Release Notes for S-PLUS 6.1 for Windows
(May 2002)

These release notes are current as of May 21, 2002. For updates to the release notes that are made after this date as well as other useful information, please see the Web site www.insightful.com/support/splus61win.

This file contains the following information:

About this Release

Version-Specific Information

What's New in S-PLUS 6.1

Bugs Fixed in S-PLUS 6.1

Supported Platforms and System Requirements

Installation Instructions

Running S-PLUS

Getting Help in S-PLUS

Compilers/Linkers

Contact Information for Feedback

Notes and Known Issues

ABOUT THIS RELEASE

S-PLUS 6.1 for Windows is a full 32-bit Windows application with an Office 97/2000-compatible graphical user interface. The help system in S-PLUS 6.1 uses Microsoft’s current help standard, HTML Help, and contains help for both the graphical user interface and the S-PLUS engine.

The new features in S-PLUS 6.1 for Windows improve upon S-PLUS 6.0 in two main areas: Java connectivity and globalization.

VERSION-SPECIFIC INFORMATION

The majority of these release notes are written for S-PLUS 6.1 Professional Edition. Information specific to other versions of S-PLUS 6.1 is noted here.

S-PLUS 6.1 Professional Trial Edition

The Trial Edition of S-PLUS 6.1 for Windows is a full copy of S-PLUS 6.1 Professional Edition. The software expires 30 days after the date of initial installation.

S-PLUS 6.1 Professional Network Edition

The Network Edition of S-PLUS 6.1 for Windows is a license-managed version of S-PLUS 6.1 Professional Edition. It provides all the capabilities of S-PLUS 6.1 Professional plus while providing floating licenses through a license manager. The network edition is based on a client/server architecture, where the application is installed on a server machine and accessed from one or more clients (or workstations). This type of architecture allows the clients to access the full application across the network from the server, for example, which saves disk space on each of the workstations. It also simplifies the update process; instead of updating and migrating numerous separate installations of S-PLUS when patches are released, you need only to update the single network installation.

For complete installation instructions and details on the supported platforms and system requirements for the network edition, consult the manual S-PLUS 6 Network Installation Guide. This manual is included as the PDF file winnet.pdf in the network folder of your S-PLUS 6.1 CD. For instructions on installing S-PLUS modules with the network edition, see the document modinst_winnet.pdf, also located in the network folder of your S-PLUS 6.1 CD.

Although Novell NetWare was supported in the Network Edition of S-PLUS 6.0, it is no longer supported in S-PLUS 6.1.

S-PLUS 6.1 Academic Site Edition

The Academic Site Edition of S-PLUS 6.1 for Windows is a full copy of S-PLUS 6.1 Professional Edition. It is intended for customers at university and college campuses that have academic site licenses with Insightful Corporation. The software expires one year after the date of initial installation.

S-PLUS 6.1 Student Edition

The Student Edition of S-PLUS 6.1 for Windows is a copy of S-PLUS 6.1 Professional Edition with a few limitations. It is intended for students at university and college campuses and expires one year after the date of initial installation.

The limitations in the Student Edition of S-PLUS include:

S-PLUS 6.1 Standard Edition

The Standard Edition of S-PLUS 6.1 for Windows is the deployment version of S-PLUS 6.1 Professional Edition. It is a low-cost licensing option for non-distributed deployments of custom S-PLUS applications. The standard edition provides the complete S-PLUS 6.1 graphical user interface, but does not provide an interface to the S language. Instead, the standard edition should be modified through the use of initialization files (such as S.init) and custom libraries before it is deployed on the desktop. The standard edition also enables you to run custom data analyses created by S-PLUS programmers using the functionality in S-PLUS 6.1 Professional Edition. This gives companies a cost-effective way for large groups of people within an organization to standardize analytics and more effectively share information between workgroups.

