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Easy Statistics for Food Science with R
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Easy Statistics for Food
Science with R

Abbas F.M. Alkarkhi

Malaysian Institute of Chemical & Bioengineering Technology Universiti Kuala Lumpur,
(UniKL, MICET), 78000, Melaka, Malaysia

Wasin A.A. Alqaraghuli

Skill Education Center, PA, A-07-03 Pearl Avenue, Sungai Chua, 43000 Kajang,
Selangor, Malaysia
Academic Press is an imprint of Elsevier
125 London Wall, London EC2Y 5AS, United Kingdom
525 B Street, Suite 1650, San Diego, CA 92101, United States
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The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
Copyright r 2019 Elsevier Inc. All rights reserved.
No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical,
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This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as
may be noted herein).
Notices
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understanding, changes in research methods, professional practices, or medical treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any
information, methods, compounds, or experiments described herein. In using such information or methods they should
be mindful of their own safety and the safety of others, including parties for whom they have a professional
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To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for
any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any
use or operation of any methods, products, instructions, or ideas contained in the material herein.
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library
Library of Congress Cataloging-in-Publication Data
A catalog record for this book is available from the Library of Congress
ISBN: 978-0-12-814262-2

For Information on all Academic Press publications

visit our website at https://www.elsevier.com/books-and-journals

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Acquisition Editor: Megan R. Ball
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 Dedication

Abbas
To the memory of my parents (deceased)
To my children Atheer, Hibah, and Farah
Wasin
To the memory of my father (deceased)
To my mother
This page intentionally left blank
Contents

Preface ix 4. Measures of Location and

Dispersion
4.1 Descriptive Statistics 33
4.2 Descriptive Statistics in R 33
4.3 Measures of Location 35
1. Introduction 4.3.1 The Arithmetic Mean for
1.1 Why Should Multivariate Analysis Univariate 35
be Studied? 1 4.3.2 Multivariate (Mean Vector) 38
1.2 Organization of Multivariate Data 1 4.4 Measure of Dispersion (Variation) 40
1.3 Examples of Multivariate Data 2 4.4.1 Variance and Standard Deviation
1.4 Multivariate Normal Distribution 6
for Univariate 40
Further Reading 9
4.5 Covariance 42
4.5.1 Covariance Matrices (Multivariate) 42
4.6 Correlation 42
2. Introduction to R 4.6.1 Correlation Matrices 43
2.1 Introduction to R Statistical Software 11 4.7 Scatter Plot 47
2.2 Installing R 12
4.7.1 The Scatter-plot Matrix 48
2.2.1 R Documentation 14 4.8 Distance 49
2.2.2 Installing R Packages 15 Reference 52
2.3 The R Console 15 Further Reading 52
2.4 Expression and Assignment in R 17
2.5 Variables and Vectors in R 18
2.5.1 Matrix in R 20
2.6 Basic Definitions 22
2.7 Graphs in R 23 5. Hypothesis Testing
2.8 Installing RStudio 24 5.1 What Is Hypothesis Testing? 53
2.8.1 Navigate RStudio 24 5.2 Hypothesis Testing in R 53
2.9 Importing Data 26 5.3 General Procedure for Hypothesis
Further Reading 27 Testing 55
5.3.1 Definitions 55
5.3.2 Definitions 56
3. Statistical Concepts 5.4 Hypothesis Testing About a Mean
3.1 Introduction 29 Value 57
3.2 Definition of Statistics 29 5.4.1 Inference About a Mean Value
3.3 Basic Definitions 29 for One Sample (Univariate) 57
3.4 Data Collection 30 5.4.2 Inference About a Mean Vector
3.4.1 Methods of Data Collection 30 for One Sample (Multivariate) 66
3.5 Sampling Techniques 31 5.5 Comparing Two Population Means 70
3.5.1 Simple Random Sampling 31 5.5.1 Comparing the Means of Two
3.5.2 Systematic Sampling 32 Populations (One Variable) 70
3.5.3 Stratified Sampling 32 5.5.2 Comparing Two Multivariate
3.5.4 Cluster Sampling 32 Population Means 74
Further Reading 32 Further Reading 80

