Supported
Platforms and System Requirements
What's
New in S‑PLUS 8.0.4
Improvements
in S‑PLUS 8.0.4
Known
Issues in S‑PLUS 8.0.4
Module
Support
Installing
S‑PLUS
Running
S‑PLUS
Using
S‑PLUS for Solaris or Linux from a Windows Desktop
Getting
Help in S‑PLUS
Contact
Information for Feedback
Appendix:
New Functions and Data Sets
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S‑PLUS 8.0.4 for Solaris/Linux is supported on the following platforms and operating systems. The minimum recommended disk space for installing and running S‑PLUS is also included (note that the disk space includes only S‑PLUS and no modules):
| Platform | Operating System | Required Disk Space |
| Sun SPARC | Solaris 2.8, 2.9, 2.10 on SPARC processors | 475 MB |
| Linux x86 | Red Hat Enterprise Linux WS 3.0 and 4.0 | 475 MB |
| Linux x86-64 | Red Hat Enterprise Linux WS 3.0 and 4.0 | 500 MB |
NOTE: S‑PLUS 8.0.4 is not supported on HP-UX or AIX.
The minimum RAM required to run S‑PLUS from the command line is roughly 60 MB. The Java GUI requires an additional 100 MB. Note that these values are the minimum requirements; if you work with moderate sized data sets, these numbers might be insufficient for your needs.
The supported release contains the kernel and compiler for Red Hat Linux WS 3 and 4 (Enterprise), as listed below.
For more information on various Linux distributions, see http://www.distrowatch.com/.
| Red Hat OS | WS 4 (Enterprise) | WS 3 (Enterprise) |
| Kernel | 2.6.9 | 2.4.21 |
| gcc | 3.4.4 | 3.2.3 |
| libc | 2.3.4 | 2.3.2 |
| libstdc++ | 5.0.7 | 5.0.3 |
Eclipse 3.2.2, the version that S‑PLUS 8.0.4 uses, does not support SPARC/Motif for Solaris. If you are using a version of Solaris prior to version 10, you must install the GTK library. (This library is included in Solaris 10.)
The Java runtime environment (JRE) version 1.5.0_11 is included in S‑PLUS 8.0.4. Your operating system must support JRE 1.5.0_11 in order to run the Java-enabled version of S‑PLUS. Note that the JRE provided by S‑PLUS is installed as part of the S‑PLUS distribution, and under normal circumstances, it is used only by S‑PLUS. If you have a different version of the JRE on your system, the JRE used by S‑PLUS should not interfere with your other JRE applications, which will continue to use the version you have previously installed.
If you are developing new code, you will need a Java 2 development environment such as the Java 2 JDK. For S‑PLUS, the desired JDK is version 1.5. For Windows, this tool is freely available from Sun®. (Licensing restrictions prevent Insightful from redistributing the Java 2 JDK with S‑PLUS.)
For more information about version 1.5 of the JRE and the JDK, see the Sun site:
http://java.sun.com/javase/downloads/index_jdk5.jsp
Linux requirements for the JRE are available from
http://java.sun.com/j2se/1.5.0/jre/install-linux.html
These release notes indicate the Java 2 SDK Standard Edition v1.5.0 is supported on Solaris 8, 9, and 10 operating environments.
Solaris requirements for the JRE are available from
http://java.sun.com/j2se/1.5.0/jre/install-solaris.html
These release notes provide the following recommendations:
"Java 2 Runtime Environment v 1.5.0 (J2RE) is supported on i586 Intel and 100% compatible platforms running Linux. For a list of supported operating systems and desktop managers, see System Configurations."
The S‑PLUS 8.0.4 for Linux release uses the kernel and compilers listed above. Other Linux distributions, such as SuSE, are not officially supported or tested. However, if you want to use another Linux distribution, you should use one that has similar versions of the kernel and compilers (e.g., SuSE 9.0 or 9.1).
There is no separate Enterprise Developer or Professional edition in S‑PLUS 8.0.4. This release includes the Big Data library section and the Eclipse Workbench (previously available in the S‑PLUS 7.0 Enterprise Developer edition only):
S‑PLUS 8.0.4 is a major release of the S‑PLUS product family, with the following new features:
S‑PLUS packages is a system for downloading, installing, and creating a
user-defined library of functions, help files, and data for distribution.
