Doing Data Science in R An Introduction for Social Scientists

- 1st Edition

Visit the link below to download the full version of this book:

https://medipdf.com/product/doing-data-science-in-r-an-introduction-for-social-s
cientists-1st-edition/

Click Download Now

DOING DATA SCIENCE IN R
An Introduction for Social Scientists
Mark Andrews

Los Angeles
London
New Delhi
Singapore
Washington DC
Melbourne
 SAGE Publications Ltd
1 Oliver’s Yard
55 City Road
London EC1Y 1SP
SAGE Publications Inc.
2455 Teller Road
Thousand Oaks, California 91320
SAGE Publications India Pvt Ltd
B 1/I 1 Mohan Cooperative Industrial Area
Mathura Road
New Delhi 110 044
SAGE Publications Asia-Pacific Pte Ltd
3 Church Street
#10-04 Samsung Hub
Singapore 049483
© Mark Andrews 2021
Apart from any fair dealing for the purposes of research or private
study, or criticism or review, as permitted under the Copyright,
Designs and Patents Act, 1988, this publication may be reproduced,
stored or transmitted in any form, or by any means, only with the
prior permission in writing of the publishers, or in the case of
reprographic reproduction, in accordance with the terms of licences
issued by the Copyright Licensing Agency. Enquiries concerning
reproduction outside those terms should be sent to the publishers.
Library of Congress Control Number: 2020945072
British Library Cataloguing in Publication data
A catalogue record for this book is available from the British Library
ISBN 978-1-5264-8676-9
ISBN 978-1-5264-8677-6 (pbk)
Editor: Aly Owen
Assistant editor: Lauren Jacobs
Production editor: Ian Antcliff
Copyeditor: QuADS Prepress Pvt Ltd
Proofreader: Neville Hankins
 Marketing manager: Ben Griffin-Sherwood
Cover design: Shaun Mercier
Typeset by: C&M Digitals (P) Ltd, Chennai, India
Printed in the UK
At SAGE we take sustainability seriously. Most of our products are
printed in the UK using responsibly sourced papers and boards.
When we print overseas we ensure sustainable papers are used as
measured by the PREPS grading system. We undertake an annual
audit to monitor our sustainability.
CONTENTS
About the Author
Online Resources
1 Data Analysis and Data Science
Part I Fundamentals of Data Analysis and Data Science
2 Introduction to R
3 Data Wrangling
4 Data Visualization
5 Exploratory Data Analysis
6 Programming in R
7 Reproducible Data Analysis
Part II Statistical Modelling
8 Statistical Models and Statistical Inference
9 Normal Linear Models
10 Logistic Regression
11 Generalized Linear Models for Count Data
12 Multilevel Models
13 Nonlinear Regression
14 Structural Equation Modelling
Part III Advanced or Special Topics in Data Analysis
15 High-Performance Computing with R
16 Interactive Web Apps with Shiny
17 Probabilistic Modelling with Stan
References
Index
ABOUT THE AUTHOR
Mark Andrews (PhD)
is Senior Lecturer in the Department of Psychology at Nottingham
Trent University. There, he specializes in teaching statistics and data
science at all levels from undergraduate to PhD level. Currently, he
is the Chair of the British Psychological Society’s Mathematics,
Statistics, and Computing section. Between 2015 and 2018, Dr
Andrews was funded by the UK’s Economic and Social Research
Council (ESRC) to provide advanced training workshops on
Bayesian data analysis to UK-based researchers at PhD level and
beyond in the social sciences. Dr Andrews’ background is in
computational cognitive science, particularly focused Bayesian
models of human cognition. He has a PhD in Cognitive Science from
Cornell University, and was a postdoctoral researcher in the Gatsby
Computational Neuroscience Unit in UCL and also in the Department
of Psychology in UCL.
ONLINE RESOURCES

