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Using R for Data Analysis and GraphicsIntroduction, Code and Commentary
J H MaindonaldCentre for Bioinformation Science,Australian National University.
©J. H. Maindonald 2000, 2004. A licence is granted for personal study and classroom use. Redistribution inany other form is prohibited.Languages shape the way we think, and determine what we can think about (Benjamin Whorf.).
14 Novem
 ber 2004
 
 
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45 50 55Cam barvilleBellbirdW hian W hianByrangeryConondaleAllyn River Bulburinfem alem ale
 Lindenmayer, D. B., Viggers, K. L., Cunningham, R. B., and Donnelly, C. F. : Morphological variationamong populations of the mountain brushtail possum, t
richosurus
 
caninus
Ogibly(Phalangeridae:Marsupialia). Australian Journal of Zoology 43: 449-459, 1995.possum
 
n
.
1
Any of many chiefly herbivorous, long-tailed, tree-dwelling, mainly Australian marsupials, someof which are gliding animals (e.g.
brush-tailed possum
,
 flying possum
).
2
a mildly scornful term for a person.
3
 an affectionate mode of address.From the Australian Oxford Paperback Dictionary, 2
nd
ed, 1996.
 
 
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 
 
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