Insightful hosts a Web site called CSAN (Comprehensive S Archival Network)
at
csan.insightful.com.
that serves as the central repository for S‑PLUS users to exchange these S‑PLUS packages. These packages are available for download as Windows binaries and Solaris/Linux source.
Downloading, installing, and creating S‑PLUS packages requires the pkgutils library, which must be downloaded and installed from CSAN, and installed in your SHOME/library.
After you have installed S‑PLUS, cd to your installation
directory, then download and install the pkgutils library using the shell
command:
./INSTALL.PKGUTILS
This installs the pkgutils library in your; SHOME/library, where SHOME is your installation directory. You must be connected to the Internet to run this script. For more information on S‑PLUS packages, see the Guide to S‑PLUS Packages, available in your SHOME/doc directory (spluspackages.pdf).
The interactive debugger provides an environment for writing and developing functions in S‑PLUS. This application has modern debugging tools like step debugging and breakpoints. For more information on how to use the Workbench debugger, see the S‑PLUS Workbench User's Guide in your SHOME/doc directory (workbench.pdf).
S‑PLUS 8.0.4 includes new command-line graphics functionality. The new
features include support for named colors (for example, col="red"),
alternative color specification models, color palettes, and vectorized
parameters for drawing points, lines, and text. The graphics enhancements
support all devices (including transparency on java.graph and
pdf.graph) except print. For more information, see the
Guide to Graphics pdf, available in your SHOME/doc
directory (graphics.pdf).
col, font, and
cex arguments in par() controlled plot elements in a
generalized way. The color, font, and character size of a plot's title,
subtitle, axis labels, and tick mark labels could not be set independently. New
parameters have been implemented to set these display characteristics at a more
granular plot element level:col.main,
col.sub, col.axis, col.lab.
font.main,
font.sub, font.axis, font.lab.
cex.main,
cex.sub, cex.axis, cex.lab. If you specify display characteristics using the col,
font, and cex arguments, they apply only to the plot's
data representation.
If you do not specify any of these arguments, S‑PLUS uses the default values.
See the par() help file for more information.
S‑PLUS 8.0.4 introduces many new objects and data sets. See the Appendix in this document for a detailed list.
S‑PLUS 8.0.4 now implements a deprecation policy to improve the S‑PLUS product line by removing functions, function arguments, and terms that no longer serve a useful purpose or have been superseded by others. The deprecation policy divides the functions, function arguments, and terms into four states: good standing, deprecated, defunct, and discontinued.
help(Deprecated).
help(Defunct).
For a list of bugs fixed in this release, see the file FIXEDBUG.TXT in the doc directory of your installation.
For a list of issues you might encounter as a result of improvements to S‑PLUS, see the section Backwards Compatibility Considerations in S‑PLUS 8..
Prior to S‑PLUS version 7.0.6, if you imported data containing an empty column, on import, S‑PLUS would remove that column and replace it with the column immediately to its right. (For example, S‑PLUS would remove empty column C2 and populate that column with the contents of column C3.) If you have implemented custom code to work around this pre-existing issue, you could encounter problems importing data in S‑PLUS 8.
"helmert" to
"treatment"Factor contrasts changed from contr.helmert to
contr.treatment. The old value can be restored by
setting:
options(contrasts=c(factor="contr.helmert",
ordered="contr.poly"))
If this is set in the file S.init in $SHOME/local, then all users get the old contrasts.
java.graphThe java.graph window and Graphlets® now allow text
and symbols to grow without limit by setting cex= to higher values.
This also means that text and symbols will grow when zooming a
java.graph window or Graphlet, so zooming into a clump of points
does not make their distribution clearer.
By default, Java graph windows are subwindows embedded in the S‑PLUS Workbench window, instead of separate windows. To change this setting, on the Workbench menu, click Window > Preferences, and in the Preferences dialog, select the S‑PLUS page. Clear the option Integrate Java Graphs in the S‑PLUS Workbench.
n argument in readLines
has changed The default for the n argument of readLines has
changed from 1 to -1 (to read all lines, not just the
first line).