S-PLUS 6.1 Standard Edition is based on the Professional Edition of S-PLUS 6.1 but is designed to be used solely through the graphical user interface. The Commands and Script windows are not available in S-PLUS 6.1 Standard Edition, as they are intended for the S-PLUS programmer who needs to type commands in the S language. Other differences between the Standard and Professional Editions of S-PLUS 6 are as follows:

WHAT'S NEW IN S-PLUS 6.1

S-PLUS 6.1 includes specific features to add or extend S-PLUS capabilities in the following areas:

  1. Java connectivity

  2. Globalization

  3. User-defined help files

  4. Usability in the Commands and Script windows

  5. The Missing Data library

  6. The Robust library

  7. Survival analysis

  8. Other contributed libraries

  9. New binary operator %in%

  10. New error functions erf and erfc

This section briefly describes these additions and enhancements.

1. Java Connectivity

CONNECT/Java is now available with S-PLUS for Windows through the winjava library. Previously, CONNECT/Java was available only in S-PLUS for UNIX. The winjava library provides the java.graph function as well as the .JavaMethod functionality, which allows S-PLUS to call Java classes and Java applications to call S-PLUS. For detailed information, see the S-PLUS 6.1 for Windows Supplement.

Java is a powerful programming language with a variety of attractive features. Its strengths include a clean object-oriented design, a rich set of class libraries, and cross-platform capabilities. With CONNECT/ Java, S-PLUS may be used with Java in a variety of ways. Just as S-PLUS can call C and Fortran routines, it can call Java methods to perform computations. Alternatively, a Java program can call S-PLUS to perform computations and create graphs.

The winspj library still exists for backward compatibility, but is deprecated.

2. Globalization

Aspects of S-PLUS have been significantly enhanced to support globalization and locales. The concept of a locale is akin to Regional Settings in Microsoft Windows; setting a locale is a way of specifying which character sets, number formats, and collation sequences to use. This allows S-PLUS to support Western European character sets (ISO 8859-1) as well as 8-bit ASCII characters (ASCII codes 128-255) in character data and the names of objects. Globalization also permits you to import, export, and display numbers written with decimal separators other than the period, and thousands separators other than the comma.

S-PLUS 6.1 fully supports French and German locales. For complete details on the changes made to support global installation and use, see the S-PLUS 6.1 for Windows Supplement.

The implementation of locales within S-PLUS does not apply to date formats because they are handled through a separate mechanism in the timeDate set of functions. Also, it does not apply to messaging; all messages in S-PLUS are in the English language.

3. User-Defined Help Files

In S-PLUS 6.1, the process for creating and distributing custom S-PLUS help files has been greatly streamlined and documented better. For complete details, see the S-PLUS 6.1 for Windows Supplement.

S-PLUS 6.1 includes a set of tools in help\BuildHelpFiles under your S-PLUS home directory which enable you to convert old-style help files to the format used in S-PLUS 6. In particular, you can use doc_to_S.cyg to convert old-style help files and you can use build_helpchm.cyg to create compiled help files for distribution.

4. Usability in the Commands and Script Windows

The color of output text (engine output) and input text (keystrokes) can be displayed using different colors in the Commands windows. The default colors for output and input text are controlled in the Options > Command Line dialog, through the lists Output color and Input color.

The Commands and Script windows now support buffered output, in which the output from S-PLUS is displayed once the S-PLUS engine has stopped generating output, rather than continuously as it is generated. In previous releases of S-PLUS, sending output to the Commands or Script window is a slow operation compared to many engine computations. Output is sent line-by-line; for commands which compute quickly but produce significant output, the time taken to print the output can dwarf the computation time. In S-PLUS 6.1, the results of commands generating large amounts of output are displayed all at once after a short pause.

By default, buffered output is on in both the Commands and Script windows. To disable this feature in both windows, clear the Buffer output check box in the Options > General Settings dialog. To toggle buffered output in both windows, you can also use the keyboard shortcut CTRL-W. Note that the timing of "trickling" output (from the trace argument of ms, for example) may be different. If you rely on the timing of output, you may want to disable buffered output.

