Chapter 1

A Brief Introduction to R, R Studio

and MicrofiniteR

Abstract This chapter provides a short introduction to the R programming language

and the RStudio environment to facilitate familiarity with the computer codes in the
later chapters of the book. Basic instructions on relevant installations, demonstrations
of some R commands, a description of microfiniteR (developed for this book)
and a list of references for further consultations are presented.

1.1 The R Programming Language

Developed in the mid-90s at the University of Auckland by Ross Ihaka and Robert
Gentleman, R is closely associated with hardcore computational statistics and it is
often seen as an alternative to statistical packages such as Stata and SAS [1–3].
However, the language has emerged as a quality open-source platform for a variety
of scientific programming tasks [4]. In recent years, R’s appeal has spread beyond
the domain of statistical computations. This is reflected in book series dedicated to
spreading the knowledge of its usage across different fields [5, 6]. In the area of
numerical analysis, the books by Soetaert et al. [7] and Griffiths [8] presented exten-
sive coverages of solution techniques to a multitude of differential equations by well-
tested, high-precision integrators developed in R. Different concepts on numerical
quadrature, numerical differentiation, optimization and curve fitting procedures are
covered in Bloomfield [9]. Schiesser [10] features the use of the language for solu-
tions to differential equations that originate from the field of Biomedical Science and
Engineering. Recently, a demonstration of the capability of the language for finite
element analyses is presented by Mustapha [11].
One of the main challenges faced by many newcomers to R is its large ecosystem
and the question of where to start. The good news is that there are many accessible
texts on the language for beginners. In fact, some of these texts can be accessed for free
via https://bookdown.org/. Besides, a gentle introduction to scientific computing in R
can be found in Jones et al. [12]. For an example-driven approach to learning R, Albert
and Rizzo [13], Kabacoff [14] and Teetor [15] are recommended. In-depth coverage
of R can be sought in Adler [16] and Wickham [17]. Meanwhile, Allerhand [18]

© The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2019 1
K. B. Mustapha, R for Finite Element Analyses of Size-dependent Microscale
Structures, SpringerBriefs in Computational Mechanics,
https://doi.org/10.1007/978-981-13-7014-4_1
2 1 A Brief Introduction to R, R Studio and MicrofiniteR

provides a quick introduction to R in just 89 pages! There are also many excellent
web resources, e.g.:
• https://www.statmethods.net/index.html
• https://www.r-bloggers.com/
• http://www.cookbook-r.com/Basics/.

1.2 Tools for Getting Started

1.2.1 R Installer

The first step to using the language is to obtain the R installer, which can be down-
loaded from the official home of the R programming language called CRAN1 : https://
cran.r-project.org/. A screenshot of the homepage is shown in Fig. 1.1. As revealed
in this figure, the installer is available for different operating systems. Clicking on
the link that matches your operating system will re-direct you to the relevant website.
As an example, clicking on the Download R for Windows will re-direct you to the
website for Windows installer (shown in Fig. 1.2). Follow the prompts to download,
save and run the files.

Fig. 1.1 Screenshot of a segment of the CRAN website

1 CRAN stands for the Comprehensive R Archive Network.

1.2 Tools for Getting Started 3

Fig. 1.2 Windows-specific website for the R installer

1.2.2 RStudio

Once R has been installed, the next step is to install RStudio which is the popular
integrated development environment (IDE) for working with R. RStudio can be
downloaded from: https://www.rstudio.com/products/rstudio/. After the installation,
look for and click on the RStudio icon (shown in Fig. 1.3) and you should see
something similar to Fig. 1.4.
Click on the small symbol pointed to by the arrow in Fig. 1.4 to reveal the full
layout of the RStudio GUI as revealed in Fig. 1.5.

1.3 Overview of Basic Operations

R is a procedural and a high-level programming language like MATLAB, Basic,

FORTRAN, and C++. The base R program comes with an incredible list of built-in
functions and mathematical constants. It is impossible to be introduced to all of R
functionalities in one go. However, a brief coverage of some of the functionalities
are highlighted next.