vii
viii Contents

6. Comparing Several Population 8.3 Calculating Principal Components 126

Means 8.4 Principal Components From Correlation
6.1 Introduction 81 Matrix 127
6.2 ANOVA and MANOVA in R 81 8.5 Standardizing the Principal
6.3 Analysis of Variance (ANOVA) 83 Components 127
8.6 Choosing the Number of Principal
6.3.1 One-Way ANOVA 83
Components 127
6.3.2 Two-Way ANOVA 88 8.7 Principal Components Analysis in R 127
6.4 Multivariate Analysis of Variance Further Reading 141
(MANOVA) 94
6.4.1 One-Way MANOVA 94
6.4.2 Two-Way MANOVA 99
Further Reading 105
9. Factor Analysis
9.1 Introduction 143
9.2 Factor Analysis Model 143
7. Regression Models 9.3 Procedure for Factor Analysis 144
7.1 Introduction 107 9.3.1 Principal Component Method 144
7.2 Regression Analysis in R 107 9.4 Factor Analysis in R 145
7.3 Simple Linear Regression 109 Further Reading 159
7.3.1 Hypothesis Testing 109
7.3.2 Interpretation of Regression
Equation 110
7.3.3 Prediction Using a Regression 10. Discriminant Analysis
Equation 113 and Classification
7.3.4 Outliers and Influential 10.1 Introduction 161
Observations 114 10.2 Describing Discriminant Analysis
7.3.5 Residuals 116 Data 161
7.3.6 Explained and Unexplained 10.3 Discriminant Function 161
Variation 116 10.3.1 Procedure for Finding
7.3.7 Coefficient of Determination 118 the Discriminant Function 162
7.4 Multiple Regression 119 10.4 Classification 163
7.5 Hypothesis Testing in Multiple Linear 10.5 Discriminant Analysis in R 164
Regression 120 Further Reading 175
7.5.1 Test of Overall Significance of the
Regression Model 120
7.5.2 Tests on Individual Regression
Coefficients Regression Model 120 11. Cluster Analysis
7.5.3 Tests on a Subset of the Regression 11.1 Introduction 177
11.2 Measures of Distance 177
Coefficients 120
11.3 Approaches for Clustering 178
7.6 Adjusted Coefficient of Determination 121
7.7 Multivariate Multiple Linear Regression 123 11.3.1 Hierarchical Clustering 178
Further Reading 124 11.3.2 Nonhierarchical Methods 179
11.4 Cluster Analysis in R 179
Further Reading 186

8. Principal Components Analysis

8.1 Introduction 125 Appendix 187
8.2 Describing Principal Components 125 Index 213
Preface

Easy statistics for food science with R software was written in a simple way to introduce some statistical methods that
are important to graduate students, postgraduate students, and researchers who work in the food science or food engi-
neering fields with applications in food science. Specifically, this book was written to help researchers from different
fields to analyze their data and make valid decisions. The interpretation of the results is carried out in a step-by-step
manner and in an easy and clear style to enable nonstatisticians to understand and use it in their research. This book is
not comprehensive because the topics were selected based on what is commonly used in the field.
The analysis is carried out step by step, and the interpretation of the results is given for each example by matching
the results to the area of study where the data were obtained. The book focuses on the applications of univariate and
multivariate statistical methods in the field of food science. We use real data obtained from research in the School of
Industrial Technology, USM over more than 10 years of work in food science.
The development of modern statistical packages makes the analysis of data easier than before. Thus, no mathemati-
cal proofs are given in this book. Instead, the focus is on the application of statistics and correct methods for the analy-
sis and interpretation of data.
R statistical software is used throughout the book to analyze the data. The beauty of R is that it is open source, and
you can label your work based on your ideas and arrangement to produce beautiful graphs with high resolution. R is
available over the internet under the General Public License (GPL online) for the Windows, Macintosh, and Linux oper-
ating systems.
Finally, we wish to thank our colleagues and friends for their continuous support, especially Dr. Yusri Yusup for his
valuable comments. We would like to extend our thanks to the R software community and R family (R users and contri-
butors to R). This book would not have been possible without the information provided online, which is easy to obtain.
We thank the University of Kuala Lumpur (UnikL-MICET) for its support.

ix
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Chapter 1

Introduction

Learning outcomes
At the end of this chapter, you should be able
G To describe multivariate analysis.
G To understand the benefits of multivariate methods.
G To arrange the results of multivariate data to be ready for analysis.
G To understand the difference between univariate and multivariate concepts.
G To know how and where to use multivariate data.
G To comprehend the univariate normal distribution.
G To comprehend the multivariate normal distribution.