5. The Missing Data Library

The default version of of anyMissing now uses which.na instead of just stopping, if called for an object with slots that does not have its own method for anyMissing.

The preGauss function now gives warnings when non-numeric variables are deleted, and suggests using preCgm (conditional Gaussian model) instead. In addition, preGauss evaluates a subset expression (if given) before non-numeric variables are deleted.

If you call any of the following in S-PLUS 6.1, the return value is an object of class "miVariable", without call and seed attributes:

impGauss(..., return.type="matrix")
impCgm(..., return.type="matrix")
impLoglin(..., return.type="matrix")

You cannot add attributes to an object with a new-style class like "miVariable" without losing the class and component names, which makes the object no longer work with the rest of the library code.

6. The Robust Library

The choice of the robust covariance estimator used in covRob (the estim argument) is now set directly as an argument to covRob, not through the control argument. An example command from previous versions of the Robust library is:

covRob(stack.dat, control = covRob.control(estim="M"))

In S-PLUS 6.1, this command becomes:

covRob(stack.dat, estim = "M")

The function covRob.control now returns only the control parameters required for the selected estimator.

Truncated mean estimators have been added to gammaRob and weibullRob and are now the default.

The fit.models function has been modified to support user-defined fit.models methods.

The summary method for robust linear models now includes an option for obtaining bootstrap coefficient standard error estimates.

7. Survival Analysis

The survival analysis library of functions from Terry Therneau has been updated in S-PLUS 6.1. There is now a new function aareg for fitting Aalen's additive regression model for censored data. The Aalen model assumes the cumulative hazard H(t) for a subject can be expressed as a(t) + X B(t), where a(t) is a time-dependent intercept term, X is the vector of covariates for the subject (possibly time-dependent), and B(t) is a time-dependent matrix of coefficients. The estimates are inheritly non-parametric; a fit of the model will normally be followed by one or more plots of the estimates. The estimates may become unstable near the tail of a data set, since the increment to B at time t is based on the subjects still at risk at time t.

The aareg function produces objects of class "aareg". Methods for this new class include print, summary, plot, and lines.

New functions dsurvReg, psurvReg, and qsurvReg compute the density, cumulative probability, and quantiles, respectively, for the set of distributions supported by the survReg function.

The survfit function can now handle general censoring of all types (left, right, and interval as well as counting process data).

8. Other Contributed Libraries

S-PLUS 6.1 includes the MASS4 libraries (mass, class, spatial, and nnet) from Venables and Ripley. For details on specific features included in the updated libaries, see www.stats.ox.ac.uk/pub/MASS4.

S-PLUS 6.1 also includes updates to the hmisc and design libraries from F. Harrell. For details on the updates to these libraries, see hesweb1.med.virginia.edu/biostat/s/Hmisc.html.

The set of S-PLUS functions for mixed effects models has been updated to the NLME 3.3.2 library from Jose Pinheiro and Douglas Bates. See the readme.txt file in \library\nlme3 of your S-PLUS home directory for complete details.

9. New Binary Operator %in%

S-PLUS 6.1 includes the new binary operator %in% that is a synonym to the is.element function. This operator is not related to the %in% formula syntax; see the is.element help file for details.

10. New Error Functions erf and erfc

New functions erf and erfc have been added to the S-PLUS engine. These functions use pnorm to calculate estimates of the error function.

SUPPORTED PLATFORMS AND SYSTEM REQUIREMENTS

S-PLUS 6.1 for Windows is supported on the following:

S-PLUS IS NOT SUPPORTED UNDER WIN32S (that is, Windows 3.1x), nor is it supported under Windows NT 3.51 or Windows 95.

The minimum recommended system configuration is Pentium II/233 with 96MB of RAM. You must have at least 256MB of free disk space for the typical installation (and, if not installing on drive C:\, an additional 75MB free disk space on drive C:\ to unpack the distribution).