Lecturers can visit https://study.sagepub.com/andrews to find a range of additional

resources to support teaching and aid your students’ study.
INSTRUCTOR RESOURCES
PowerPoint slides covering key themes and topics from every chapter, which
are available for you to download and tailor in support of your teaching.
An instructor’s manual, providing a guide to using the book in teaching and
resources for teaching, including ideas for student activities and assessments.
Datasets for you to share with your students in class or for assignments, which
will support their mastery of data science techniques.
1 DATA ANALYSIS AND DATA SCIENCE
Introduction 2
What is data science? 3
Why R, not Python? 5
Who is this book for? 6
The style and structure of this book 7
1.1 INTRODUCTION
This book is about statistical data analysis of real-world data using modern tools. It is
aimed at those who are currently engaged in, or planning to be engaged in, analysis
of statistical data of the kind that might arise at or beyond PhD level scientific
research, especially in the social sciences. The data in these fields is complex. There
are many variables and complex relationship between them. Analysing this data
almost always requires data wrangling, exploration, and visualization. Above all, it
involves modelling the data using flexible probabilistic models. These models are
then used to reason and make predictions about the scientific phenomenon being
studied. This book aims to address all of these topics. The term we use for these
topics and their corresponding methods and tools is data science.

Figure 1.1 The data science workflow. Raw data is usually messy and not yet
amenable to analysis of any kind. Data wrangling takes the raw data and transforms
it into a new tidy format. This data is then explored and visualized in an iterative
manner, which may also include some further wrangling. This eventually leads to
probabilistic modelling, which itself involves an iterative process of statistical
inference and model evaluation. Finally, we communicate our results in articles,
presentations, webpages, etc.
As we use the term throughout this book, data science is a set of interrelated
computational or mathematical methods and tools that are used in the general data
analysis workflow that we outline in Figure 1.1. This workflow begins with data in its
nascent and raw form. Raw data is usually impossible or extremely difficult to work
with, even casually or informally. The process of transforming the data so that it
amenable to further analysis is data wrangling, and the resulting data sets are said to
be tidy. This data can then be explored and visualized. We view data exploration and
data visualization as ultimately accomplishing the same thing. One usually involves
quantitative descriptive analysis, while the other involves graphical analysis, but both
aim to discover potentially interesting patterns and behaviours in the data. The
exploratory analysis stage then leads us to posit a tentative probabilistic model of the
data. Put more precisely, it leads us to posit a tentative probabilistic model of the
phenomenon that generated the data. Inevitably, this model involves unknown
variables that must be inferred using statistical inference. This leads to a fitted model,
which may be then evaluated and possibly extended and modified, thus leading to
further inference. Eventually, we communicate our results in reports, presentations,
webpages, etc.
Each of the stages of this data science workflow involves computational and
mathematical concepts and methods. In fact, it is this combination of the
computational and the mathematical or statistical that is a defining feature or key
characteristic of data science as we conceive of it. Without using computers, and thus
performing any stages of the workflow manually in some manner, only practically
trivial types of analysis could be accomplished, and even then the analysis would be
laborious and error prone. By contrast, the more proficient we are with the relevant
computational tools, the more efficient and sophisticated our analyses can be. In this
sense, computing skills, specifically reading and writing code, are integral and vital
parts of modern data analysis. These cannot be generally sidestepped or avoided by
using graphical user interfaces (GUIs) to statistics programs. While programs like
these are sometimes suitable for novices or for casual use, they are profoundly
limited and inefficient in comparison to writing code in a high-level programming
language.
In addition to computing tools, many of the stages of the data science workflow
involve mathematical and statistical concepts and methods. This is especially true of
the statistical modelling stage, which requires a proper understanding of
mathematical and probabilistic models, and related topics such as statistical
inference. Simply being able to perform a statistical analysis computationally,
accompanied by a vague and impressionistic understanding of what the analysis is
doing and why it is doing it, will not generally be sufficient. Without a deeper and
theoretical understanding of probabilistic models, statistical inference, and related
concepts, we will not be able to make principled and informed choices concerning
which models to use for any given problem. Nor would we be able to understand the
meaning of the results of the inference, and we would be limited or mistaken in the
practical and scientific conclusions that we make when we use these models for
explanation or prediction. Moreover, statistical models of the kind that we cover in this