1.1 WHY SHOULD MULTIVARIATE ANALYSIS BE STUDIED?

Univariate statistical tests describe statistical methods for analyzing data related to a single variable. However, most
research studies require measuring several variables for each individual or object (unit, sampling units, research units,
or experimental units) in one or more samples. For example, consider assessing the flour prepared from green and ripe
banana fruits based on starch, digestible starch, resistant starch, total dietary fiber, soluble dietary fiber, and insoluble
dietary fiber. In this case, there are six variables measured for each sample, and these variables are usually correlated.
Analyzing the results by considering one variable at a time would ignore the relationships between the variables and
mislead the researcher about the real behavior of the variables in the presence of other variables. Thus, a technique that
considers the relationship between different variables is required to untangle the overlapping information indicated by
the correlated variables to understand the real structure of the phenomenon and the behavior of the different variables.
Multivariate methods can be used to analyze data with several variables without ignoring the correlation between the
variables. Multivariate analysis consists of a collection of methods that can be used for several purposes, which include
identifying groups of similar individuals (objects) using cluster analysis; reducing the number of variables to a small
number of indices without losing valuable information and enabling easier interpretation using principal or factor analy-
sis; separating the data into different groups based on the measured variables using discriminant analysis; performing
hypothesis testing based on several variables, such as MANOVA; and making predictions based on the relationships
among the variables using multivariate multiple regression analysis.

1.2 ORGANIZATION OF MULTIVARIATE DATA

Multivariate data for several variables measured from a number of samples (items) can be presented in a table. The
numbers of rows and columns of the table are specified based on the number of samples (items) and number of vari-
ables, respectively.
In general, the data for n samples (items) and k variables measured for each sample are presented in Table 1.1. In
this case, the table consists of n rows to represent the samples and k columns to represent the variables measured from
each sample.
Note
G The total number of samples (n) is usually greater than the number of variables measured, k.

Easy Statistics for Food Science with R. DOI: https://doi.org/10.1016/B978-0-12-814262-2.00001-7

© 2019 Elsevier Inc. All rights reserved. 1
2 Easy Statistics for Food Science with R

TABLE 1.1 The Arrangement of n Samples and k Variables in Multivariate Form

Variable Sample Y1 Y2 ... Yj ... Yk

1 Y11 Y12 ... Y1j ... Y1k

2 Y21 Y22 ... Y2j j ... Y2k

^ ^ ^ ... ^ ... ^

i Yi1 Yi2 ... Yij ... Yik

^ ^ ^ ... ^ ... ^

n Yn1 Yn2 ... Ynj ... Ynk

1.3 EXAMPLES OF MULTIVARIATE DATA

A few examples of multivariate data may be helpful in easier demonstrating the associated calculations or illustrating
concepts related to multivariate methods. Some real case studies of multivariate data related to food science will be pro-
vided. Different multivariate methods will be applied to these examples in subsequent chapters.
Example 1.1: Physicochemical properties of a banana—The physicochemical properties of banana pulp and peel
flour prepared from green and ripe Cavendish bananas were investigated. The physicochemical properties, such as the
pH; total soluble solids (TSS, o Brix); water-holding capacity (WHC, g water/g dry sample); oil-holding capacity
(OHC, g oil/g dry sample) at 40, 60, and 80
C; color values (L* (lightness), a* (redness),and b* (yellowness)); back
extrusion force (BEF) in N (Newtons); and viscosity were measured. The four types of flours are green peel (Gpe), ripe
peel (Rpe), green pulp (Gpu), and ripe pulp (Rpu). The data are given in Table 1.2.
The objective of this study was to compare green and ripe Cavendish banana flour based on the selected physico-
chemical properties of the pulp and peels. Furthermore, the data were used to discriminate between the four types of
flour, Gpe, Rpe, Gpu, and Rpu. The last objective was to identify the most appropriate physicochemical methods to dif-
ferentiate the flours. The data will be used to identify the source of variation in the data themselves using principal
components analysis (PCA).
Example 1.2: Heavy metal in cockles—A researcher wants to assess the concentration of arsenic (As) and six heavy
metals (chromium (Cr), cadmium (CD), zinc (Zn), copper (Cu), lead (Pb), and mercury (Hg)) in cockles obtained from
two locations. The two locations, with 20 sampling points at each location, were Kuala Juru (the Juru River) and Bukit
Tambun (the Jejawi River) in the Penang State of Malaysia. The data were analyzed for the concentration of arsenic
(As) and heavy metals using a graphite flame atomic absorption spectrometer (GF-AAS) for Cr, Cu, Pb, Cd, Zn, As,
and a cold vapor atomic absorption spectrometer (CV-AAS) for Hg. Arsenic and heavy metals concentration were mea-
sured (mg/L) at 20 different sites. The data are given in Table 1.3.
To assess whether the cockles obtained from these rivers are polluted or not, the relationship between different para-
meters should be considered for more information on the behavior of each variable in the presence of other variables,
which helps the researcher identify the source of the variation and use the data to discriminate between different loca-
tions. Furthermore, the contribution of each parameter in explaining the total variation in the data can be observed using
multivariate methods. This study may assist in the evaluation of the impact of industry and agricultural discharge on
aquaculture products in the selected area.
Example 1.3: Quality characteristics for tapioca deep-fried food—A researcher wants to investigate the quality
characteristics of “tapioca” or “cassava,” a popular Malaysian snack prepared by deep frying. Seven different brands of
tapioca were selected based on the packaging type (polyethylene zip-lock, laminated gas packaging, and typical trans-
parent polypropylene). Furthermore, T1 (packed in laminated pouches bag with gas packaging) was obtained from a
kiosk; T2 (packed in transparent polyethylene zip-lock packaging) was acquired from an established supermarket chain;
and T3, T4, T5, and T7 (all packed in transparent polypropylene plastic bag packaging) were acquired from various
stores. Lastly, T6 (packed in laminated gases packaging) was obtained from a supermarket. The samples were analyzed
to determine their fat oxidation (Peroxide (PV), p-anisidine (p-AV), acid value (AV) [mg KOH/g] and thiobarbituric
acid (TBA) [mg MAD/kg]), fat content (%), fatty acid composition (%) (saturated fatty acid (SFA), polyunsaturated
TABLE 1.2 The Physicochemical Properties of Banana Pulp and Peel Flours Prepared From Green and Ripe Fruits

