R For Dummies by Meys, Joris -- Read -- Imperial Library of Trantor

Index

Introduction

About This Book Conventions Used in This Book What You’re Not to Read Foolish Assumptions How This Book Is Organized

Part I: R You Ready? Part II: Getting Down to Work in R Part III: Coding in R Part IV: Making the Data Talk Part V: Working with Graphics Part VI: The Part of Tens

Icons Used in This Book Where to Go from Here

Part I: R You Ready?

Chapter 1: Introducing R: The Big Picture

Recognizing the Benefits of Using R

It comes as free, open-source code It runs anywhere It supports extensions It provides an engaged community It connects with other languages

Looking At Some of the Unique Features of R

Performing multiple calculations with vectors Processing more than just statistics Running code without a compiler

Chapter 2: Exploring R

Working with a Code Editor

Exploring RGui Dressing up with RStudio

Starting Your First R Session

Saying hello to the world Doing simple math Using vectors Storing and calculating values Talking back to the user

Sourcing a Script Navigating the Workspace

Manipulating the content of the workspace Saving your work Retrieving your work

Chapter 3: The Fundamentals of R

Using the Full Power of Functions

Vectorizing your functions Putting the argument in a function Making history

Keeping Your Code Readable

Following naming conventions Structuring your code Adding comments

Getting from Base R to More

Finding packages Installing packages Loading and unloading packages

Part II: Getting Down to Work in R

Chapter 4: Getting Started with Arithmetic

Working with Numbers, Infinity, and Missing Values

Doing basic arithmetic Using mathematical functions Calculating whole vectors To infinity and beyond

Organizing Data in Vectors

Discovering the properties of vectors Creating vectors Combining vectors Repeating vectors

Getting Values in and out of Vectors

Understanding indexing in R Extracting values from a vector Changing values in a vector

Working with Logical Vectors

Comparing values Using logical vectors as indices Combining logical statements Summarizing logical vectors

Powering Up Your Math with Vector Functions

Using arithmetic vector operations Recycling arguments

Chapter 5: Getting Started with Reading and Writing

Using Character Vectors for Text Data

Assigning a value to a character vector Creating a character vector with more than one element Extracting a subset of a vector Naming the values in your vectors

Manipulating Text

String theory: Combining and splitting strings Sorting text Finding text inside text Substituting text Revving up with regular expressions

Factoring in Factors

Creating a factor Converting a factor Looking at levels Distinguishing data types Working with ordered factors

Chapter 6: Going on a Date with R

Working with Dates Presenting Dates in Different Formats Adding Time Information to Dates Formatting Dates and Times Performing Operations on Dates and Times

Addition and subtraction Comparison of dates Extraction

Chapter 7: Working in More Dimensions

Adding a Second Dimension

Discovering a new dimension Combining vectors into a matrix

Using the Indices

Extracting values from a matrix Replacing values in a matrix

Naming Matrix Rows and Columns

Changing the row and column names Using names as indices

Calculating with Matrices

Using standard operations with matrices Calculating row and column summaries Doing matrix arithmetic

Adding More Dimensions

Creating an array Using dimensions to extract values

Combining Different Types of Values in a Data Frame

Creating a data frame from a matrix Creating a data frame from scratch Naming variables and observations

Manipulating Values in a Data Frame

Extracting variables, observations, and values Adding observations to a data frame Adding variables to a data frame

Combining Different Objects in a List

Creating a list Extracting elements from lists Changing the elements in lists Reading the output of str() for lists Seeing the forest through the trees

Part III: Coding in R

Chapter 8: Putting the Fun in Functions

Moving from Scripts to Functions

Making the script Transforming the script Using the function Reducing the number of lines

Using Arguments the Smart Way

Adding more arguments Conjuring tricks with dots Using functions as arguments

Coping with Scoping

Crossing the borders Using internal functions

Dispatching to a Method

Finding the methods behind the function Doing it yourself

Chapter 9: Controlling the Logical Flow

Making Choices with if Statements Doing Something Else with an if...else Statement Vectorizing Choices

Looking at the problem Choosing based on a logical vector

Making Multiple Choices

Chaining if...else statements Switching between possibilities

Looping Through Values

Constructing a for loop Calculating values in a for loop

Looping without Loops: Meeting the Apply Family

Looking at the family features Meeting three of the members Applying functions on rows and columns Applying functions to listlike objects

Chapter 10: Debugging Your Code

Knowing What to Look For Reading Errors and Warnings

Reading error messages Caring about warnings (or not)

Going Bug Hunting

Calculating the logit Knowing where an error comes from Looking inside a function