book should not be seen as a list of independent tools in a big toolbox, each one
designed for a different task or application, and each with its own rules and principles.
Rather, more generally, we should view statistical modelling as a systematic
framework, or even a language, for building mathematical models of scientific
phenomena using observed data. While we may talk about normal linear models, or
zero-inflated Poisson models, etc., these are just examples of the infinitely many
models that we can build to model the scientific problem at hand. Being aware of
statistical modelling as a flexible and systematic framework that is based on
pragmatic and theoretical principles allows us to more competently and confidently
perform statistical analysis, and also greatly increases the range and scope of the
analyses that are readily available to us.
1.2 WHAT IS DATA SCIENCE?
Even if we accept the nature and the value of the data analysis workflow that we’ve
just outlined, it is reasonable to ask whether it should properly be called ‘data
science’. Is this not just using a new word, even a buzzword, in place of much more
established terms like ‘statistics’ or ‘statistical data analysis’? We are using the term
‘data science’ rather than ‘statistics’ per se or some variant thereof because data
analysis as we’ve outlined it arguably goes beyond the usual focus of statistics, at
least as it is traditionally understood. Mathematical statistics as a scientific or
mathematical discipline has focused largely on the statistical modelling component of
the programme we outlined above. As we’ve hopefully made clear, this component is
of profound importance, and in fact we would argue that it is the single most
important part and even ultimate goal of data analysis. Nonetheless, in practice, data
wrangling alone occupies far more of our time and effort in any analysis, and
exploration and visualization should be seen as necessary precursors to, and even
continuous with, the statistical modelling itself. Likewise, traditional statistics often
marginalizes the practical matter of computing tools. In statistics textbooks, even
excellent ones, for example, code examples may not be provided for all analyses,
and the code may not be integrated tightly with the coverage of the statistical
methods. In this sense, traditional statistics does not thoroughly deal with all the parts
of the data analysis workflow that we have outlined. This is not a criticism of statistics,
but just a recognition of its particular focus.
This general point about real-world data analysis being more than just the traditional
focus of mathematical statistics was actually made decades ago by Tukey (1962).
There, Tukey, who was one of the most influential statisticians of the twentieth
century and a pioneer of exploratory data analysis and data visualization, preferred
the term data analysis as the general term for what he and other statistical analysts
actually do in practice. For Tukey, inferential statistics and statistical modelling were
necessary and vital, but only as a component of a much bigger and multifaceted
undertaking, which he called ‘data analysis’.
While the general spirit of the argument about the breadth and scope of data analysis
that Tukey (1962) outlined is very much in keeping with the perspective we follow
here, modern data analysis has a character that goes beyond Tukey’s vision,
however broad and comprehensive it was. This is due to the computing revolution.
For example, when Tukey was writing in the early 1960s, the world’s fastest
computers1 were capable of around 1 million calculations per second. Approximately
60 years later in 2020, the world’s fastest computer2 is capable of around 500
quadrillion (5 × 1017) calculations per second, and a typical consumer desktop can
perform hundreds of billions of calculations per second. This revolution has
transformed all aspects of data analysis, and now computing is as vital and integral a
part of data analysis as are mathematics and statistics. It was largely the recognition
of the vital and transformative role of computing that lead Cleveland (2001) to coin
the term ‘data science’. As we use the term, therefore, data science is the blend of
computational and statistical methods applied to all the aspects of data analysis.
1 https://en.wikipedia.org/wiki/Atlas_(computer)
2
https://en.wikipedia.org/wiki/Fugaku_(supercomputer)
Even if we accept that the defining feature of data science is generally the combined
application of computational tools and statistical methods to data analysis, the term
‘data science’ has some popular connotations that are somewhat at odds with the
more general understanding of the term that we are following in this book. In
particular, for some people, data science is all about concepts like predictive
analytics, big data, machine learning, deep learning, data mining of massive
unstructured data sets including natural language corpora. It is seen as largely a
branch of computer science and engineering, and is something that is done in the big
tech companies like Google, Amazon, Facebook, Apple, Netflix and Twitter. It is
absolutely true that data science, particularly as it is practised in industry, heavily
avails tools like machine learning and big data analysis software, and is applied to the
analysis of massive unstructured data sets. As real and important as these activities
are, we see them here as just one application of data science as we generally
understand the term. Also, in this particular application of data science, some topics
and issues take precedence over or dominate others. For example, in these contexts,