Fig. 1.3 The RStudio icon

4 1 A Brief Introduction to R, R Studio and MicrofiniteR

Fig. 1.4 The RStudio GUI

Environment
Editor

Files Pane

Console

Prompt Symbol

Fig. 1.5 Full layout of RStudio GUI

1.3.1 Using RStudio Console as a Calculator

The window pane named (Console) in Fig. 1.5 is typically used to display results of
computations or error messages. However, it can also be used as a powerful calculator,
which is a good way to start experimenting with R.
Type each of the expressions below in the console and hit the Enter key after each
(ignore the part of the expression with #).
1.3 Overview of Basic Operations 5

> # A line preceded by the "#" (without the quotes) is a comment in R

> 2*5 # Simple multiplication
[1] 10
> 3^4 # Exponentiation
[1] 81
> 3**4 # Another way to do exponentiation
[1] 81
> 10 + 30 - 56/3 + 90 # Combination of operators
[1] 111.3333
> round(111.333,0) # Rounding the number 111.333
[1] 111
> x = 35 # Assigning a variable
> y = x + 100 # Assigning and using the earlier
defined variable
> y # Print the value of y
[1] 135
> (Area = pi * x^2) # Using a built-in variable pi
[1] 3848.451
> vec = c(20, 32, 14, 63, 91, 8) # The command c() is used to form a
vector
> min(vec) # Obtain the smallest number in the
vector named vec
[1] 8
> max(vec) # Obtain the maximum number in vec
[1] 91
> vec[1] # Obtain the first element of vec
[1] 20
> vec[1:3] # Obtain the first 3 elements of vec
[1] 20 32 14
> rep(vec,2) # Repeat vec two times
[1] 20 32 14 63 91 8 20 32 14 63 91 8
> vec/2 # Divide all elements of vec by 2
[1] 10.0 16.0 7.0 31.5 45.5 4.0
> vec2 <- 1:8 # Another assignment operator ( <- )
> vec2 # Print vec2 is created with colon operator
[1] 1 2 3 4 5 6 7 8
> sqrt(vec2) # Find square root of vec2
[1] 1.000000 1.414214 1.732051 2.000000 2.236068 2.449490 2.645751 2.828427
> exp(1) # Exponential function
[1] 2.718282
> sin(pi/2) # Calculates the sin x, in radians

Entering and executing commands in R as done in the preceding lines of code

is called the Interactive Mode [3]. Via this interactive mode, we have had a rather
cursory exposure to some of the concepts listed below.
• Basic arithmetic operators in R
• + (Addition)
• — (Subtraction)
6 1 A Brief Introduction to R, R Studio and MicrofiniteR

• ˆ or ** (Exponentiation)
• / (Division)
• Examples of built-in functions in R
• round()
• min ()
• max()
• c()
• rep()
• sin()
• exp()
• sqrt()
• Variables and the assignment operators (there are more than two in R, the second
is the most preferred by hardcore R users)
• =
• <-
• Creating simple vectors via
• c() (combine function)
• : (colon operator)
A comprehensive discussion on these and related concepts can be explored further
in one of the many excellent references highlighted in Sect. 1.1. However, the R
documentation is also amazingly rich in content that knowing how to get help from
it is a necessary step to proficiency in R.

1.3.2 Getting Help

There are several ways to get help in R. For a start, the manuals, resources and
documentations on a myriad of functions can be accessed by typing the following in
R console:

> help.start()

Hit the Enter key after typing help.start(), and the file pane (labelled in
Fig. 1.5) will reveal links to several resources as shown in Fig. 1.6. Further, if you
click on the “Home” symbol, which is pointed to using an arrow in Fig. 1.6, the file
pane will also provide you with access to RStudio resources as shown in Fig. 1.7.
To know more about a specific function, a very handy method is to use a question
mark followed by the name of the function. This functionality is especially useful
to find more detail information about all the functions developed for this book. For
1.3 Overview of Basic Operations 7

Fig. 1.6 Accessing manuals and references on R through the RStudio GUI

Fig. 1.7 Accessing manuals and references on RStudio through the GUI

instance, say we wish to know more about the function called plot (apparently used
for plotting), we do this:
?plot

The result will be information about this function as shown in the file pane in
Fig. 1.8. Meanwhile, after populating the console with many commands and you
wish to clear it, use Ctrl+L.
8 1 A Brief Introduction to R, R Studio and MicrofiniteR

Fig. 1.8 Searching for help with “?”

1.3.3 Using RStudio’s Editor

The RStudio’s editor is appropriate for dealing with situations that demand that
multiple lines of code be executed at once rather than interactively as we have been
doing. For instance, type the following commands in the editor (as shown in Fig. 1.9).
After typing the codes, highlight all the lines and click the “run” button as depicted
in Fig. 1.10. The output will be printed in the console (see Fig. 1.11). All the codes
used in the analyses presented in this book are first written in the editor and then
run as demonstrated here. It is therefore a straightforward matter to replicate all the
analysis reported in this book by copying the codes to the editor and running them.
a = 40; b = -20; d = 100 #Define three variables
x = a + b + c # Assign the sum of the variables to x
vecy = c(12, 89, 21, 23, 100, 12) # A simple vector with c()
matrixA = matrix(vecy, nrow = 2, byrow = T) # Convert vecy to a matrix
vecy[1,] # Extract first element of vecy
matrixA[1,] # Extract first element of matrixA

