Introduction to S-Plus

1
Introduction to S-Plus

• by
• Francesco Ferretti
• Analysis of Biological Data Course
• Winter term 2007
• Dalhousie University

2
Introduction

• S-plus and R are statistical programs using the S
  language.
• Developed in the Bell Labs of ATT in 1970s by
  Rick Becker, John Chambers and Allan Wilks
• In 1987 Douglas Martin at the University of
  Washington created the present Insightful
  Corporation. He made S more popular, compatible
  with many hardware platforms, and provided with
  the necessary support for technical and
  statistical problems. S become S-plus
• In 1997 the R project started. It was created by
  Ross Ihaka and Robert Gentelman at the university
  of Auckland, New Zealand. R is Similar to S-plus
  and freely available.

3
S-Plus and R

• Flexible and powerful statistical program
• Particularly appealing for its graphical
  capabilities
• Can be problematic with large amount of data
• SAS is more powerful in these cases

4
GUI (Grafical User Interface)

• Main toolbar and several windows
• Object Explorer
• Overview of what is available on the system.
• Computational Engine
• data frames, list, matrices, vectors
• Interface Objects
• Search path, menu items, toolbars, dialogs
• Documet objects Outputs
• Graph sheets, Scripts and Reports
• Object explorer visualize all the objects you
  have in your work directory

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GUI (Grafical User Interface)

• Import data
• FilegtImport DatagtFrom file
• Export data
• FilegtExport Datagtto file
• chose among all the data frames present in your
  working directory, give location and extension
• Creating graphs
• Highlight a dataset in object explorer
• Select variables (Ctrl-select)
• Click on 2D plots
• Chose the preferred graph type
• Save graphs
• Default .sgr (s-plus graph sheet)
• Eventually you can choose your preferred picture
  extension with FilegtExport Graph.. then specify
  location, name and extension then click OK

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GUI (Grafical User Interface)

• Summary statistics
• From object explorer select a data frame
• On the main toolbar select StatisticsgtSummary
  Statistics
• Select data, variables and statistics to be shown
  then click OK

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Programming mode

• Full potential and flexibility of S-plus. Highly
  recommended! While GUI can perform much of the
  S-Plus commands and functions, programming mode
  allows you to resolve potentially all problems
  you will encounter in data manipulation, analysis
  and plotting.
• Command window
• Can be used step by step interactively
• Writing functions
• Using a text editor (notepad, emacs, editplus,
  etc.) or directly on the command line

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Command line (the basic)

• S-plus is case sensitive
• commenting sign
• ? Call help
• q() quit S-plus
• lt- assignment sign. This is to associate a value
  or a function to a variable name

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Use of S-Plus in programming mode

• Calculator
• /-, , log, exp, sqrt, , sin, cos
• Follow the same arithmetic rules / before - and
  () before /
• Manipulate data
• Fitting models to data
• Plotting graphs

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Logical Values

• Boolean Values True, False
• lt (less than), gt, lt (less than or equal to),
• gt, (equal to), ! (not equal to)
• Conditional expressions and operators
• If, else, ifelse
• (and) (or)

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Brackets

• () to enclose arguments of functions and perform
  arithmetic calculations
• indexing objects
• xlt-c(1,5,7,8) then x3 7
• to enclose groups of commands
• Function bodies
• If else statements
• loops

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S-plus common objects

• Vector
• Ordered group of numbers or strings
• Xlt-c(45,29,27)
• zlt-c(180,180,165)
• ylt-c(Hall,Francesco,Sara)
• Matrix
• rectangular layout of cells each one containing
  a value
• AHlt-matrix(c(45,29,27,180,180,165),nrow 3)
• AHlt-matrix(c(x,z),nrow3)
• Array
• Multidimentional matrix
• Data frame
• AHPlt-data.frame(x,z,y)
• AHPlt-data.frame(x,z,y,)
• List
• group together data not having the same
  structure. Output or summary come out as list.
  You can access or use part of these output.

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Functions

• Set of commands performed on specified variables
• Ylt-mean(x) or..ylt-(x1x2x3x4)/4 ..or..
  ylt-sum(x)/4 ..or..ylt-sum(x)/length(x)
• You can build your own functions
• In command line
• SDlt-function(x)sqrt(var(x)) function will be
  saved in your working directory..SD(x)

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Functions

• Creating a file with an s extension (file.s, sort
  of a library where you can store one ore more
  functions)
• Open and editor
• Write the function
• this function create the dataset buddy and
• plot its variables one against the other
• buddylt-function()
• xlt-c(2,3,5,6,8,10)
• ylt-c(4,6,10,12,16,20)
• buddylt-data.frame(x,y)
• plot(buddyx,buddyy,xlabx,ylaby,typel
  )
• print(buddy)
• Save the file as an s file c\buddy.s
• Open the file with source(c\\buddy.s)
• Access the funtion calling it as buddy()

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Use of S-Plus in programming mode (Manipulation
of data)

• Dataset never ready for analyses
• Importing datasets read.table()
• Subsetting object
• Creating new variables
• seq(), rep(), sort(), unique(), length()
• Merging and binding datasets
• merge(), cbin(),rbin()

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Graphical analysis

• Plotting to the active device s-plus window or
  file
• pdf.graph(file,horizontal)
• postscript(file,horizontal)
• graphsheet(file,format)
• Important functions
• par(), plot(), hist(), boxplot(), pairs()

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Fitting a model to data

• Take SharkLife data
• Summary of the data, summary()
• EDA (Exploratory Data Analysis), pairs(), hist(),
  boxplot(), plot()
• Fitting a linear regression model between Lmax
  and birth.size, model1lt-lm()
• Checking the model (using statistics and plots),
  summary(model), plot(model)

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Programming mode

• Script window
• Mode where you can write programs, run them and
  keep track of your operations for future work
• FilegtNewgtScript File

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Useful Reference Books

• The Basic of S-Plus by Krause A. and Olson M.
• Statistical computing with S-Plus by Crawley M.J.
• Modern Applied Statistics with S-plus by
• Venables W.N. and Ripley B.D
• much more in the internet