The R Primer

Cover
Half Title
Title Page
Copyright Page
Contents
Preface
CHAPTER 1 Importing and exporting data
	1.1 IMPORT AN R DATASET FROM A PACKAGE
	1.2 LOAD AND SAVE R DATA FILES
	1.3 READ AND WRITE TEXT FILES
	1.4 READ AND WRITE CSV FILES
	1.5 READ DATA FROM THE CLIPBOARD
	SPREADSHEETS
		1.6 READ AND WRITE DATA FROM A SPREADSHEET
		1.7 READ AND WRITE EXCEL FILES
	STATISTICAL SOFTWARE PROGRAMS
		1.8 IMPORT AND EXPORT SAS DATASETS
		1.9 IMPORT AND EXPORT SPSS DATASETS
		1.10 IMPORT OR EXPORT A STATA DATASET
		1.11 IMPORT A SYSTAT DATASET
	DATA EXCHANGE FORMATS AND DATABASES
		1.12 IMPORT A JSON DATASET
		1.13 READ DATA FROM A SIMPLE XML FILE
		1.14 READ DATA FROM AN XML FILE
		1.15 EXPORT A DATA FRAME TO XML
		1.16 IMPORT DATA FROM AN HTML TABLE
		1.17 SCRAPE DATA FROM AN HTML WEB PAGE
		1.18 IMPORT FROM A MYSQL/POSTGRESQL DATABASE
		1.19 READ DATA FROM AN SQL DATABASE USING ODBC
CHAPTER 2 Manipulating data
	2.1 USE MATHEMATICAL FUNCTIONS
	2.2 USE COMMON VECTOR OPERATIONS
	2.3 WORK WITH CHARACTER VECTORS
	2.4 READ NON-ASCII CHARACTER VECTORS
	2.5 SORT AND ORDER DATA
	2.6 TRANSFORM A VARIABLE
	2.7 FIND THE VALUE OF X CORRESPONDING TO THE MAXIMUM OR MINIMUM OF Y
	2.8 CHECK IF ELEMENTS IN ONE OBJECT ARE PRESENT IN ANOTHER OBJECT
	2.9 APPLY A FUNCTION TO SUBSETS OF A VECTOR
	2.10 FILL IN MISSING VALUES WITH PREVIOUS VALUES
	2.11 CONVERT COMMA AS DECIMAL MARK TO PERIOD
	2.12 LAG OR SHIFT A VECTOR
	2.13 CALCULATE THE AREA UNDER A CURVE
	MATRICES, ARRAYS, AND TABLES
		2.14 APPLY FUNCTION TO MARGINS OF A MATRIX/ARRAY
		2.15 COMPUTE A MATRIX/ARRAY OF PROPORTIONS
		2.16 TRANSPOSE A MATRIX (OR DATA FRAME)
		2.17 CREATE A TABLE OF COUNTS
		2.18 CONVERT A TABLE OF COUNTS TO A DATA FRAME
	DATES AND TIMES
		2.19 PARSING DATES AND TIMES
		2.20 EXTRACT AND FORMAT DATE/TIME INFORMATION
	FACTORS
		2.21 CONVERT A FACTOR TO NUMERIC
		2.22 CONVERT A FACTOR TO CHARACTER STRINGS
		2.23 ADD A NEW LEVEL TO AN EXISTING FACTOR
		2.24 COMBINE THE LEVELS OF A FACTOR
		2.25 REMOVE UNUSED LEVELS OF A FACTOR
		2.26 CHANGE THE REFERENCE LEVEL
		2.27 CUT A NUMERIC VECTOR INTO A FACTOR
	DATA FRAMES AND LISTS
		2.28 SELECT A SUBSET OF A DATA FRAME
		2.29 SELECT THE COMPLETE CASES OF A DATA FRAME
		2.30 DELETE A VARIABLE FROM A DATA FRAME
		2.31 APPLY FUNCTION TO EACH VARIABLE IN A DATA FRAME
		2.32 SPLIT DATA FRAME INTO SUBSETS AND APPLY FUNCTION TO EACH PART
		2.33 APPLY FUNCTION TO EACH ROW OF A DATA FRAME
		2.34 COMBINE TWO DATASETS
		2.35 MERGE DATASETS
		2.36 ADD NEW OBSERVATIONS TO A DATA FRAME
		2.37 STACK THE COLUMNS OF A DATA FRAME TOGETHER
		2.38 RESHAPE A DATA FRAME FROM WIDE TO LONG FORMAT OR VICE VERSA
		2.39 CONVERT A DATA FRAME TO A VECTOR
CHAPTER 3 Statistical analyses
	DESCRIPTIVE STATISTICS
		3.1 COMPUTE SUMMARY STATISTICS
