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Dedication To the memory of Gregory Boivin, DVM, MBA, who provided encouragement and much needed data for this endeavor iv Biostatistics Using JMP: A Practical Guide Contents Dedication ............................................................................................................................... iii Acknowledgments ................................................................................................................. xi About This Book ................................................................................................................... xiii About the Author ................................................................................................................. xvii Chapter 1: Introduction ......................................................................... 1 1.1 Background and Overview .............................................................................................. 1 1.2 Getting Started with JMP ................................................................................................ 2 1.3 General Outline ................................................................................................................ 4 1.4 How to Use This Book ..................................................................................................... 5 1.5 Reference .......................................................................................................................... 5 Chapter 2: Data Wrangling: Data Collection ......................................... 7 2.1 Introduction ...................................................................................................................... 7 2.2 Collecting Data from Files ............................................................................................... 8 2.2.1 JMP Native Files ..................................................................................................... 8 2.2.2 SAS Format Files .................................................................................................... 9 2.2.3 Excel Spreadsheets .............................................................................................. 10 2.2.4 Text and CSV Format ........................................................................................... 11 2.3 Extracting Data from Internet Locations ..................................................................... 14 2.3.1 Opening as Data ................................................................................................... 14 2.3.2 Opening as a Webpage ........................................................................................ 15 2.4 Data Modeling Types ..................................................................................................... 17 2.4.1 Incorporating Expression and Contextual Data ................................................ 18 2.5 References ...................................................................................................................... 19 Chapter 3: Data Wrangling: Data Cleaning ......................................... 21 3.1 Introduction .................................................................................................................... 21 3.2 Tables .............................................................................................................................. 21 3.2.1 Stacking Columns ................................................................................................ 24 3.2.2 Basic Table Organization ..................................................................................... 26 3.2.3 Column Properties ............................................................................................... 31 3.3 The Sorted Array ............................................................................................................ 32 vi 3.4 Restructuring Data ......................................................................................................... 34 3.4.1 Combining Columns ............................................................................................. 35 3.4.2 Separating Out a Column (Text to Columns) ..................................................... 36 3.4.3 Creating Indicator Columns ................................................................................ 36 3.4.4 Grouping Inside Columns .................................................................................... 38 3.5 References ...................................................................................................................... 41 Chapter 4: Initial Data Analysis with Descriptive Statistics ................. 45 4.1 Introduction .................................................................................................................... 45 4.2 Histograms and Distributions ....................................................................................... 45 4.2.1 Histograms ............................................................................................................ 46 4.2.2 Box Plots ............................................................................................................... 55 4.2.3 Stem-and-Leaf Plots ............................................................................................ 57 4.2.4 Pareto Charts ........................................................................................................ 58 4.3 Descriptive Statistics ..................................................................................................... 64 4.3.1 Sample Mean and Standard Deviation ............................................................... 66 4.3.2 Additional Statistical Measures .......................................................................... 67 4.4 References ...................................................................................................................... 69 Chapter 5: Data Visualization Tools ..................................................... 71 5.1 Introduction .................................................................................................................... 71 5.2 Scatter Plots ................................................................................................................... 72 5.2.1 Coloring Points ..................................................................................................... 75 5.2.2 Copying Better-Looking Figures ......................................................................... 77 5.2.3 Multiple Scatter Plots ........................................................................................... 79 5.3 Charts .............................................................................................................................. 81 5.4 Multidimensional Plots .................................................................................................. 84 5.4.1 Parallel Plots ......................................................................................................... 84 5.4.2 Cell Plots ............................................................................................................... 87 5.5 Multivariate and Correlations Tool ............................................................................... 89 5.5.1 Correlation Table .................................................................................................. 91 5.5.2 Correlation Heat Maps ......................................................................................... 92 5.5.3 Simple Statistics ................................................................................................... 93 5.5.4 Additional Multivariate Measures ....................................................................... 93 5.6 Graph Builder and Custom Figures .............................................................................. 94 5.6.1 Graph Builder Custom Colors ............................................................................. 