When importing from SPSS, S‑PLUS now imports value labels for string variables. Previously, S‑PLUS imported value labels for numeric variables only.
optim() function added to core S‑PLUSThe optimization function optim has moved from Venables and
Ripley's MASS library (with Brian Ripley's permission) to core S‑PLUS. This is a
general-purpose optimization based on Nelder-Mead, quasi-Newton, and
conjugate-gradient algorithms, and includes an option for box-constrained
optimization. See the help file for optim for more information.
regexpr() uses a new regular expression matching algorithm and
accepts "extended regular expressions."The functions regexpr, substituteString,
grep, and the new functions sub, gsub,
and strsplit use a newer regular expression matching code. The
default is to use "extended regular expressions" (not "basic" or "obsolete"
regular expressions).
var.equal changed from TRUE to
FALSEThe default value for var.equal in the two-sample t-test was
changed from TRUE to FALSE. This change was made in
the function t.test, and in the Windows and Java GUI dialogs for
two-sample comparisons.
correlation argument in
summary.lm changed from TRUE to
FALSEThe default value for the correlation argument in
summary.lm (and all summary functions with an lm
object) has been set to FALSE.
parseXMLPathFile and
parseXMLPathString support parsing based on white spaceNew arguments were added to parseXMLPathFile and
parseXMLPathString to support parsing data. For example, you can
now retrieve and parse <x>a b c</x> as individual
values, "a" "b" "c", rather than as "a b c".
Previously, to load Java, you had to load it when starting S‑PLUS using
Splus -j. Now, it is possible to load Java during an S‑PLUS session
by calling library(spjava). In addition, if a Java-dependent
function such as .JavaMethod, .JavaField, or
java.graph is called when the JVM is not running, it automatically
loads Java, thereby saving system resources until you need to use them.
Major elements of S‑PLUS require using the Java Virtual Machine (JVM). By
default, the memory heap size is now set to 400mb. If you see a
java.lang.OutOfMemoryError, you can now increase the limit more
easily.
On Solaris and Linux, increase the JVM memory heap size by setting the
JAVA_OPTIONS environmental variable to 600MB (for example) by
executing the following S‑PLUS
expressions: setenv("JAVA_OPTIONS",
"-Xmx600m");library(spjava)
NOTE You must set the
JAVA_OPTIONS environment variable before the JVM is started;
setting it afterward has no effect. For more information about setting other
JVM options, see the Sun documentation.
Exceptions to the above changes include when you are running the S‑PLUS
Workbench and when you are running S‑PLUS commands on a remote application
server. For more information about changing the JVM memory heap size in the
Workbench, see the S‑PLUS Workbench documentation. To increase the memory heap
size when you are running commands on a remote server, set it in the Solaris or
Linux shell initialization file (such as the .cshrc file, if
you use csh.)
USE.NAMES=T added to sapply()This addition makes sapply() similar to R functionality with the
addition of this argument.
sub function name changed to subscript2dTo avoid a name conflict with R's sub function
(substituteString) the S‑PLUS sub function (which does
subscripting) has been renamed to subscript2d.
This was supported under 32-bit. Now connectivity to DB2 and Oracle is supprted under Linux 64-bit.
NAColumns containing NA are imported as character (instead of
numeric, as they were in previous versions of S‑PLUS).
Previously, conversions of empty lists to logical and numeric objects would
give an error. Conversions are now allowed for as.logical(list()),
as.numeric(list()), as.integer(list()), and
as.complex(list()).
Certain improvements to S‑PLUS 8.0.4 might result in existing scripts not working as expected. This is especially true for workarounds for pre-existing issues, or for the new graphics enhancements. Some issues you might encounter include the following.
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 col, font, and cex arguments,
they apply only to the plot's data representation. See the section Element-Specific
Arguments Add Graph Flexibility for more information.
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
S‑PLUS 8.0.4, 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 issue described in the section Missing Columns now preserved, you could encounter problems importing data in S‑PLUS 8.
Changes to substituteString's replacement
argument. Treatment of backslashes (\\) in
substituteString's replacement argument in S‑PLUS 8 has changed, so
it is no longer compatible with previous versions of S‑PLUS. This change
accommodates R's implementation of string replacement. See the help for
substituteString for more information.
Workbench: S‑PLUS Console deprecated. Because of implementation changes in the view, the S‑PLUS Console view available in previous releases is being deprecated. If you use a workspace created prior to this release, you will see a label indicating that the Console view is deprecated (S‑PLUS Console (deprecated)); however, the new view is available to you.
To change to the new Console view permanently:
The deprecated S‑PLUS Console view will still work as expected in this release, and its functionality is the same as the new Console view; however, it will follow the deprecation policy described above.