		3.2 CREATE DESCRIPTIVE TABLE
	LINEAR MODELS
		3.3 FIT A LINEAR REGRESSION MODEL
		3.4 FIT A MULTIPLE LINEAR REGRESSION MODEL
		3.5 FIT A POLYNOMIAL REGRESSION MODEL
		3.6 FIT A ONE-WAY ANALYSIS OF VARIANCE
		3.7 MAKE POST-HOC PAIRWISE COMPARISONS
		3.8 FIT A TWO-WAY ANALYSIS OF VARIANCE
		3.9 FIT A LINEAR NORMAL MODEL
		3.10 FIT A PENALIZED REGRESSION MODEL
	GENERALIZED LINEAR MODELS
		3.11 FIT A LOGISTIC REGRESSION MODEL
		3.12 FIT A CONDITIONAL LOGISTIC REGRESSION MODEL
		3.13 FIT AN ORDINAL LOGISTIC REGRESSION MODEL
		3.14 FIT A MULTINOMIAL LOGISTIC REGRESSION MODEL
		3.15 FIT A POISSON REGRESSION MODEL
	METHODS FOR ANALYSIS OF REPEATED MEASUREMENTS
		3.16 FIT A LINEAR MIXED-EFFECTS MODEL
		3.17 FIT A LINEAR MIXED-EFFECTS MODEL WITH SERIAL CORRELATION
		3.18 FIT A GENERALIZED LINEAR MIXED MODEL
		3.19 FIT A GENERALIZED ESTIMATING EQUATION MODEL
		3.20 ANALYZE TIME SERIES USING AN ARIMA MODEL
		3.21 DECOMPOSE A TIME SERIES INTO TREND, SEASONAL, AND RESIDUAL COMPONENTS
	SPECIFIC METHODS
		3.22 COMPARE POPULATIONS USING T TEST
		3.23 FIT A NONLINEAR MODEL
		3.24 FIT A CENSORED REGRESSION MODEL
		3.25 FIT A ZERO-INFLATED REGRESSION MODEL
		3.26 FIT A SMOOTH CURVE
		3.27 FIT A GENERALIZED ADDITIVE MODEL
		3.28 USE META ANALYSIS TO COMBINE AND SUMMARIZE THE RESULTS FROM SEVERAL STUDIES
		3.29 USE RANDOM FOREST FOR CLASSIFICATION AND REGRESSION
		3.30 FIT A LINEAR QUANTILE REGRESSION MODEL
	MODEL VALIDATION
		3.31 TEST FOR NORMALITY OF A SINGLE SAMPLE
		3.32 TEST VARIANCE HOMOGENEITY ACROSS GROUPS
		3.33 VALIDATE A LINEAR OR GENERALIZED LINEAR MODEL
	CONTINGENCY TABLES
		3.34 ANALYZE TWO-DIMENSIONAL CONTINGENCY TABLES
		3.35 ANALYZE TWO-DIMENSIONAL CONTINGENCY TABLES WITH ORDINAL CATEGORIES
		3.36 ANALYZE TWO-DIMENSIONAL CONTINGENCY TABLES WITH PAIRED MEASUREMENTS
		3.37 ANALYZE CONTINGENCY TABLES USING LOG-LINEAR MODELS
	AGREEMENT
		3.38 CREATE A BLAND–ALTMAN PLOT OF AGREEMENT TO COMPARE TWO QUANTITATIVE METHODS
		3.39 DETERMINE AGREEMENT AMONG SEVERAL METHODS OF A QUANTITATIVE MEASUREMENT
		3.40 CALCULATE COHEN’S KAPPA FOR AGREEMENT
	MULTIVARIATE METHODS
		3.41 FIT A MULTIVARIATE REGRESSION MODEL
		3.42 CLUSTER OBSERVATIONS
		3.43 USE PRINCIPAL COMPONENT ANALYSIS TO REDUCE DATA DIMENSIONALITY
		3.44 FIT A PRINCIPAL COMPONENT REGRESSION MODEL
		3.45 CLASSIFY OBSERVATIONS USING LINEAR DISCRIMINANT ANALYSIS
		3.46 USE PARTIAL LEAST SQUARES REGRESSION FOR PREDICTION
	RESAMPLING STATISTICS AND BOOTSTRAPPING
		3.47 NON-PARAMETRIC BOOTSTRAP ANALYSIS
		3.48 USE CROSS-VALIDATION TO ESTIMATE THE PERFORMANCE OF A MODEL OR ALGORITHM
		3.49 CALCULATE POWER OR SAMPLE SIZE FOR SIMPLE DESIGNS
	NON-PARAMETRIC METHODS
		3.50 TEST MEDIAN WITH WILCOXON’S SIGNED RANK TEST
		3.51 USE MANN–WHITNEY’S TEST TO COMPARE TWO GROUPS