Generating Your Own Messages

Creating errors Creating warnings

Recognizing the Mistakes You’re Sure to Make

Starting with the wrong data Having your data in the wrong format

Chapter 11: Getting Help

Finding Information in the R Help Files

When you know exactly what you’re looking for When you don’t know exactly what you’re looking for

Searching the Web for Help with R Getting Involved in the R Community

Using the R mailing lists Discussing R on Stack Overflow and Stack Exchange Tweeting about R

Making a Minimal Reproducible Example

Creating sample data with random values Producing minimal code Providing the necessary information

Part IV: Making the Data Talk

Chapter 12: Getting Data into and out of R

Getting Data into R

Entering data in the R text editor Using the Clipboard to copy and paste Reading data in CSV files Reading data from Excel Working with other data types

Getting Your Data out of R Working with Files and Folders

Understanding the working directory Manipulating files

Chapter 13: Manipulating and Processing Data

Deciding on the Most Appropriate Data Structure Creating Subsets of Your Data

Understanding the three subset operators Understanding the five ways of specifying the subset Subsetting data frames

Adding Calculated Fields to Data

Doing arithmetic on columns of a data frame Using with and within to improve code readability Creating subgroups or bins of data

Combining and Merging Data Sets

Creating sample data to illustrate merging Using the merge() function Working with lookup tables

Sorting and Ordering Data

Sorting vectors Sorting data frames

Traversing Your Data with the Apply Functions

Using the apply() function to summarize arrays Using lapply() and sapply() to traverse a list or data frame Using tapply() to create tabular summaries

Getting to Know the Formula Interface Whipping Your Data into Shape

Understanding data in long and wide format Getting started with the reshape2 package Melting data to long format Casting data to wide format

Chapter 14: Summarizing Data

Starting with the Right Data

Using factors or numeric data Counting unique values Preparing the data

Describing Continuous Variables

Talking about the center of your data Describing the variation Checking the quantiles

Describing Categories

Counting appearances Calculating proportions Finding the center

Describing Distributions

Plotting histograms Using frequencies or densities

Describing Multiple Variables

Summarizing a complete dataset Plotting quantiles for subgroups Tracking correlations

Working with Tables

Creating a two-way table Converting tables to a data frame Looking at margins and proportions

Chapter 15: Testing Differences and Relations

Taking a Closer Look at Distributions

Observing beavers Testing normality graphically Using quantile plots Testing normality in a formal way

Comparing Two Samples

Testing differences Comparing paired data

Testing Counts and Proportions

Checking out proportions Analyzing tables Extracting test results

Working with Models

Analyzing variances Evaluating the differences Modeling linear relations Evaluating linear models Predicting new values

Part V: Working with Graphics

Chapter 16: Using Base Graphics

Creating Different Types of Plots

Getting an overview of plot Adding points and lines to a plot Different plot types

Controlling Plot Options and Arguments

Adding titles and axis labels Changing plot options Putting multiple plots on a single page

Saving Graphics to Image Files

Chapter 17: Creating Faceted Graphics with Lattice

Creating a Lattice Plot

Loading the lattice package Making a lattice scatterplot Adding trend lines

Changing Plot Options

Adding titles and labels Changing the font size of titles and labels Using themes to modify plot options

Plotting Different Types

Making a bar chart Making a box-and-whisker plot

Plotting Data in Groups

Using data in tall format Creating a chart with groups Adding a key

Printing and Saving a Lattice Plot

Assigning a lattice plot to an object Printing a lattice plot in a script Saving a lattice plot to file

Chapter 18: Looking At ggplot2 Graphics

Installing and Loading ggplot2 Looking At Layers Using Geoms and Stats

Defining what data to use Mapping data to plot aesthetics Getting geoms

Sussing Stats Adding Facets, Scales, and Options

Adding facets Changing options

Getting More Information

Part VI: The Part of Tens

Chapter 19: Ten Things You Can Do in R That You Would’ve Done in Microsoft Excel

Adding Row and Column Totals Formatting Numbers Sorting Data Making Choices with If Calculating Conditional Totals Transposing Columns or Rows Finding Unique or Duplicated Values Working with Lookup Tables Working with Pivot Tables Using the Goal Seek and Solver

Chapter 20: Ten Tips on Working with Packages

Poking Around the Nooks and Crannies of CRAN Finding Interesting Packages Installing Packages Loading Packages Reading the Package Manual and Vignette Updating Packages Unloading Packages Forging Ahead with R-Forge Conducting Installations from BioConductor Reading the R Manual

Appendix: Installing R and RStudio

Installing and Configuring R

Installing R Configuring R Installing RStudio Configuring RStudio

Cheat Sheet

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