Practicing R for Statistical Computing

This book is designed to provide a comprehensive introduction to R programming for data analysis, manipulation and presentation. It covers fundamental data structures such as vectors, matrices, arrays and lists, along with techniques for exploratory data analysis, data transformation and manipulation. The book explains basic statistical concepts and demonstrates their implementation using R, including descriptive statistics, graphical representation of data, probability, popular probability distributions and hypothesis testing. It also explores linear and non-linear modeling, model selection and diagnostic tools in R. The book also covers flow control and conditional calculations by using ‘‘if’’ conditions and loops and discusses useful functions and resources for further learning. It provides an extensive list of functions grouped according to statistics classification, which can be helpful for both statisticians and R programmers. The use of different graphic devices, high-level and low-level graphical functions and adjustment of parameters are also explained. Throughout the book, R commands, functions and objects are printed in a different font for easy identification. Common errors, warnings and mistakes in R are also discussed and classified with explanations on how to prevent them. Preface Contents About the Authors 1 R Language: Introduction 1.1 R Introduction 1.2 R and S: History and Background 1.3 The R Foundation 1.4 What Is CRAN? 1.5 R-Forge 1.6 Why R Language? 1.6.1 What Does R Do? 1.7 R Packages: An Introduction Bibliography 2 Obtaining and Installing R Language 2.1 Downloading and Installation of R 2.1.1 Running R 2.1.2 The R User Interface or Layout 2.1.3 Updating the R Installation 2.1.4 Accessing Available Data in R Packages 2.1.5 Choosing Repositories 2.1.6 Setting a Default CRAN Mirror 2.2 Managing Directories 2.3 R Session 2.4 Workspace 2.5 Command History Bibliography 3 Using R as a Calculator 3.1 Computing Mathematical Expression in R 3.2 Basic Algebraic Expressions 3.3 Assigning Values to Variables 3.3.1 Rules for Naming a Variable 3.4 Logical Expressions 3.4.1 [basicstyle=]xor(x, Y) Exclusive OR 3.4.2 [basicstyle=]isTRUE(x) 3.5 Built-in Mathematical Functions 3.6 Built-in Constants Bibliography 4 Data Mode and Data Structure 4.1 Mode: Physical Type 4.2 Class: Abstract Type 4.2.1 Numeric 4.2.2 Integer 4.2.3 Complex 4.2.4 Logical 4.2.5 Character 4.2.6 Date and Time 4.3 Data Structure 4.3.1 Vectors 4.3.2 Matrix 4.3.3 Factors 4.3.4 Data Frame 4.3.5 List 4.3.6 Arrays 4.4 Functions for Rounding of Numbers Bibliography 5 Working with Data 5.1 Entering Data Within R 5.2 Saving and Loading Data 5.2.1 Loading Data 5.2.2 Saving Data 5.3 Editing Data 5.4 Importing from External Files 5.5 Importing Data from Different Software 5.6 Importing Data from Excel Files 5.7 Listing Variables 5.8 Exporting Data 5.9 Preparing and Managing Data 5.9.1 Appending Observations to a Data Set 5.9.2 Combining Data Sets 5.9.3 Converting Mode of Data and Structured Data Type 5.9.4 Binning Data 5.9.5 Subsetting 5.10 Data Cleaning 5.10.1 Checking Structure of Data 5.10.2 Checking Variables Names 5.10.3 Checking Missing/ Null Values 5.10.4 Imputing the Missing Values 5.10.5 Checking Data Type of a Variable 5.10.6 Removing Extra Spaces 5.10.7 Removing Duplicate Rows 5.10.8 Deleting Variables or Functions 5.11 Generating Data 5.11.1 Generating Numeric Sequences 5.11.2 Generating Factors 5.11.3 Generating Repetitions Patterns 5.12 Recycling Rule 5.13 Performing Vector Arithmetic 5.13.1 Some Basic