96 5.6.2 Incorporating Contextual Data ............................................................................ 98 5.7 References ...................................................................................................................... 99 vii Chapter 6: Rates, Proportions, and Epidemiology ............................. 101 6.1 Introduction .................................................................................................................. 101 6.2 Rates ............................................................................................................................. 101 6.2.1 Crude Rates ........................................................................................................ 101 6.2.2 Adjusted Rates ................................................................................................... 105 6.3 Geographic Visualizations .......................................................................................... 108 6.3.1 National Visualizations ....................................................................................... 108 6.3.2 County and Lower Level Visualizations ........................................................... 116 6.4 References .................................................................................................................... 120 Chapter 7: Statistical Tests and Confidence Intervals ....................... 123 7.1 Introduction .................................................................................................................. 123 7.1.1 General Hypothesis Test Background ............................................................. 124 7.1.2 Selecting the Appropriate Method ................................................................... 125 7.2 Testing for Normality ................................................................................................... 126 7.2.1 Histogram Analysis ............................................................................................ 126 7.2.2 Normal Quantile/Probability Plot ...................................................................... 128 7.2.3 Goodness-of-Fit Tests ....................................................................................... 131 7.2.4 Goodness-of-Fit for Other Distributions .......................................................... 132 7.3 General Hypothesis Tests ........................................................................................... 133 7.3.1 Z-Test Hypothesis Test of Mean ....................................................................... 133 7.3.2 T-Test Hypothesis Test of Mean ....................................................................... 135 7.3.3 Nonparametric Test of Mean (Wilcoxon Signed Rank) .................................. 136 7.3.4 Standard Deviation Hypothesis Test ................................................................ 140 7.3.5 Tests of Proportions........................................................................................... 141 7.4 Confidence Intervals .................................................................................................... 144 7.4.1 Mean Confidence Intervals ................................................................................ 144 7.4.2 Mean Confidence Intervals with Different Thresholds ................................... 144 7.4.3 Confidence Intervals for Proportions ............................................................... 145 7.5 Chi-Squared Analysis of Frequency and Contingency Tables ................................ 146 7.6 Two Sample Tests ........................................................................................................ 150 7.6.1 Comparing Two Group Means .......................................................................... 150 7.6.2 Paired Comparison, Matched Pairs .................................................................. 154 7.7 References .................................................................................................................... 156 Chapter 8: Analysis of Variance (ANOVA) and Design of Experiments (DoE) ................................................................................................. 159 8.1 Introduction .................................................................................................................. 159 viii 8.2 One-Way ANOVA .......................................................................................................... 161 8.2.1 One-Way ANOVA with Fit Y by X ....................................................................... 161 8.2.2 Means Comparison, LSD Matrix, and Connecting Letters ............................ 165 8.2.3 Fit Y by X Changing Significance Levels .......................................................... 168 8.2.4 Multiple Comparisons, Multiple One-Way ANOVAs ........................................ 169 8.2.5 One-Way ANOVA via Fit Model ......................................................................... 171 8.2.6 One-Way ANOVA for Unequal Group Sizes (Unbalanced) ............................. 176 8.3 Blocking ........................................................................................................................ 179 8.3.1 One-Way ANOVA with Blocking via Fit Y by X................................................. 179 8.3.2 One-Way ANOVA with Blocking via Fit Model ................................................. 182 8.3.3 Note on Blocking ................................................................................................ 183 8.4 Multiple Factors ........................................................................................................... 183 8.4.1 Experimental Design Considerations ............................................................... 184 8.4.2 Multiple ANOVA .................................................................................................. 188 8.4.3 Feature Selection and Parsimonious Models .................................................. 191 8.5 Multivariate ANOVA (MANOVA) and Repeated Measures ....................................... 196 8.5.1 Repeated Measures MANOVA Background .................................................... 196 8.5.2 MANOVA in Fit Model ......................................................................................... 197 8.6 References .................................................................................................................... 201 Chapter 9: Regression and Curve Fitting ........................................... 205 9.1 Introduction .................................................................................................................. 205 9.2 Simple Linear Regression ........................................................................................... 206 9.2.1 Fit Y by X for Bivariate Fits (One X and One Y) ................................................ 206 9.2.2 Special Fitting Tools ........................................................................................... 208 9.3 Multiple Regression ..................................................................................................... 211 9.3.1 Fit Model .............................................................................................................. 211 9.3.2 Stepwise Feature Selection ............................................................................... 214 9.3.3 Analysis of Covariance (ANCOVA) .................................................................... 222 9.4 Nonlinear Curve Fitting and a Nonlinear Platform Example .................................... 226 9.5 References .................................................................................................................... 232 Chapter 10: Diagnostic Methods for Regression, Curve Fitting, and ANOVA ............................................................................................... 233 10.1 Introduction ................................................................................................................ 