When FUN is a generic function, lapply and sapply
sometimes will not find the proper function when you call
lapply(X,FUN). It works if you use
lapply(X,function(x)FUN(x)). This applies to any function that
takes another function as an argument, not just to lapply and sapply. For
example:
sapply(as.bdFrame(fuel.frame)[,-5],
floor)
will cause an error; the recommended workaround is:
sapply(as.bdFrame(fuel.frame)[,-5], function(x)
floor(x))
lapply, sapply,
and so on.When FUN is a generic function, lapply and
sapply will sometimes not find the proper function when you call
lapply(X,FUN). It works if you use
lapply(X,function(x)FUN(x)). This applies to any function that
takes another function as an argument, not just to lapply and
sapply. For example, sapply(as.bdFrame(fuel.frame)[,-5],
floor) will cause an error; the recommended workaround is
sapply(as.bdFrame(fuel.frame)[,-5], function(x) floor(x)).
Exporting using direct Oracle drivers (e.g.,
exportData(type="DIRECT-ORACLE")) converts the exported column
names to uppercase.
Direct database accessdoes not work in the Big Data library on LINUX 64.
S‑PLUS cannot import files created by MATLAB version 7 or higher, and MATLAB
version 7 or higher cannot load
Workaround: Files created by MATLAB version 7 or higher can be imported into
S‑PLUS if the -v6 option is used when saving the file in
MATLAB.
S‑PLUS -g)If you see a message that contains:
"Cannot connect to X11 window server using ...as the value
of the DISPLAY variable" when attempting to start S‑PLUS, this most likely means you forgot to set
your DISPLAY environment variable. See Running S‑PLUS for
details.
If you see messages about a connection to your display being refused by the
server, you might need to use the Solaris or Linux xhost command to
allow access to your X server from the S‑PLUS server.
The Data Set lists in dialog boxes display the names of data frames in your working directory. To see built-in example data sets, assign them to your working directory by typing commands similar to the following in the Commands window:
fuel.frame <- fuel.frame
catalyst <- catalyst
environmental <- environmentalAlternatively, you can click View > New Data Viewer, and then type the name of a built-in example data set into the Data Set text box
The Java menus and dialog boxes are equipped with keyboard shortcuts that allow you to use your keyboard instead of the mouse to navigate the GUI. The keyboard shortcuts are indicated by underscores in menu and field names; combine these with the ALT key or its equivalent to navigate the main menu. For example, ALT-F opens the File menu, and once that menu is displayed, pressing E displays the Export Data dialog box. Similarly, ALT-G will open the Graph menu, and then pressing S displays the Scatter Plot dialog box.
Within dialog boxes, use the ALT key together with the indicated keyboard shortcuts to navigate to a desired field. For example, in the Scatter Plot dialog box, use ALT-F to navigate to the x Axis Value box.
The GUI (including JavaHelp) uses the GUI-standard CTRL-C/CTRL-V for cutting and pasting. Because CTRL-C can be interpreted as a copy command, the GUI version of S‑PLUS uses ESC as its interrupt key. On some X displays, you might need to double-middle-click to execute a paste in the Commands window.
To run the Java GUI on a remote display, you must have a display that supports the X Window System. This might be either a Solaris or Linux display or a PC running an X server such as X-Win32 or Reflection X. A text-only connection such as telnet does not support graphical applications.
Java has a number of known problems displaying on a remote display using the X Window System. For this reason, we suggest (if possible) that you limit your use of the Java-based GUI in this release to the console of the machine on which S‑PLUS is installed. That is, treat this release of the Java-based GUI as a workstation release, rather than as a network client/server release.
Known problems with remote display include the following:
The amount of memory available to a particular user in Solaris or Linux is controlled by various limits. To see them, type:
% limitat a shell prompt on your system. The defaults returned might be too small for S‑PLUS. On one machine at Insightful Corporation, for example:
% limit datasizeis 131072 kbytes by default. This can lead to S‑PLUS running out of dynamic memory sooner than it otherwise should. The fix is to increase the limit, as in the following command:
% limit datasize unlimitedSome user limits are constrained by system limits that must be set by the superuser. If you maximize your user settings but still have dynamic memory problems, you might need to contact your system administrator to raise the system limits.
