we will need
to specify the file path. To avoid typing the path every time we can specify
a working directory.
 To set the working directory click File > Change dir... or type
setwd(file path)

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Workspace
 The workspace is where all the objects you create during a session are
located.
 When you close R you will be prompted to “Save workspace image?” If
you say yes, the next time you open R from the same working directory the
workspace will be restored. That is all of the objects you created during
your last session will still be available. Also see save.image().
 Depending on what you are working on, it is usually wiser to write a script
and then run the entire script with each new session. This way you know
exactly what objects you have created; sometimes lingering objects can
cause errors in programs. If a particular object is very important then save
it to a file.
 Managing the Workspace
 To list what variables you have created in the current session, ls()
 To see what libraries and dataframes are loaded, search()
 To see what libraries have been installed, library()
 To remove an object, rm(object names)
 To remove all objects, rm(list=ls())

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options()
 The function options() sets several global options that affect how R
computes and displays results.
 To look at the value of a single option, getOption("option name")
 Options reset to the defaults with each new R session, even if you save the
workspace.
 For example suppose we want to change the maximum number of digits
printed from 7 (default) to 15.
> defaults <- options() # Save all default options
> getOption("digits")
[1] 7
> pi
[1] 3.141593
> options(digits=15) # Change to 15 digits
> pi
[1] 3.14159265358979
> options(defaults) # Restore all default options
> getOption("digits")
[1] 7
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