Do NOT install this release over any existing version of S-PLUS. Instead, designate a clean installation directory for S-PLUS 6.1 and proceed with the Setup program as described below.

INSTALLING S-PLUS

The instructions in this section apply to all standalone versions of S-PLUS 6.1. For complete installation instructions for the Network Edition of S-PLUS 6.1, consult the manual S-PLUS 6 Network Installation Guide. This manual is included as the PDF file winnet.pdf in the network folder of your S-PLUS 6.1 CD. Although Novell NetWare was supported in the Network Edition of S-PLUS 6.0, it is no longer supported in S-PLUS 6.1.

For instructions on installing S-PLUS modules with the network edition, see the document modinst_winnet.pdf located in the network folder of your S-PLUS 6.1 CD. For instructions on installing S-PLUS modules with all other editions of S-PLUS 6.1, see the file modist.pdf in the help folder under your S-PLUS installation directory.

If the operating system of your machine is Windows NT, Windows 2000, or Windows XP Professional, you must have full Administrator priveleges to install S-PLUS. This is because the installation program must write to both the C:\WINNT\System folder and the registry, which is possible only if you have the correct privileges. This is a restriction imposed by InstallShield, the installation program that S-PLUS uses.

The S-PLUS Setup program offers a variety of options:

Typical

Installs all of the S-PLUS files in the selected directory, including the release notes (this document), program files, online help, sample files, development support files, and supported libraries.

Recommended for most users.

Compact

 

Installs minimum files required by S-PLUS in the target directory you choose, including the release notes (this document) and the program files.

Custom

 

Installs only selected parts of S-PLUS. Choose whether to install the release notes (this document), program files, online help, sample files, development support files, and supported libraries.

Any files you choose not to install can be installed later by selecting the icon for Add/Remove Programs in the Control Panel. See below for more details.

Recommended for advanced users.

Installing S-PLUS from the CD-ROM

  1. Insert the CD-ROM into the CD-ROM drive.

  2. If your system has CD-ROM AutoPlay enabled, the S-PLUS Setup program starts automatically. Otherwise, click the Start button, then Run, then type x:\setup (where x is the drive letter of the CD-ROM). Alternatively, double-click the setup.exe file in the CD-ROM drive of Windows Explorer.

  3. The S-PLUS Setup window appears.

  4. Follow the Setup instructions on the screen. For most installations, the default settings are recommended. It is a good idea to turn off other applications while installing S-PLUS, in particular virus checkers and screen savers.

  5. During installation, you are prompted for your S-PLUS serial number. Note that the serial number format has changed dramatically in S-PLUS 6.1; you can find your new serial number on the S-PLUS 6.1 CD-ROM jewel case. The serial number you enter during installation is recorded and you can retrieve it later by selecting Help > About S-PLUS from the main S-PLUS menu. If you do not enter a serial number during installation, the Trial Edition of S-PLUS 6.1 is automatically installed and timebombed to expire in 30 days.

Adding and Removing Components of S-PLUS

To add or remove parts of S-PLUS from your system, select the Add/Remove Programs icon in the Control Panel. Choose S-PLUS from the list of installed programs, and then click the Add/Remove button. Once in the S-PLUS Setup program, select the Modify option. Use the tree of components provided to add (select) or remove (deselect) parts of S-PLUS.

Uninstalling S-PLUS from Your Computer

To uninstall S-PLUS, select the Add/Remove Programs icon in the Control Panel. Choose S-PLUS from the list of installed programs, and then click the Add/Remove button. Once in the S-PLUS Setup program, select the Remove option.

RUNNING S-PLUS

The S-PLUS program group contains the following options:

After installing S-PLUS, the S-PLUS program group appears as an option under Programs when you click the Start button.