the software and hardware problems of being able to analyse data that is on such a
large scale are the major practical issues. Likewise, for some applications, being able
to perform successful predictions using statistical methods is the only goal, and so
the assumed statistical models on which these predictions are based are less
important or even irrelevant (see Breiman, 2001, for a well-known early discussion of
these two different general ‘cultures’ of using statistical methods).
In summary, in this book, we use the term ‘data science’ as the general term for
modern data analysis, which is something that always involves a tight integration of
computational and statistical methods and tools. In this, we are hopefully faithfully
following the broad and general understanding of what real-world data analysis
entails as described by Tukey (1962), albeit with the additional vital feature of
intensive use of computational tools. In some contexts, data science has a more
particular focus on big data, data mining, machine learning and related concepts.
That particular focus is not the focus of this book, and so this book is probably not
ideal for anyone keen to learn more about data science in just this sense of the term.
1.3 WHY R, NOT PYTHON?
We have stated repeatedly that computational methods and tools are vital for doing
data science. In this book, the computing language and environment that we use is
the R Project for Statistical Computing, simply known as R. More specifically, we use
the modern incarnation of R that is based on the so-called tidyverse. In Chapter 2 we
provide a proper introduction to R. Here, we wish to just outline why R is our choice
of language and environment, what the alternatives are, and what this entails in terms
of the our conception of what data science is and how it is practised.
Given our conception of the data science workflow that we outlined in Figure 1.1, R is
an inevitable choice. We believe that R is simply the best option for performing all the
major components that we outline there. For example, for the data wrangling
component, which can be extremely laborious, R packages that are part of the
tidyverse such as readr, dplyr and tidyr, which we cover in Chapter 3, make
data wrangling fast and efficient and even pleasurable. For data visualization, the
ggplot2 package provides us with essentially a high-level and expressive language
for data visualization. For the statistical modelling loop, which we cover in all the
chapters of Part II of this book, R provides a huge treasure trove of packages for
virtually every conceivable type of statistical methods and models. Also, R is the
dominant environment, using packages like rstan and brms, for doing Bayesian
probabilistic modelling using the Stan probabilistic programming language. We cover
Bayesian models throughout the chapters of Part II. For communication, R provides
us with the ability to produce reproducible data analysis reports using RMarkdown,
Knitr and other tools, which we describe in Chapter 7.
Everything we cover in this book could be done using another programming
language, or possibly using some set of different languages. Chief among these
alternatives is Python. Python is close to being the most widely used general-purpose
programming language of any kind. It has been very popular for almost two decades,
and its dominance and popularity have been increasing in recent years. Moreover,
one of Python’s major domains of application is data science, with some arguing that
it should preferred over R for data science generally. For the big data, big tech, data
mining, machine learning sense of data science that we mentioned above, Python
certainly ought to be the dominant choice over R. This is for multiple reasons. First,
Python is now the principal computing language for doing machine learning, deep
learning and related activities. Also, because Python is a general-purpose
programming language and one that is widely used on the back end of web
applications, this makes integrating data science tools with the ‘production’ web
server software much easier and scalable. Likewise, Python is a very powerful and
well-designed general-purpose programming language, which means that it is easier
to write complex highly structured software applications in Python than in a
specialized language like R. This again facilitates the integration of Python data
science tools with production- or enterprise-level software applications. Nonetheless,
for the more general conception of data science that we are following in this book,
Python is more limited than R. For example, for data wrangling of typical rectangular
data structures, Python’s pandas package, as excellent as it is, is not as high level
and expressive as R’s tidyverse-based packages like dplyr and tidyr. This entails
that wrangling data into shape in R can be easier and involve less lower-level
procedural and imperative code than when using Python. Likewise for data
visualization, Python’s matplotlib package is very powerful but is also lower-level
than ggplot2. This entails that relatively complex visualization requires considerably
more procedural or imperative code, which is harder and slower to read and write
than using the more expressive high-level code of ggplot2. The higher-level
counterpart of matplotlib is seaborn, which is excellent, but seaborn is less
powerful and extensive in terms of its features than ggplot. For statistical modelling,
at the moment, there frankly is no competition between R and Python. Even though
Python has excellent statistics packages like statsmodels, these provide only a
fraction of the statistical models and methods that are available from R packages.
