Release Notes for TIBCO Spotfire S+® 8.1 for UNIX®/Linux® (November 2008)

Supported Platforms and System Requirements
Overview of Spotfire S+ 8.1
What's New in Spotfire S+ 8.1
Improvements in Spotfire S+ 8.1
Known Issues in Spotfire S+ 8.1
R Compatibility
Module Support
Using Spotfire S+ for Solaris or Linux from a Windows Desktop
Getting Help in Spotfire S+
Technical Support
Appendix: New Functions in Spotfire S+ 8.1

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Supported Platforms and System Requirements

You can use Spotfire S+ 8.1 on the following Linux and UNIX-based platforms:

Overview of Spotfire S+ 8.1

S-PLUS is now TIBCO Spotfire S+. For more information on this change, please visit http://spotfire.tibco.com/iful.

This version of Spotfire S+ introduces new packages, expanded package features, and improvements to the Spotfire S+ language, the Big Data library, and other libraries. We have added features to support working remotely with the Spotfire S+ Server. Also, we have updated third-party components, such as Java and Eclipse.

These release notes are intended to provide you with a high-level view of changes. We encourage you to read more detailed descriptions of the new and changed features in the Spotfire S+ documentation.

What's New in Spotfire S+ 8.1

Packages

New resample Package

Spotfire S+ now offers the new resample Package, which was previously available as a package from CSAN or from the Insightful research download site. The package is now included with Spotfire S+ 8.1. To load the package, use library(resample).

New sjdbc Package

The sjdbc package, formerly available on CSAN, now ships with Spotfire S+. The sjdbc package provides an interface to databases using Java's JDBC connectivity. For more information, from the Spotfire S+ prompt, type

library(sjdbc)
help(sjdbc)
New rtftools Package

The rtftools package contains Spotfire S+ functions for writing out RTF files, including initialization, writing paragraphs, modifying text styles, writing tables, and writing WMF files to RTF. See RTFCodeExample.ssc for examples of some of the package functionality.

Wavelets, Environmental Statistics, and Spatial Statistics Now Included As Packages

The Wavelets and Spatial Statistics modules are now included with core Spotfire S+ as packages. Environmental Statistics is now included with core Spotfire S+ on Windows.

New Sweave Package

Spotfire S+ now offers on the CSAN Website (http://spotfire.tibco.com/csan) the Sweave package. Sweave is a convenient way for package authors to integrate Spotfire S+ code and Latex documentation for vignettes, analyses, and reports.

New FlexBayes Package

Spotfire S+ now offers the FlexBayes package on Windows. FlexBayes provides tools for modeling data using the Bayesian paradigm for statistical inference. Bayesian modeling offers the following advantages over classical or frequentist modeling:

Finding and Updating Packages in the Spotfire S+ Workbench

The Spotfire S+ Workbench now provides user interface support for finding packages from a Web server (via URL) or from a specified local repository. Also, it supports updating packages that you currently have on your system. The Spotfire S+ Workbench also provides support for exporting a package. See the Spotfire S+ Workbench User's Guide for more information.

Creating Spotfire S+ GUIs for Packages

The Guide to Packages is updated to include information about creating grapical user interfaces for packages on Windows. The pkgutils package has been enhanced to support building these on Winodws

Support for Remote Script Execution

The Spotfire S+ Workbench now supports sending a remote script request to a Spotfire S+ Server. Using the interface provided in the Workbench, you can send:

You must have access to a Spotfire S+ Server to use remote script execution. For more information about using this new feature, see the Spotfire S+ Workbench User's Guide.

Support for Association Rules ("Market Basket Analysis") in the Big Data Library

The Big Data library now includes three functions:

These functions support finding interesting association rules for transactions. See their Help files and the Big Data User's Guide for more information.

Obsolete and Deprecated Features and Functions

Improvements in Spotfire S+ 8.1

For a list of bugs fixed since the last release (S-PLUS 8.0.4), see the file FIXEDBUG.TXT in the doc directory of your installation.