Starting S-PLUS with the Full Graphical User Interface

  1. From the Start menu, choose Programs.

  2. Choose the S-PLUS program group.

  3. Choose S-PLUS 6.1.

Starting S-PLUS as a Console Application Without the GUI

  1. From the Start menu, choose Programs.

  2. Choose the S-PLUS program group.

  3. Choose S-PLUS Console.

GETTING HELP IN S-PLUS

S-PLUS offers an online HTML Help system to make learning and using S-PLUS easier. Under the Help menu, you will find help on using the S-PLUS graphical user interface. In addition, an extensive Language Reference provides detailed help on each function in the S-PLUS language. You can also access the Language Reference through the Commands window by typing help() at the S-PLUS prompt. Context-sensitive help is available by clicking the Help buttons in dialogs or the context-sensitive Help button on toolbars, as well as by pressing the F1 key while S-PLUS is active.

In S-PLUS 6, the help files for GUI and command line functions are completely separate. To access all of the GUI help files, select Help > Available Help > S-PLUS Help; to access all of the command-line help files, select Help > Available Help > Language Reference. If you ask for help primarily by clicking on Help buttons in dialogs, you'll want to access S-PLUS Help on a regular basis for its Contents, Index, and Search tabs. Likewise, if you ask for help primarily through the help or ? functions, you'll want to access the Language Reference on a regular basis for the Contents, Index, and Search tabs available there.

For lists of additional S-PLUS resources, see the S-PLUS 6.1 for Windows Supplement.

COMPILERS/LINKERS

S-PLUS 6.1 is built with Microsoft VC++6.0 and Compaq/DEC Fortran 6.0. All samples shipped with S-PLUS 6.1 have been tested with VC++6.0 and Compaq/DEC Fortran 6.0. If you use Microsoft VC++6.0 and Compaq/DEC Fortran 6.0 in your projects that link to S-PLUS, use the import libraries in SHOME\lib. For example, sqpe.lib is the import library for sqpe.dll containing the core S-PLUS interpreter, and sconnect.lib is the import library for sconnect.dll containing the CONNECT/C++ class library.

Previous builds of S-PLUS 6 for Win32 used Visual Studio 6.0 service pack 3 to build the engine, GUI, and all samples and utilities shipped with the program. To fix some issues in MFC (the Microsoft Foundation Classes) that S-PLUS is based on, we updated the compiler to service pack 5. If you have built any C/C++ or Fortran applications using CONNECT/C++ or have modified one of the sample applications for your own purposes, you should install the Visual Studio 6.0 service pack 5 update and recompile and relink these applications to ensure there will be no runtime problems related to changes that may have occurred in Microsoft shared dll files.

File input and output is fully supported in C code called from S-PLUS, but input and output directed to the standard streams STDIN, STDOUT, and STDERR requires special handling. This special handling is provided by the header file newredef.h, which is included in S.h and sconnect.h. If you need to disable this behavior, define NO_NEWIO before S.h or sconnect.h. For example:

#define NO_NEWIO
#include "S.h"

CONTACT INFORMATION FOR FEEDBACK

Please feel free to contact us with questions or feedback about this release. Send all technical support queries and general comments to one of the locations listed below.

North, Central, and South America

Contact Technical Support at Insightful Corporation:

Telephone: 206.283.8802 or 1.800.569.0123, ext. 235
Monday-Friday, 6:00 a.m. PST (9:00 a.m. EST) to 5:00 p.m. PST (8:00 p.m. EST)

Fax: 206.283.8691

E-mail: support@insightful.com

Web: www.insightful.com/support

All Other Locations

Contact the European Headquarters of Insightful Corporation:

Christoph Merian-Ring 11, 4153 Reinach, Switzerland

Telephone: +41 61 717 9340

Fax: +41 61 717 9341

E-mail: info@ch.insightful.com

We are very interested in receiving information on possible bugs and usability enhancements from all users. Bug reports can be sent to the following e-mail address:

bugs@insightful.com

General information about this release of S-PLUS is available at:

www.insightful.com/support/splus61win

The list of S-PLUS Frequently Asked Questions is available from:

www.insightful.com/support/faq.asp

NOTES AND KNOWN ISSUES

These notes detail some characteristics and issues known to exists in this release.