If you compile C or Fortran code for use with S‑PLUS 8.0.4, note that 32-bit
and 64-bit versions of S‑PLUS 8.0.4 both produce makefiles that create shared
libraries named S.so by default. These libraries are incompatible between
versions and must be compiled for either 32-bit or 64-bit versions of S‑PLUS. We
recommend creating shared libraries with different names for each platform (such
as S_64.so and S_32.so). You can then use dyn.open to open these
libraries, if desired.
If you exceed your processor's integer limit, S‑PLUS now returns NA and generates a warning indicating that you have reached integer overflow. For example, on a computer with a 32-bit processor, if you calculate the following:
46341 * 46341you will see the integer overflow warning. You can avoid this problem by using floating point numbers. For example,
46341. * 46341The following functions do not support the graphics color enhancements
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 S‑PLUS 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 S‑PLUS, 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.
To change any variable
names to names that the S language recognizes, use the make.names
function, which converts character strings into legal S‑PLUS names. See the Help
topic for make.names for more information.
Eclipse 3.2.2, the version that S‑PLUS 8.0.4 uses, does not support SPARC/Motif for Solaris. If you are using a version of Solaris prior to version 10, you must install the GTK library. (This library is included in Solaris 10.)
Using the debugger and profiler can tax speed, memory usage. When you use the debugger or the profiler in the S‑PLUS Workbench, you might notice a slowdown in running your code or an extra draw on memory usage. This behavior is typical of process-heavy tools and can be especially problematic with larger data sets. To help mitigate this effect, try running the debugger or profiler against several small samples of your data and examining the results.
S‑PLUS 8.0.4 will support the following S‑PLUS modules. These modules require a license to use; please contact Support at support@insightful.com for more information. For module version information, see the module's release notes in the SHOME/modulename directory.
| Module | Platform |
| S+ArrayAnalyzer® | Windows, Linux 64-bit |
| S+FinMetricsTM | Windows, Solaris, Linux 32/64-bit |
| S+NuOPT | Windows, Solaris, Linux 32-bit |
| S+WaveletsTM | Windows, Solaris, Linux 32-bit |
| S+EnvironmentalStatsTM | Windows |
| S+SeqTrialTM | Windows |
| S+SpatialStatsTM | Windows, Solaris, LINUX 32/64-bit |
For complete installation instructions, see the document INSTALL.TXT, located at the top level of your S‑PLUS 8.0.4 CD-ROM.
Do NOT install this release over any existing version of S‑PLUS. Instead, designate a clean installation directory for S‑PLUS 8.0.4.
From the top-level directory, type
rm -rf <filelist>where <filelist> is the S‑PLUS directory.
Before installing S‑PLUS, you must do the following:
DISPLAY environment variable to your local machine,
if necessary.
To use the Java related features of S‑PLUS, you must be able to connect to
your local X window server. Thus, you must have the environmental variable
DISPLAY set and the X window server on your local machine must
allow the S‑PLUS server to create windows on your machine; see the Solaris/Linux
programs xauth or xhost. Typically, if you can run
xclock on your machine, then S‑PLUS should also be able to access
the X server.
To set your display from a C-like shell (csh, tcsh,
etc.), use the setenv command:
% setenv DISPLAY <display_name>where <display_name> is the name of your local machine.
From the Bourne- and Korn-like shells (including sh,
ksh, bash, etc.), use the following commands:
% DISPLAY=<display_name>;export
DISPLAYYou do not need to do this if your DISPLAY variable is set
already; check the output from echo $DISPLAY to be sure.
Creating an S‑PLUS chapter is necessary for storing the data objects and external files you create in S‑PLUS. The following commands create an S‑PLUS chapter named mysplus for you to work in (be sure you do not have a mysplus directory in your home directory before typing these commands).
% cd
% mkdir mysplus
% cd mysplus
% Splus
CHAPTER
If you do not create a chapter, S‑PLUS automatically creates one for you
named MySwork the first time you start S‑PLUS.