Statistical Functions Bibliography 6 Descriptive Statistics 6.1 Summary Statistics for Ungroup Data 6.1.1 Measures of Location 6.1.2 Measures of Position 6.1.3 Measures of Dispersion 6.2 Summary Statistics by Groups 6.2.1 Using [basicstyle=]tapply() Function 6.2.2 Using [basicstyle=]aggregate() Function 6.2.3 Using [basicstyle=]by() Function 6.2.4 Using [basicstyle=]describeBy() Function 6.3 Graphical Representation of Group Data 6.3.1 Bar Chart 6.3.2 Cluster/Stacked Bar Chart 6.3.3 Pie Chart 6.3.4 Histogram 6.3.5 Boxplot 6.3.6 Stem and Leaf Display 6.3.7 Q-Q plot 6.3.8 Scatter Plot Bibliography 7 Probability and Probability Distributions 7.1 Generating Sample Spaces 7.1.1 Extracting Event from Sample Space 7.1.2 Union, Intersection, Difference, and Compliment of Sets 7.1.3 Counting: Permutation and Combination 7.1.4 Generating Combination 7.2 Computing Probability 7.2.1 Conditional Probability 7.2.2 Independent Events 7.2.3 Bayes' Rule 7.3 Random Variable 7.3.1 Marginal Distributions 7.3.2 Mean and Variance of Discrete Random Variable 7.4 Probability Distributions 7.4.1 Computing p-Value 7.4.2 Discrete Distributions 7.4.3 Continuous Distributions 7.4.4 The distr Package 7.4.5 The distrEx Package 7.5 Examining the Distribution of Univariate Data Set Bibliography 8 Confidence Intervals and Comparison Tests 8.1 Confidence Intervals 8.1.1 CI for Means 8.1.2 CI for Proportion 8.1.3 CI for Variance 8.1.4 CI for Differences Between Means 8.2 Hypothesis Testing 8.2.1 One-Sample t-Test 8.2.2 Two-Sample t-Test 8.2.3 Paired Sample t-Test 8.2.4 Two-Sample Proportion Test 8.2.5 One-Way Analysis of Variance 8.2.6 The Chi-Squared Test 8.2.7 Effect Size Bibliography 9 Correlation and Regression Analysis 9.1 Covariance, Correlation, and Testing 9.2 Defining Statistical Models in R 9.3 Linear Models 9.3.1 Extracting Model Information 9.3.2 Updating Fitted Model 9.3.3 Comparing Models 9.3.4 Computing Durbin–Watson Value 9.3.5 Visualizing Regression Graphically Bibliography 10 Graphing in R 10.1 Managing Graphics 10.1.1 Opening Several Graphical Devices 10.2 Partitioning a Graphic 10.3 High-level Graphical Functions 10.4 Low-level Plotting Commands 10.5 Interacting with Graphics 10.6 Adding Mathematical Expression on a Plot 10.7 Graphical Parameters 10.7.1 Graphical Elements 10.7.2 Axes and Tick Marks 10.7.3 Figure Margins 10.7.4 Multiple Figure Environment 10.8 A Detailed Example 10.9 The grid and lattice Package 10.9.1 Some Advance Examples 10.9.2 More on Panel Functions 10.10 The ggplot2 Package Bibliography 11 Control Flow: Selection and Iteration 11.1 Selection Control Structure 11.1.1 [basicstyle=]if Statement 11.1.2 [basicstyle=]if Else Statement 11.1.3 [basicstyle=]if Else if Ladder 11.1.4 Nested [basicstyle=]if else Statement 11.1.5 Vectorized [basicstyle=]if 11.1.6 Switch Statement 11.2 Repetition/Loop 11.2.1 [basicstyle=]for Loop 11.2.2 [basicstyle=]while Loop 11.2.3 [basicstyle=]repeat Loop Bibliography 12 Functions and R Resources 12.1 Some Important Functions 12.1.1 [basicstyle=]print() Function 12.1.2 [basicstyle=]cat() function 12.1.3 [basicstyle=]ls() function 12.1.4 [basicstyle=]split() Function 12.1.5 [basicstyle=]rm() Function 12.2 Useful Features of R 12.3 Literature on R 12.3.1 Manuals 12.3.2 Frequently Asked Questions 12.3.3 Online Resources 12.3.4 Mailing Lists 12.3.5 R News 12.3.6 Citing R in a Publication Bibliography 13 Common Errors and Mistakes 13.1 Avoiding Common Mistakes 13.1.1 Difference in 1, l, i, I, 0, o, O, and | 13.1.2 Forgetting the Function Parenthesis 13.1.3 Forgetting double Backslashes 13.1.4 Space Between ``