JRE Updated for Spotfire S+ 8.1.

Spotfire S+ now ships with version 1.6 of the JRE.

java.graph() now interprets file extensions.

In previous versions of Spotfire S+, java.graph() required the format argument for file types other than JPEG. Now, if you specify a file extension in the file argument, java.graph() interprets that extension to produce the specified format. If no extension, or an unsupported extension is specified, java.graph() defaults to JPEG.

Multiple Random Number Generators Now Supported

Spotfire S+ now includes the function RNGkind() for specifying the type of random number generator to use. Also, Spotfire S+ supports using the Mersenne-Twister random number generator. See the RNGkind Help file for details.

Importing and Exporting changes

STATA version 10 data files are now supported for import and export.

Support for STATA export includes the new type STATASE, which can handle exporting datasets with up to 32,767 variables. (The number of observations is limited only by the amount of RAM in your computer.) Note that exporting using the type="STATA" limits the number of variables to 2,047.

When you import regular Stata or Stata/SE files, just use type="STATA". Specify type="STATASE" only when you call exportData to export data having more than 2,047 variables.

Changes and Updates to the Spotfire S+ Workbench

For more information on using these new features, see the Spotfire S+ Workbench User's Guide.

Changes to the Big Data Library

Spotfire S+ now contains discrete distribution functions.

The following functions have been added to Spotfire S+ to provide density, cumulative probability, quantiles, and random generation for a discrete distribution. See their Help topic for more information.

New Functions and Updates to Spotfire S+

Known Issues in Spotfire S+ 8.1

Branding Update  In this version, you might see inconsistencies in product names, images, and branding as we migrate to our new name and identity. We appreciate your patience as we work though the name and branding processes.

Big Data library does not convert variable names on import.  When you import data using the argument bigdata=T, variables containing characters considered "illegal" by the standard S language are retained. (That is, while the S language does not recognize any character other than a-z, A-Z, 0-9 and period, the Big Data library allows all characters.) When standard Spotfire S+ converts input data to a data frame, it modifies any variable names containing an illegal character, replacing any illegal characters with a period (".") character. For example, if a variable name includes a space ("a b") or an underscore ("a_b"), then in standard Spotfire S+, a period replaces the space or underscore ("a.b"). The Big Data library does not follow this convention; rather, it retains variable names on import.

Backwards Compatibility Considerations in Spotfire S+ 8.1

If you are upgrading from S-PLUS version 8.0 to Spotfire S+ 8.1, the following items do not apply; however, certain improvements to Spotfire S+ 8.1 might result in scripts written for versions of S-PLUS prior to 8.0 not working as expected. This is especially true for workarounds for pre-existing issues, or for the new graphics enhancements.

The par("col") value is now a character string representing an RGB value.  Previously, par("col") was an integer. If you have code that did numeric operations on the par("col") value (for example, col=par("col")+1), the code now fails. Note that you can still set col to a number (for example, par(col=3)).

Changes to cex, font, and col  If you specify display characteristics using the cex, font, and col arguments, they apply only to the plot's data representation.

Setting color maps can produce unexpected results.  Device-specific colormap settings and manipulations apply only when use.device.palette(T) (or when use.legacy.graphics(T) because it sets use.device.palette(T)). Because of this issue, by default, setting Color Schemes from the Options menu does not affect command-line graphics. See the help topic for use.device.palette() for more information.

Big Data library section no longer loaded by default   The S-PLUS 7 Enterprise Developer edition included the Big Data library section, and this library section was loaded by default. In Spotfire S+ 8.1, it is no longer loaded automatically. To load it at startup, add library(bigdata) to your SHOME/local/S.init. Note that SHOME/S.init should not be used. Instructions for editing this S.init file are in SHOME/local/README.