		3.52 COMPARE GROUPS USING KRUSKAL–WALLIS’ TEST
		3.53 COMPARE GROUPS USING FRIEDMAN’S TEST FOR A TWO-WAY DESIGN
	SURVIVAL ANALYSIS
		3.54 FIT A KAPLAN–MEIER SURVIVAL CURVE TO EVENT HISTORY DATA
		3.55 FIT A COX REGRESSION MODEL (PROPORTIONAL HAZARDS MODEL)
		3.56 FIT A COX REGRESSION MODEL (PROPORTIONAL HAZARDS MODEL) WITH TIME-VARYING COVARIATES
	MISCELLANEOUS
		3.57 CORRECT P-VALUES FOR MULTIPLE TESTING
		3.58 USE A BOX–COX TRANSFORMATION TO MAKE NON-NORMALLY DISTRIBUTED DATA APPROXIMATELY NORMAL
CHAPTER 4 Graphics
	4.1 USE GREEK LETTERS AND FORMULAS IN GRAPHS
	4.2 SET COLORS IN R GRAPHICS
	4.3 SET COLOR PALETTES IN R GRAPHICS
	HIGH-LEVEL PLOTS
		4.4 CREATE A SCATTER PLOT
		4.5 CREATE A BUBBLE PLOT
		4.6 CREATE A HISTOGRAM
		4.7 CREATE A HANGING ROOTOGRAM
		4.8 CREATE A VIOLIN- OR BOXPLOT
		4.9 CREATE A BAR PLOT
		4.10 CREATE A BAR PLOT WITH ERROR BARS
		4.11 CREATE A PLOT WITH ESTIMATES AND CONFIDENCE INTERVALS
		4.12 CREATE A PIE CHART
		4.13 CREATE A PYRAMID PLOT
		4.14 PLOT MULTIPLE SERIES
		4.15 MAKE A 2D SURFACE PLOT
		4.16 MAKE A 3D SURFACE PLOT
		4.17 PLOT A 3D SCATTER PLOT
		4.18 CREATE A HEAT MAP PLOT
		4.19 PLOT A CORRELATION MATRIX
		4.20 MAKE A QUANTILE-QUANTILE PLOT
		4.21 GRAPHICAL MODEL VALIDATION FOR LINEAR MODELS
		4.22 CREATE A VENN OR EULER DIAGRAM
	TWEAKING GRAPHICS
		4.23 ADD A BROKEN AXIS TO INDICATE DISCONTINUITY
		4.24 CREATE A PLOT WITH TWO Y-AXES
		4.25 ROTATE AXIS LABELS
		4.26 MULTIPLE PLOTS
		4.27 ADD A LEGEND TO A PLOT
		4.28 ADD A TABLE TO A PLOT
		4.29 LABEL POINTS IN A SCATTER PLOT
		4.30 IDENTIFY POINTS IN A SCATTER PLOT
		4.31 VISUALIZE POINTS, SHAPES, AND SURFACES IN 3D AND INTERACT WITH THEM IN REAL-TIME
	WORKING WITH GRAPHICS
		4.32 EXPORTING GRAPHICS
		4.33 PRODUCE GRAPHICS IN LATEX-READY FORMAT
		4.34 EMBED FONTS IN POSTSCRIPT OR PDF GRAPHICS
CHAPTER 5 R
	GETTING INFORMATION
		5.1 GETTING HELP
		5.2 FINDING R SOURCE CODE FOR A FUNCTION
		5.3 TIMING R COMMANDS AND FUNCTIONS
	R PACKAGES
		5.4 INSTALLING R PACKAGES
		5.5 UPDATE INSTALLED R PACKAGES
		5.6 UNLOAD A PACKAGE
		5.7 INSTALL AN R PACKAGE FROM A REPOSITORY
		5.8 INSTALL A PACKAGE FROM BIOCONDUCTOR
		5.9 LIST THE INSTALLED PACKAGES
		5.10 LIST THE CONTENT OF A PACKAGE
		5.11 UNINSTALL AN R PACKAGE
		5.12 LIST OR VIEW VIGNETTES
		5.13 PERMANENTLY CHANGE THE DEFAULT DIRECTORY WHERE R INSTALLS PACKAGES
		5.14 AUTOMATICALLY LOAD A PACKAGE AT STARTUP
	THE R WORKSPACE
		5.15 LIST OR DELETE OBJECTS
		5.16 CHANGE THE CURRENT WORKING DIRECTORY
		5.17 SAVE AND LOAD WORKSPACES
		5.18 SAVE AND RESTORE HISTORIES
		5.19 INTERACT WITH THE FILE SYSTEM
		5.20 LOCATE AND CHOOSE FILES INTERACTIVELY
		5.21 INTERACT WITH THE OPERATING SYSTEM
		5.22 GET SESSION INFORMATION
Bibliography
Index