usingrfordataanalysisandgraphics资源-CSDN文库

4星 · 超过85%的资源需积分: 9 55 浏览量 2008-05-31 09:45:25 上传评论收藏 2.14MB PDF 举报

资源推荐

资源详情

资源评论

Using R for Data Analysis and Graphics

Introduction, Code and Commentary

J H Maindonald

Centre for Bioinformation Science,

Australian National University.

©J. H. Maindonald 2000, 2004. A licence is granted for personal study and classroom use. Redistribution in

any other form is prohibited.

Languages shape the way we think, and determine what we can think about (Benjamin Whorf.).

14 November 2004

Introduction ..................................................................................................................................................................1

1. Starting Up ................................................................................................................................................................3

1.1 Getting started under Windows ......................................................................................................................3

1.2 Use of an Editor Script Window .....................................................................................................................4

1.3 A Short R Session............................................................................................................................................5

1.4 Further Notational Details.............................................................................................................................7

1.5 On-line Help....................................................................................................................................................7

1.6 The Loading or Attaching of Datasets...........................................................................................................7

1.7 Exercises..........................................................................................................................................................8

2. An Overview of R .....................................................................................................................................................9

2.1 The Uses of R .......................................................................................................................................................9

2.2 R Objects ............................................................................................................................................................11

*2.3 Looping.............................................................................................................................................................12

2.4 Vectors ................................................................................................................................................................12

2.5 Data Frames ......................................................................................................................................................15

2.6 Common Useful Functions ................................................................................................................................16

2.7 Making Tables....................................................................................................................................................17

2.8 The Search List ..................................................................................................................................................17

2.9 Functions in R ....................................................................................................................................................18

2.10 More Detailed Information .............................................................................................................................19

2.11 Exercises...........................................................................................................................................................19

3. Plotting.....................................................................................................................................................................21

3.1 plot () and allied functions ................................................................................................................................21

3.2 Fine control – Parameter settings ....................................................................................................................21

3.3 Adding points, lines and text .............................................................................................................................22

3.4 Identification and Location on the Figure Region ..........................................................................................24

3.5 Plots that show the distribution of data values................................................................................................25

3.6 Other Useful Plotting Functions.......................................................................................................................27

3.7 Plotting Mathematical Symbols ........................................................................................................................29

3.8 Guidelines for Graphs .......................................................................................................................................29

3.9 Exercises.............................................................................................................................................................30

3.10 References ........................................................................................................................................................31

4. Lattice graphics ......................................................................................................................................................33

4.1 Examples that Present Panels of Scatterplots – Using xyplot() ..............................................................33

4.2 An incomplete list of lattice Functions .............................................................................................................34

4.3 Exercises.............................................................................................................................................................35

5. Linear (Multiple Regression) Models and Analysis of Variance....................................................................37

5.1 The Model Formula in Straight Line Regression ............................................................................................37

5.2 Regression Objects ............................................................................................................................................37

5.3 Model Formulae, and the X Matrix ..................................................................................................................38

5.4 Multiple Linear Regression Models .................................................................................................................40

5.5 Polynomial and Spline Regression ...................................................................................................................43

5.6 Using Factors in R Models ...............................................................................................................................46

5.7 Multiple Lines – Different Regression Lines for Different Species ................................................................48

5.8 aov models (Analysis of Variance) ...................................................................................................................49

5.9 Exercises.............................................................................................................................................................51

5.10 References ........................................................................................................................................................52

6. Multivariate and Tree-based Methods ...............................................................................................................55

6.1 Multivariate EDA, and Principal Components Analysis ................................................................................55

6.2 Cluster Analysis .................................................................................................................................................56

6.3 Discriminant Analysis .......................................................................................................................................56

6.4 Decision Tree models (Tree-based models).....................................................................................................57

6.5 Exercises.............................................................................................................................................................58

6.6 References ..........................................................................................................................................................58

*7. R Data Structures ................................................................................................................................................59

7.1 Vectors ................................................................................................................................................................59

7.2 Missing Values ...................................................................................................................................................59

7.3 Data frames........................................................................................................................................................60

7.4 Data Entry ..........................................................................................................................................................61

7.5 Factors and Ordered Factors ...........................................................................................................................62

7.6 Ordered Factors ................................................................................................................................................63

7.7 Lists.....................................................................................................................................................................64

*7.8 Matrices and Arrays ........................................................................................................................................64

7.9 Exercises.............................................................................................................................................................66

8. Functions .................................................................................................................................................................67

8.1 Functions for Confidence Intervals and Tests .................................................................................................67

8.2 Matching and Ordering.....................................................................................................................................67

8.3 String Functions.................................................................................................................................................67

8.4 Application of a Function to the Columns of an Array or Data Frame.........................................................68

*8.5 aggregate() and tapply() .................................................................................................................................68

*8.7 Merging Data Frames .....................................................................................................................................69

8.8 Dates...................................................................................................................................................................69

8.9. Writing Functions and other Code ..................................................................................................................70

8.10 Exercises...........................................................................................................................................................73

*9. GLM, and General Non-linear Models ............................................................................................................75

9.1 A Taxonomy of Extensions to the Linear Model ..............................................................................................75

9.2 Logistic Regression............................................................................................................................................76

9.3 glm models (Generalized Linear Regression Modelling) ...............................................................................79

9.4 Models that Include Smooth Spline Terms .......................................................................................................79

9.5 Survival Analysis................................................................................................................................................79

9.6 Non-linear Models .............................................................................................................................................80

9.7 Model Summaries ..............................................................................................................................................80

9.8 Further Elaborations.........................................................................................................................................80

9.9 Exercises.............................................................................................................................................................80

9.10 References ........................................................................................................................................................80

*10. Multi-level Models, Repeated Measures and Time Series...........................................................................81

10.1 Multi-Level Models, Including Repeated Measures Models.........................................................................81

10.2 Time Series Models..........................................................................................................................................85

10.3 Exercises...........................................................................................................................................................85

10.4 References ........................................................................................................................................................86

*11. Advanced Programming Topics ......................................................................................................................87

11.1. Methods ...........................................................................................................................................................87

11.2 Extracting Arguments to Functions ................................................................................................................87

11.3 Parsing and Evaluation of Expressions .........................................................................................................88

11.4 Plotting a mathematical expression ...............................................................................................................89

11.4 Searching R functions for a specified token...................................................................................................90

12. Appendix 1 ............................................................................................................................................................91

12.1 R Packages for Windows.................................................................................................................................91

12.2 Contributed Documents and Published Literature........................................................................................91

12.3 Data Sets Referred to in these Notes ..............................................................................................................92

12.4 Answers to Selected Exercises ........................................................................................................................92

剩余98页未读，继续阅读

评论收藏

内容反馈