Group pH TSS L* a* b* WHC40 WHC60 WHC80 OHC40 OHC60 OHC80 Viscosity Texture
Gpe 4.64 1.83 45.16 5.28 21.01 5.15 5.21 5.70 0.78 0.68 1.10 60.07 32.70

Gpe 4.32 1.73 43.10 6.03 23.02 5.16 4.87 5.97 0.78 0.77 1.06 46.90 34.16

Gpe 4.60 1.77 44.72 6.42 23.38 5.03 5.14 5.65 0.79 0.75 1.17 55.70 33.88

Gpe 4.59 1.57 37.82 5.89 21.35 5.15 4.95 6.16 0.76 0.75 1.02 49.97 37.06

Gpe 4.55 1.53 38.64 5.67 24.30 5.20 5.37 6.50 0.74 0.78 0.95 58.83 37.26

Gpe 4.33 1.67 39.85 5.36 23.73 4.99 5.53 6.00 0.80 0.77 1.02 57.53 38.02

Gpe 4.30 1.60 37.04 5.52 22.88 4.58 5.36 6.21 0.69 0.76 1.05 57.70 38.89

Gpe 5.08 1.70 36.35 4.94 21.81 5.20 5.85 5.97 0.75 0.80 1.01 46.73 39.20

Gpe 5.31 1.80 48.73 3.79 26.58 4.34 5.53 5.15 0.73 0.71 1.03 55.03 38.80

Gpe 5.33 1.80 38.42 4.38 22.66 4.97 4.81 5.71 0.85 0.75 1.02 54.53 36.90

Gpe 5.24 1.83 45.93 4.26 27.07 4.14 5.27 5.88 0.76 0.78 0.96 52.97 39.68

Gpe 5.26 1.90 34.83 4.89 21.45 5.03 4.82 5.64 0.72 0.78 0.97 54.87 40.91

Rpe 4.86 3.30 32.43 5.26 11.16 5.39 6.43 6.65 0.94 0.94 1.30 66.90 54.19

Rpe 5.31 3.20 35.61 4.77 13.10 6.10 6.56 8.10 1.06 0.98 1.33 73.47 43.99

Rpe 5.32 3.60 35.25 5.29 11.55 5.55 6.34 8.19 0.97 1.04 1.28 77.23 35.94

Rpe 5.31 3.53 32.50 5.52 11.02 6.19 6.64 8.10 0.97 0.92 1.07 79.50 55.17

Rpe 5.45 3.23 39.85 5.53 12.57 6.34 6.58 8.48 0.90 1.01 1.24 80.20 42.62

Rpe 5.69 3.47 40.31 5.55 13.07 6.21 6.72 9.26 1.01 0.96 1.39 83.90 42.62

Rpe 5.61 3.53 38.14 5.74 12.49 6.21 6.47 9.26 0.89 0.92 1.26 76.27 45.43

Rpe 5.65 3.57 39.29 5.98 12.79 6.16 6.23 8.29 1.00 0.97 1.30 79.40 47.50

Rpe 5.65 3.47 36.68 5.72 12.08 5.94 6.47 8.31 0.78 1.00 1.21 82.90 59.92

Rpe 5.68 3.50 41.08 5.32 12.97 6.17 5.90 7.92 0.96 0.98 1.37 78.30 63.24

Rpe 5.58 3.53 39.95 5.57 12.81 6.55 6.20 7.84 0.90 1.02 1.29 66.80 57.61

Rpe 5.47 3.63 40.37 6.34 14.01 6.34 5.59 7.88 0.81 1.05 1.31 72.73 59.93

