Analyzing Medical Data Using S-PLUS

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Springer Science & Business Media, Sep 21, 2001 - Computers - 485 pages
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This book covers a range of statistical methods useful in the analysis of medical data, from the simple to the sophisticated, and shows how they may be applied using the latest versions of S-PLUS and S-PLUS 6. In each chapter several sets of medical data are explored and analysed using a mixture of graphical and model fitting approaches. At the end of each chapter the S-PLUS script files are listed, enabling readers to reproduce all the analyses and graphics in the chapter. These script files can be downloaded from a web site. The aim of the book is to show how to use S-PLUS as a powerful environment for undertaking a variety of statistical analyses from simple inference to complex model fitting, and for providing informative graphics. All such methods are of increasing importance in handling data from a variety of medical investigations including epidemiological studies and clinical trials. The mix of real data examples and background theory make this book useful for students and researchers alike. For the former, exercises are provided at the end of each chapter to increase their fluency in using the command line language of the S-PLUS software. Professor Brian Everitt is Head of the Department of Biostatistics and Computing at the Institute of Psychiatry in London and Sophia Rabe-Hesketh is a senior lecturer in the same department. Professor Everitt is the author of over 30 books on statistics including two previously co-authored with Dr. Rabe-Hesketh.
 

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Contents

Medical Statistics
1
An Introduction to SPLUS
5
13 Elementary commands
7
14 Vectors
9
15 Matrices
13
16 Logical expressions and subsetting matrices and vectors
14
17 List objects
16
18 Data frames
18
104 Diagnostics
234
106 Using SPLUS
237
107 Exercises
242
Linear Mixed Models I
243
113 Mixed effects ANOVA model
248
114 Linear regression with a random intercept
251
115 Random coefficient models
256
116 Summary
260

19 Reading in data
19
110 Some commonly used SPLUS functions for data analysis
21
111 Data manipulation
22
112 Modeling in SPLUS
25
113 User functions
26
114 Graphics using the command line approach
29
115 The SPLUS GUI
34
Describing Data
37
23 Graphing and summarizing categorical data
44
24 Dotplots for classified continuous data
50
25 Summary
51
26 Using SPLUS
55
27 Exercises
60
Basic Inference
63
322 Paired ttests
70
33 Distribution free tests
72
332 A distributionfree signed rank testWilcoxon test
74
342 Fishers exact test
77
343 The MantelHaenszel test
78
35 An introduction to the bootstrap
81
36 Summary
82
37 Using SPLUS
83
38 Exercises
86
Scatterplots Simple Regression and Smoothing
89
421 Jittering a scatterplot
93
423 Convex hull trimming of bivariate data
95
424 The aspect ratio of a scatterplot
96
43 Estimating bivariate densities
102
44 Simple regression and locally weighted regression
105
45 Summary
107
46 Using SPLUS
110
47 Exercises
118
Analysis of Variance and Covariance
121
53 Multiple comparison procedures
125
54 A factorial experiment
127
55 Unbalanced designs
130
56 Analysis of covariance
132
57 Summary
136
58 Using SPLUS
138
59 Exercises
141
The Analysis of Longitudinal Data
143
63 Summary measure analysis of longitudinal data
149
64 Summary
152
65 Using SPLUS
153
66 Exercises
156
More Graphics
157
72 The bubbleplot
158
73 The scatterplot matrix
161
74 Conditioning plots
162
75 Trellis graphics
168
76 Summary
169
77 Using SPLUS
173
78 Exercises
176
Multiple Linear Regression
179
821 Anesthesia example
180
83 Identifying a good model
188
832 Stepwise methods
190
residuals and other regression diagnostics
194
85 The linear model
195
86 Summary
199
87 Using SPLUS
200
88 Exercises
203
Generalized Linear Models I Logistic Regression
205
92 Logistic regression for grouped data
206
93 Logistic regression for individual level data
213
94 Casecontrol studies
215
95 Summary
216
96 Using SPLUS
218
97 Exercises
222
Generalised linear models II Poisson regression
223
102 Poisson regression examples
225
103 Overdispersion
230
117 Using SPLUS
262
118 Exercises
268
Linear Mixed Models II
269
123 Heteroscedasticity
272
124 Multilevel models
274
125 Assessing model assumptions
277
126 Summary
282
127 Using SPLUS
283
128 Exercises
287
Generalized Additive Models
291
132 Additive models
292
134 Some examples of the use of additive models
294
135 Using a logistic additive model
296
136 Summary
298
137 Using SPLUS
301
138 Exercises
303
Nonlinear models
305
143 Two examples of nonlinear models
306
144 Age of onset of schizophrenia
314
145 Summary
317
146 Using SPLUS j
322
147 Exercises
326
Regression Trees
327
152 Treebased models
328
153 Birthweight of babies
330
1531 Some simple examples of regression trees for the birthweight data
332
154 More complex trees for the birthweight data
335
155 Summary
337
156 Using SPLUS
342
157 Exercises
344
Survival Analysis I
345
162 The survivor function
346
163 The logrank test
350
164 The hazard function
352
165 Summary
353
166 Using SPLUS
356
167 Exercises
358
Survival Analysis II Coxs Regression
361
173 Left truncation
364
174 Stratification
368
175 Diagnostics and assessing the proportional hazards assumption
370
176 Summary
373
177 Using SPLUS
375
178 Exercises
378
Principal Components and Factor Analysis
381
1821 Principal components analysis of head lengths
382
1822 Principal components analysis of nutrients in foodstuffs
384
183 Exploratory factor analysis
389
184 Principal components analysis and factor analysis compared
393
185 Summary
396
186 Using SPLUS
397
187 Exercises
399
Cluster Analysis
401
1921 Clustering foodstuffs
402
193 kmeans clustering
403
194 Classification maximum likelihood
409
195 Summary
412
196 Using SPLUS
413
197 Exercises
416
Discriminant Function Analysis
417
202 The linear discriminant function
418
203 Discriminant functions when group covariance matrices cannot be assumed to be equal
424
204 Discriminant analysis with more than two groups
425
205 Summary
431
206 Using SPLUS
433
207 Exercises
437
The SPLUS GUI
439
A3 Graphics using the GUI
443
Answers to selected exercises
447
References
465
Index
473
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