233 10.2 Computing Residuals with Fit Y by X and Fit Model .............................................. 234 10.2.1 Fit Y by X ............................................................................................................ 234 10.2.2 Fit Model ............................................................................................................ 234 10.3 Checking for Normality ............................................................................................. 235 ix 10.4 Checking for Nonconstant Error Variance (Heteroscedasticity) .......................... 236 10.5 Checking for Outliers ................................................................................................. 238 10.6 Checking for Nonindependence ............................................................................... 242 10.7 Multiple Factor Diagnostics ...................................................................................... 243 10.8 Nonlinear Fit Residuals ............................................................................................. 245 10.9 Developing Appropriate Models ............................................................................... 246 10.10 References ................................................................................................................ 247 Chapter 11: Categorical Data Analysis .............................................. 249 11.1 Introduction ................................................................................................................ 249 11.2 Clustering .................................................................................................................... 250 11.2.1 Hierarchical Clustering .................................................................................... 250 11.2.2 K-means Clustering ......................................................................................... 260 11.3 Classification .............................................................................................................. 263 11.3.1 JMP Data Preliminaries for Classification ..................................................... 265 11.3.2 Example Data Sets ........................................................................................... 267 11.4 Classification by Logistic Regression ..................................................................... 268 11.4.1 Logistic Regression in Fit Y by X .................................................................... 268 11.4.2 Logistic Regression in Fit Model .................................................................... 270 11.5 Classification by Discriminant Analysis ................................................................... 273 11.5.1 Discriminant Analysis Loadings ...................................................................... 275 11.5.2 Stepwise Discriminant Analysis ...................................................................... 276 11.6 Classification with Tabulated Data .......................................................................... 277 11.7 Classifier Performance Verification ......................................................................... 280 11.8 References .................................................................................................................. 284 Chapter 12: Advanced Modeling Methods ......................................... 287 12.1 Introduction ................................................................................................................ 287 12.2 Principal Components and Factor Analysis ............................................................ 288 12.2.1 Principal Components in JMP ......................................................................... 288 12.2.2 Dimensionality Assessment ............................................................................ 291 12.2.3 Factor Analysis in JMP .................................................................................... 293 12.3 Partial Least Squares ................................................................................................ 296 12.4 Decision Trees ............................................................................................................ 302 12.4.1 Classification Decision Trees in JMP ............................................................. 303 12.4.2 Predictive Decision Trees in JMP ................................................................... 308 12.5 Artificial Neural Networks ......................................................................................... 310 12.5.1 Neural Network Architecture .......................................................................... 311 12.5.2 Classification Neural Networks in JMP .......................................................... 312 12.5.3 Predictive Neural Networks in JMP ................................................................ 315 x 12.6 Control Charts ............................................................................................................ 317 12.7 References .................................................................................................................. 321 Chapter 13: Survival Analysis ............................................................ 323 13.1 Introduction ................................................................................................................ 323 13.2 Life Distributions ........................................................................................................ 323 13.3 Kaplan-Meier Curves ................................................................................................. 327 13.3.1 Simple Survival Analysis .................................................................................. 327 13.3.2 Multiple Groups ................................................................................................ 330 13.3.3 Censoring .......................................................................................................... 331 13.3.4 Proportional Hazards ....................................................................................... 335 13.4 References .................................................................................................................. 336 Chapter 14: Collaboration and Additional Functionality .................... 339 14.1 Introduction ................................................................................................................ 339 14.2 Saving Scripts and SAS Coding................................................................................ 339 14.2.1 Saving Scripts to Data Table ........................................................................... 340 14.2.2 SAS Coding Functionality ................................................................................ 341 14.3 Collaboration .............................................................................................................. 342 14.3.1 Journals ............................................................................................................. 342 14.3.2 Web Reports ..................................................................................................... 344 14.4 Add-Ins ........................................................................................................................ 347 14.4.1 Finding Add-Ins ................................................................................................. 347 14.4.2 Developing Add-Ins .......................................................................................... 348 14.4.3 Example Add-In: Forest Plot / Meta-analysis ............................................... 348 14.4.4 Add-In Version Control .................................................................................... 351 14.5 References .................................................................................................................. 352 Index ................................................................................................. 331