Gpu 4.49 1.07 70.97 3.15 15.57 3.83 5.56 6.07 0.91 0.54 0.87 35.07 0.54

Gpu 4.37 1.17 71.70 3.41 15.22 3.72 5.52 6.03 0.91 0.57 0.83 37.00 0.63

(Continued )
TABLE 1.2 (Continued)

Group pH TSS L* a* b* WHC40 WHC60 WHC80 OHC40 OHC60 OHC80 Viscosity Texture
Gpu 4.75 1.20 68.23 3.67 15.09 4.07 5.37 6.15 0.87 0.54 0.86 40.13 0.66

Gpu 5.64 1.03 64.37 3.53 14.69 4.01 5.52 6.24 0.81 0.59 0.84 38.60 0.72

Gpu 4.73 1.17 74.10 2.83 15.34 4.03 5.60 6.35 0.84 0.42 0.97 42.27 0.72

Gpu 4.59 1.13 79.25 2.49 17.69 4.08 5.78 6.53 0.77 0.47 0.85 39.13 0.70

Gpu 4.54 1.23 79.15 2.54 17.46 3.93 5.80 6.43 0.79 0.53 0.88 38.73 0.71

Gpu 5.37 1.23 78.70 1.57 16.77 3.89 5.61 6.21 0.89 0.42 0.87 40.20 0.81

Gpu 5.58 1.27 74.78 1.86 19.54 3.93 5.58 6.43 0.71 0.43 0.71 42.53 0.70

Gpu 5.65 1.37 76.62 1.68 19.29 3.74 5.79 6.43 0.73 0.45 0.79 44.67 0.68

Gpu 5.53 1.30 77.08 1.66 20.04 4.02 5.74 6.46 0.71 0.45 0.85 47.47 0.58

Gpu 5.47 1.43 75.19 1.99 21.69 3.97 5.99 6.44 0.64 0.64 0.81 45.53 0.63

Rpu 5.60 4.33 74.39 2.52 11.51 1.53 1.61 4.86 0.81 0.82 1.15 84.13 2.36

Rpu 5.57 4.03 72.00 2.88 11.85 1.50 1.74 4.04 0.82 0.84 1.03 85.17 2.49

Rpu 4.76 3.77 67.38 5.07 20.23 1.52 1.81 4.98 0.77 0.81 1.13 91.67 2.46

Rpu 5.56 4.10 70.00 3.13 12.07 1.69 1.76 5.03 0.79 0.83 1.15 87.40 2.72

Rpu 4.95 3.97 68.14 4.10 16.71 1.42 1.77 4.04 0.80 0.83 0.99 87.23 2.39

Rpu 4.84 4.40 69.82 3.67 16.11 1.28 1.56 5.01 0.69 0.87 0.94 87.33 2.39

Rpu 5.07 4.50 70.82 2.70 12.40 1.25 1.68 5.01 0.79 0.85 1.05 86.90 2.23

Rpu 4.94 4.43 72.20 2.67 12.96 1.08 1.68 4.84 0.87 0.78 1.00 90.00 2.29

Rpu 5.04 4.30 67.12 3.87 15.93 1.54 1.88 4.83 0.79 0.83 1.11 86.97 2.08

Rpu 4.93 4.57 72.69 2.59 13.31 1.18 1.58 3.99 0.70 0.73 0.95 89.73 2.20

Rpu 5.05 4.30 70.82 3.00 13.71 1.26 1.78 4.77 0.80 0.83 1.07 90.27 1.97

Rpu 5.21 4.40 74.86 2.42 12.97 1.24 1.63 4.59 0.83 0.80 1.04 87.70 2.30
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