Finally, although dynamic notebooks like Jupyter3 are widely used by Python users,
and are excellent too, it is not as easy to create reproducible reports, for example for
publication in scientific journals, using Jupyter as it is using RMarkdown and knitr. In
fact, currently the easiest way to write a Python-based reproducible manuscript is to
use Python within R using the reticulate package.
3
https://jupyter.org/
1.4 WHO IS THIS BOOK FOR?
As mentioned at the start of this chapter, the prototypical audience at whom this book
is aimed are those engaged in data analysis in scientific research, specifically
research at or beyond PhD level. In scientific research, statistics obviously plays a
vital role, and specifically this is based on using data to build and interpret statistical
or probabilistic models of the scientific phenomenon being studied. This book is
heavily focused on this particular kind of statistical data analysis. As we’ve
mentioned, in data science as it is practised in industry and business, often the other
‘culture’ of statistics (see Breiman, 2001), namely predictive analytics and algorithms,
is the dominant one, and so this book is not ideal for those whose primary data
science interests are of that kind.
We’ve explicitly stated that this book is intended for those doing research in the social
sciences, but this also requires some explanation. The explicit targeting of the social
sciences is largely just to keep some focus and limits to the sets of examples that are
used throughout the book. However, beyond the example data sets that are used,
there is little about this content that is of relevance to only those doing research in
social science disciplines. All the content on data wrangling, exploration and
visualization, statistical modelling, etc., is hopefully just as relevant to someone doing
research in some field of biology as it is to someone doing research in the social
sciences. The nature of the data in terms of its complexity, and the nature of the
analysis of this data using complex statistical models, are traditionally very similar in
biology and social sciences. In fact, the statistics practised in all of these fields has all
arisen from a common original source, particularly the early twentieth-century
pioneering work of R. A. Fisher (e.g. Fisher, 1925).
We assume that the readers of this book will already be familiar with statistics to an
extent. For example, we assume that they’ve taken undergraduate-level courses
introducing statistics as it is used and applied in some discipline of science. We will
present the statistical methods that we cover from a foundational perspective, and so
not assume that readers are already confident and familiar with the fundamental
principles of statistical inference and modelling. However, we do assume that they will
have already had an introduction to statistics so that concepts like the ‘normal
distribution’, ‘linear regression’ and ‘confidence intervals’ will be relatively familiar,
even if they don’t have a very precise grasp of their technical meaning. On the other
hand, we do not assume any familiarity with any computing methods, nor R in
particular. In fact, we assume that many readers will be brand new to R.
1.5 THE STYLE AND STRUCTURE OF THIS BOOK
Apart from this brief introductory chapter, all the remainder of the book is a blend of
expository text, R code, mathematical equations, diagrams and R-based plots. It is
intended that people will read this book while using R to execute all the code
examples and so produce all the results that are presented either as R output or as
figures. Of course, if readers wish to read first and then run the code later, perhaps
on a second reading, that is entirely a matter of preference. However, all the code
that we present throughout this book is ready to run, and does not require anything
other than the R packages that are explicitly mentioned in the code and the relevant
data sets, which are all available on the website that accompanies the book.
The book is divided into three parts. Part I is all about the parts of the data science
workflow shown in Figure 1.1 except for the statistical modelling loop part. Thus, in
Part I we provide a comprehensive general introduction to R, a chapter on data
wrangling using dplyr, tidyr, etc., a chapter on data visualization, and another on
data exploration. We then go into more detail about programming in R, and conclude
Part I with a chapter on doing reproducible data analysis using tools like RMarkdown
and Git. Part II of the book, which is the largest part, is all about the statistical
modelling loop part of the data science workflow. There, we provide a general
introduction to statistical inference, and then cover all the major types of regression
models, specifically normal linear regression, generalized linear models, multilevel
models, nonlinear regression, and path analysis and related models. In Part III, which
is the shortest part, we cover some specialized topics that are not necessarily part of
the statistical modelling topics, but not general or introductory either. Specifically, in
Part III, we provide an introduction to using R for high-performance computing,
making interactive graphics web apps using Shiny, and a general introduction to
Bayesian probabilistic programming using Stan.
PART I FUNDAMENTALS OF DATA
ANALYSIS AND DATA SCIENCE
PART I CONTENTS
Chapter 2: Introduction to R 11
Chapter 3: Data Wrangling 51
Chapter 4: Data Visualization 101
Chapter 5: Exploratory Data Analysis 153
Chapter 6: Programming in R 185
Chapter 7: Reproducible Data Analysis 221