1.4 Packages in R

In R, packages are the “fundamental unit of shareable code” [19]. Primarily, a package
is a collection of functions along with the associated documentation, but it may also
include other details beyond these two.
1.4 Packages in R 9

Fig. 1.9 Multiple lines of code in RStudio Editor

Fig. 1.10 Selecting and running multiple lines of code

10 1 A Brief Introduction to R, R Studio and MicrofiniteR

Fig. 1.11 Outputs are produced in the console for the lines of codes run in the editor

Although R comes with a rich set of built-in functions, extensive availability of

special-purpose user-contributed packages developed for specific applications is one
of its strength. A list of packages available from the CRAN website can be seen here:
https://cran.r-project.org/web/packages/available_packages_by_name.html.
A quick way to install a package is to use the
install.packages(“packagename”) function. To see how this works, you
may try to install a package that is needed to download the package developed for
this book from GitHub (the devtools package). To do so, type the following in
R console and hit the Enter key:
> install.packages("devtools")

Executing the above will connect to the CRAN website to download and install
devtools. After a package has been installed, it can be called by using the
library() function.

1.5 Package—MicrofiniteR

A package named microfiniteR is developed for this book to ease the com-
putational tasks. As illustrated in Fig. 1.12, the package is a collection of relevant
functions developed in Chaps. 2–4. There are three benefits to having the package.
First, readers only need to load the package once, and all the implemented functions
for the finite element models in this book will be loaded in the computer memory.
Second, the description of the functions, the meanings of the input parameters and the
1.5 Package—MicrofiniteR 11

Fig. 1.12 Highlight of functions contained in microfiniteR

value returns by each of the developed functions can be accessed by using the query
approach (question mark, followed by the function name) demonstrated in sect. 1.3.2.
Third, it is likely that there will be future updates to the functions. In this case, getting
the update will be a straightforward step of downloading the updated package from the
code’s repository on GitHub https://github.com/khameelbm/microfiniteR. Nonethe-
less, for first time usage, the package can be installed using the following command:

devtools::install_github(“khameelbm/microfiniteR”)

1.6 Summary
In this chapter, a brief historical account and a short introduction to R are provided.
Instructions on how to install the required tools for R are discussed. A limited number
of built-in functions in R are examined via the RStudio console and editor. A highlight
of the package developed for this book is presented. A list of references that can be
consulted for further explorations follows this summary.

References

1. R. Ihaka, R. Gentleman, R: a language for data analysis and graphics. J. Comput. Graph. Stat.
5, 299–314 (1996)
2. M.J. Crawley, The R Book (Wiley, Hoboken, 2007)
12 1 A Brief Introduction to R, R Studio and MicrofiniteR

3. N. Matloff, The Art of R Programming: A Tour of Statistical Software Design (No Starch Press,
2011)
4. R.C. Team, R: A Language and Environment for Statistical Computing, ed. Vienna, Austria: R
Foundation for Statistical Computing
5. Use R! Available: https://www.springer.com/series/6991
6. The R Series. Available: https://www.crcpress.com/go/the-r-series
7. K. Soetaert, J. Cash, F. Mazzia, Differential equations, in Solving Differential Equations in R
(Springer, 2012), pp. 1–13
8. G.W. Griffiths, Numerical Analysis Using R (Cambridge University Press, Cambridge, 2016)
9. V.A. Bloomfield, Using R for Numerical Analysis in Science and Engineering (Chapman and
Hall/CRC, 2014)
10. W.E. Schiesser, Differential Equation Analysis in Biomedical Science and Engineering: Ordi-
nary Differential Equation Applications with R (Wiley, Hoboken, 2014)
11. K.B. Mustapha, Finite Element Computations in Mechanics with R: A Problem-Centered Pro-
gramming Approach (CRC Press, Boca Raton, 2018)
12. O. Jones, R. Maillardet, A. Robinson, Introduction to Scientific Programming and Simulation
Using R (CRC Press, Boca Raton, 2009)
13. J. Albert, M. Rizzo, R by Example (Springer, New York, 2012)
14. R. Kabacoff, R in Action: Data Analysis and Graphics with R (Manning, 2015)
15. P. Teetor, R Cookbook (O’Reilly, 2011)
16. J. Adler, R in a Nutshell: A Desktop Quick Reference (O’Reilly Media, 2010)
17. H. Wickham, Advanced R (Taylor & Francis Limited, Abingdon, 2017)
18. M. Allerhand, A Tiny Handbook of R (Springer, Heidelberg, 2011)
19. H. Wickham, R Packages (O’Reilly Media, 2015)