Graphics functions no longer accept list values.  Previously, the graphics system accepted single-element lists as arguments for many functions. For example, the labels argument to the axis() function could be a list, such as the following:
   axis(side=3, at=c(2,6), labels=list(c("a","b")))

The new graphics system no longer supports this behavior, and the above example causes an error. If your existing code breaks because of this change, call the unlist() function to transform the list value.

Workarounds for importing missing columns could cause problems.  If you have implemented custom code to work around the pre-existing issues, you could encounter problems importing data in Spotfire S+ 8.1.

Changes to substituteString()'s replacement argument.  Treatment of backslashes (\\) in substituteString()'s replacement argument in Spotfire S+ 8.1 has changed, so it is no longer compatible with previous versions of S-PLUS (7.0 and earlier). This change accommodates R's implementation of string replacement. See the help for substituteString() for more information.

R Compatibility

For a more thorough listing of R versus Spotfire S+ comparisons, see the TIBCO Spotfire support Web site FAQ.

aggregate.rts() has changed and new arguments for R compatibility.

Previously, aggregate.rts() was defined as follows:

     aggregate(x, nf=1, fun=sum, ndeltat=1)

Now it is:

     aggregate(x, nfrequency=1, FUN=sum, ndeltat=1, ts.eps = .Options$ts.eps, ..., fun)

For more information, see its Help file.

Logical values have changed for R compatibility.

Logical values are now printed as TRUE and FALSE, not T and F. (Note that Expressions involving T and F still print them as T and F, because they are stored by name, not by value, in expressions.)

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Module Support

Spotfire S+ 8.1 will support the following Spotfire S+ modules. For module version information, see the module's release notes in the SHOME/module/modulename directory.

Module Platform
S+FinMetricsTM Windows, Solaris, Linux 32/64-bit
S+NuOPT Windows, Solaris, Linux 32/64-bit
S+SeqTrialTM Windows

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Getting Help in Spotfire S+

To get help on a particular function, use the help() or ? functions. The help system contains online help files for all the Spotfire S+ libraries that are attached at startup; help files for other libraries are available once the libraries are attached.

These manuals are also available as Adobe Acrobat PDF files in $SHOME/doc:

Book Name File Name
TIBCO Spotfire S+ 8.1 Application Developer’s Guideadg.pdf
TIBCO Spotfire S+ 8.1 Installation and Administration Guideadmin.pdf
Big Data Library User’s Guide for TIBCO Spotfire S+ 8.1bigdata.pdf
TIBCO Spotfire S+ 8.1 Function Guidefunctionguide.pdf
Getting Started with TIBCO Spotfire S+ 8.1 for UNIX/Linuxgetstart.pdf
TIBCO Spotfire S+ 8.1 Guide to Graphicsgraphics.pdf
TIBCO Spotfire S+ 8.1 Guide to Packagesspluspackages.pdf
TIBCO Spotfire S+ 8.1 Programmer's Guidepg.pdf
TIBCO Spotfire S+ 8.1 Guide to Statistics, Volume 1statman1.pdf
TIBCO Spotfire S+ 8.1 Guide to Statistics, Volume 2statman2.pdf
TIBCO Spotfire S+ 8.1 for for UNIX/Linux User’s Guideuguide.pdf
TIBCO Spotfire S+ 8.1 Workbench User's Guideworkbench.pdf

Also, you can find the TIBCO Spotfire S+ 8.1 Installation and Administration Guide (admin.pdf) at the root level of your installation media.

