Notes on S-PLUS:
A Programming Environment for
Data Analysis and Graphics

The University of Adelaide

Version 2.1, July, 1992

• Introduction and Preliminaries
  • Reference manuals
  • S-PLUS and X-windows
  • Using S-PLUS interactively
  • An introductory session
  • S-PLUS and UNIX
  • Getting help with functions and features
  • S-PLUS commands. Case sensitivity.
  • Recall and correction of previous commands
    • S-PLUS
    • Vanilla S
  • Executing commands from, or diverting output to, a file
  • Data directories. Permanency. Removing objects.
• Simple manipulations; numbers and vectors
  • Vectors
  • Vector arithmetic
  • Generating regular sequences
  • Logical vectors
  • Missing values
  • Character vectors
  • Index vectors. Selecting and modifying subsets of a data set
• Objects, their modes and attributes
  • Intrinsic attributes: mode and length
  • Changing the length of an object
  • attributes() and attr()
  • The class of an object
• Categories and factors
  • A specific example
  • The function tapply() and ragged arrays
• Arrays and matrices
  • Arrays
  • Array indexing. Subsections of an array
  • Index arrays
  • The array() function
    • Mixed vector and array arithmetic. The recycling rule
  • The outer product of two arrays
    • An example: Determinants of 2x2 digit matrices
  • Generalized transpose of an array
  • Matrix facilities. Multiplication, inversion and solving linear equations.
  • Forming partitioned matrices. cbind() and rbind().
  • The concatenation function, c(), with arrays.
  • Frequency tables from factors. The table() function
• Lists, data frames, and their uses
  • Lists
  • Constructing and modifying lists
    • Concatenating lists
  • Some functions returning a list result
    • Eigenvalues and eigenvectors
    • Singular value decomposition and determinants
    • Least squares fitting and the QR decomposition
  • Data frames
    • Making data frames
    • attach() and detach()
    • Working with data frames
    • Attaching arbitrary lists
• Reading data from files
  • The scan() function
  • The read.table() function
  • Other facilities; editing data
• More language features. Loops and conditional execution
  • Grouped expressions
  • Control statements
• Writing your own functions
  • Defining new binary operators.
  • Named arguments and defaults. ``...''
  • Assignments within functions are local. Frames.
  • More advanced examples
    • Efficiency factors in block designs
    • Dropping all names in a printed array
    • Recursive numerical integration
  • Customizing the environment. .First and .Last
  • Classes, generic functions and object orientation
• Statistical models in S-PLUS
  • Defining statistical models; formulæ
  • Regression models; fitted model objects
  • Generic functions for extracting information
  • Analysis of variance; comparing models
    • ANOVA tables
  • Updating fitted models. The ditto name ``.''
  • Generalized linear models; families
    • Families
    • The glm() function
    • The gaussian family
    • The binomial family
    • Poisson models
    • Quasi-likelihood models
  • Nonlinear regression models; parametrized data frames
    • Changes to the form of the model formula
    • Specifying the parameters
    • Example
  • Some non-standard models
• Graphical procedures
  • High-level plotting commands
    • The plot() function
    • Displaying multivariate data
    • Display graphics
    • Arguments to high-level plotting functions
  • Low-level plotting commands
  • Interactive graphics functions
  • Using graphics parameters
    • Permanent changes: the par() function
    • Temporary changes: arguments to graphics functions
  • Graphics parameters list
    • Graphical elements
    • Axes and Tick marks
    • Figure Margins
    • Multiple figure environment
  • Device drivers
    • PostScript diagrams for typeset documents.
    • Multiple graphics devices
• S-PLUS: An Introductory Session
• The Inbuilt Command Line Editor in S-PLUS
  • Preliminaries
  • Editing Actions
  • Command Line Editor Summary
• Exercises
  • The Cloud Point Data
    • Description
    • Data
  • The Janka Hardness Data
    • Description
    • Data
  • The Tuggeranong House Price Data
    • Description
    • Data
  • Yorke Penninsula Wheat Data
    • Description
    • Data
  • The Iowa Wheat Yield Data
    • Description
    • Data
  • The Gasoline Yield Data
    • Description
    • Data
  • The Michaelson-Morley Speed of Light Data
    • Description
    • Data
  • The Rat Genotype Data
    • Description
    • Data
  • Fisher's Sugar Beet Data
    • Description
    • Data
  • A Barley Split Plot Field Trial.
    • Description
    • Data
  • The Snail Mortality Data
    • Description
    • Data
  • The Kalythos Blindness Data
    • Description
    • Data
    • Problems
  • The Stormer Viscometer Data
    • Description
    • Data
  • The Chlorine availability data
    • Description
    • Data
  • The Saturated Steam Pressure Data
    • Description
    • Data
  • Count Rumford's Friction Data
    • Description
    • Data
  • The Jellyfish Data.
    • Description
    • Data
  • Archaelogical Pottery Data
    • Description
    • Data
  • The Beaujolais Quality Data
    • Description
    • Data
  • The Painter's Data of de Piles
    • Description
    • Data

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  Preface

  These notes were originally intended only for local consumption at the University of Adelaide, South Australia. After some encouraging comments from students, the author decided to release them to a larger readership in the hope that in some small way they promote good data analysis. S (or S-PLUS) is no panacea, of course, but in offering simply a coherent suite of general and flexible tools to devise precisely the right kind of analysis, rather than a collection of packaged standard analyses, in my view it represents the single complete environment most conducive to good data analysis so far available.

  Some evidence of the local origins of these notes is still awkwardly apparent. For example they use the Tektronics graphics emulations on terminals and workstations, which at the time of writing is still the only one available to the author. The X11 windowing system, which allows separate windows for characters and graphics simultaneously to be displayed, is much to be preferred and it will be used in later versions. Also the local audience would be very familiar with MINITAB, MATLAB, Glim and Genstat, and various echoes of these persist. At one point some passing acquaintance with the Australian States is assumed, but the elementary facts are given in a footnote for foreign readers.

  Comments and corrections are always welcome. Please address email correspondence to the author at wvenable@stats.adelaide.edu.au.

  The author is indebted to many people for useful contributions, but in particular Lucien W. Van Elsen, who did the basic to conversion and Rick Becker who offered an authoritative and extended critique on an earlier version. Responsibility for this version, however, remains entirely with the author, and the notes continue to enjoy a fully unofficial and unencumbered status.

  These notes may be freely copied and redistributed for any educational purpose provided the copyright notice remains intact. Where appropriate, a small charge to cover the costs of production and distribution, only, may be made.

  Bill Venables, University of Adelaide, 16th December, 1990.

  Addendum: Version 2.0, April 1992

  As foreshadowed above the present version of the notes contains references to the use of S in a workstation environment, although I hope they remain useful to the user on an ordinary graphics terminal. Of much greater importance, however, are the language developments that have taken place in S itself in the August 1991 release. These are only partially addressed in this version of the notes, as a complete coverage would require a document of much greater length than was ever intended. I trust however that the sketches given here are useful and a spur to the reader to seek further enlightenment in the standard reference materials.

  The present notes are also centred around S-PLUS rather than plain vanilla S. This simply reflects a change in the implementation of S made available to my students and me by my employer. It should not be read as any sort of endorsement one way or another.

  My sincere thanks to David Smith, James Pearce and Ron Baxter for many useful suggestions.

  Bill Venables, University of Adelaide, 13th April, 1992.

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