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Using Spotfire S+ for Solaris or Linux from a Windows Desktop

Solaris/Linux versions of Spotfire S+ might be accessed remotely from a Windows desktop using X-server software for displaying graphics. Spotfire S+ has been tested with the following products:

The graphical user interface (GUI) performance of Spotfire S+ depends upon the X-server software. The performance of the underlying Spotfire S+ engine is not affected. The following notes describe configurations that have been found to produce the best results. No significant issues were noted. Following are some observations that pertain to X-Win32:

When using some versions of X-Win32 to start-up X-applications on your desktop, we have found that the "multiple windows" setting causes some latency in GUI response and some defects in displaying GUI elements. We recommend running in "single window" mode. If you are connecting with XDMCP, then running in "single window" mode should present you with a default window manager from which you might run Spotfire S+. If you are connecting with rsh or rexec in "single window" mode, the application might be displayed in a "raw" X-session that lacks a window manager. We recommend that you start the Solaris default window manager (/usr/dt/bin/dtwm) using either the X-Win32 "Command" option, or from an xterm on the Solaris host. Once the window manager has been launched, the Spotfire S+ application should run and display successfully.

NOTE : the graphical user interface for Spotfire S+ on UNIX/Linux is deprecated in this release.

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Technical Support

For technical support, please visit http://spotfire.tibco.com/support and register for a support account.

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Appendix: New Functions in Spotfire S+ 8.1

Function name(s) Description
bd.assoc.rulesGenerates association rules.
bd.assoc.rules.get.item.countsCounts association rule items.
bd.assoc.rules.graphCreates a plot of a set of association rules.
bd.cache.temp.dirSets and retrieves the directory used for creating temporary cache files.
bd.object.infoExtracts internal information about a bdFrame or bdVector object.
bd.run.iminer.worksheetFrom the Spotfire S+ Server, runs an Insightful Miner worksheet in batch mode.
bd.tallyMeasures internal Big Data operations.
combinationsReturns all combinations or permutations of size k elements out of n.
combnGenerates combinations of m elements out of x.
contentsDataGets the names of all data sets, sheets, or tables in a specified data file or database.
ddiscreteGets the density for a discrete distribution.
emf.graphCreates an enhanced metafile file.
groupAlls, groupAlls.data.frame,
groupAlls.default
Computes group sums, means, variances, standard deviations for a vector or columns of an array.
groupAnys, groupAnys.data.frame,
groupAnys.default
Computes group sums, means, variances, standard deviations, or other summaries for a vector or columns of an array.
groupMaxs, groupMaxs.data.frame,
groupMaxs.default
Computes group max for a vector or columns of an array.
groupMeans, groupMeans.data.frame,
groupMeans.default
Computes group means for a vector or columns of an array.
groupMins, groupMins.data.frame,
groupMins.default
Computes group mins for a vector or columns of an array.
groupProds, groupProds.data.frame,
groupProds.default
Computes group products for a vector or columns of an array.
groupRanges, groupRanges.data.frame,
groupRanges.default
Computes group ranges for a vector or columns of an array.
groupStdevsComputes group standard deviations for a vector or columns of an array.
groupSums, groupSums.data.frame,
groupSums.default
Computes group sums for a vector or columns of an array.
groupVars, groupVars.data.frame,
groupVars.default
Computes group variances for a vector or columns of an array.
isTRUETest for logical object of length one with value TRUE.
java.new.plot.actionJava graphics action on a new plot. (spjava package)
packageDescriptionGets the description of the specified package.
panel.hexbinPanel function for hexbins.
panel.hexbin.lmlinePanel function for hexbins.
panel.hexbin.loessPanel function for hexbins.
panel.hexbin.smooth.splinePanel function for hexbins.
pdiscreteGets the cumulative probability for a discrete distribution.
permutationsReturns all combinations or permutations of size k elements out of n.
qdiscreteGets the quantiles for a discrete distribution.
rdiscreteGets the random generation for a discrete distribution.
rectDraws and shades rectangles
RNGkindSets and inspects the state of the random number generator.
strwrapWraps character strings for paragraph formatting.
subtractMeansSubtract group means from each entry for a vector or columns of an array.
Sys.setenvSets environment variables for use by other processes called from S-PLUS.
tempdirReturns the name of the directory in which temporary files will be made.
write.dcfReads and writes data in DCF format.

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