You are now ready to start S‑PLUS. S‑PLUS might be launched in a variety of modes. The following table lists each command-line expression and the corresponding mode for launching it. In all of the commands below, Splus refers to the script you use to launch S‑PLUS 8 on your system.
| Command-line Expression | S‑PLUS Mode |
% Splus |
S‑PLUS command line without Java. |
% Splus ‑j |
S‑PLUS command line supporting Java calls, Java graphics, and the Java help interface. |
% Splus ‑bigdata |
S‑PLUS command line with the Big Data library. Also loads Java. |
% Splus ‑gor % Splus ‑g & |
S‑PLUS graphical user interface. The second command using the ampersand "&" puts the GUI process into the background, freeing your xterm for other uses. The -e flag might be added to either of the first three modes to enable command-line editing. The Commands window in the graphical user interface always allows basic editing. |
‑helpoff |
S‑PLUS without the automatic invisible startup of the help system. The
-helpoff flag is useful only with the -g flag. The invisible startup improves initial responsiveness of the help system but adds a significant memory footprint to the current session. If you want to optimize your available memory, this flag might prove useful. |
% Splus ‑wor % Splus ‑workbench |
S‑PLUS Workbench, the Eclipse IDE plug-in that provides a work environment integrated with S‑PLUS. |
% Splus ‑w ‑bigdata & |
Loads the S‑PLUS Workbench and the big data library. |
Solaris/Linux versions of S‑PLUS might be accessed remotely from a Windows desktop using X-server software. S‑PLUS has been tested with the following products:
The graphical user interface (GUI) performance of S‑PLUS depends upon the X-server software. The performance of the underlying S‑PLUS 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 S‑PLUS. 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 S‑PLUS application should run and display successfully.
The GUI version of S‑PLUS 8.0.4 for Solaris/Linux uses JavaHelp 2.0 as its
main help system. You can use the help.start and
help.off functions to turn the help system on and off,
respectively, throughout your S‑PLUS session. To get help on a particular
function, use the help or ? functions. The help system
contains online help files for all the S‑PLUS libraries that are attached at
startup; help files for other libraries are available once the libraries are
attached.
To get help for a particular dialog box, click the Help
button in that dialog box. For replacement functions such as
"dim<-", look for help on the corresponding regular function,
such as dim. Look up Arithmetic, Assignment, and Comparison,
respectively, for arithmetic, assignment, and
comparison operators.
The installation notes are available in $SHOME/INSTALL.TXT
S‑PLUS 8.0.4 has two printed manuals:
| Book Name | File Name |
| Getting Started with S‑PLUS 8 | getstart.pdf |
| S‑PLUS 8 Installation and Administration Guide | admin.pdf |
These manuals are also available as Adobe Acrobat PDF files in $SHOME/doc:
| Book Name | File Name |
| Getting Started with S‑PLUS 8 | getstart.pdf |
| Guide to Packages | spluspackages.pdf |
| Guide to Graphics | graphics.pdf |
| S‑PLUS 8 Big Data Library User’s Guide |
bigdata.pdf |
| S‑PLUS 8 Workbench User’s Guide |
workbench.pdf |
| S‑PLUS 8 Application Developer’s Guide | adg.pdf |
| S‑PLUS 8 Programmer's Guide | pg.pdf |
| S‑PLUS 8 User’s Guide | uguide.pdf |
| S‑PLUS 8 Function Guide | functionguide.pdf |
| S‑PLUS 8 Guide to Statistics, Volume 1 | statman1.pdf |
| S‑PLUS 8 Guide to Statistics, Volume 2 | statman2.pdf |
We are very interested in receiving information on possible bugs and
usability enhancements from all users in this release. Please send any feedback
to:
bugs@insightful.com
General information about this release of S‑PLUS is available at:
http://www.insightful.com/support/splus80unix/
You can search the S‑PLUS Frequently Asked Questions (FAQ) Knowledgebase
at:
http://www.insightful.com/insightful_faq/search.asp
This section contains names and short description of new objects and data sets in S‑PLUS 8.0.4. For more information about any one of these, see its individual help file.
New
Functions for Graphics Colors
String
Manipulation Functions
Misc.
Functions - Many Added for R Compatibility
Functions
Related to the Package System
File
/ Directory Manipulation Functions
Color
Data Sets
Other
New Data Sets
| Function name | Description |
add.color.values |
Modifies the table of named colors. |
cm.colors |
Creates color sets suitable for image palettes. |
col2rgb |
Converts the specified color to RGB integer triplet. |
color.values |
Gets color names and values. |
colors |
Gets color names and values. |
gray |
Generates shades of gray at different levels. |
gray.colors |
Generates gamma-corrected shades of gray. |
grey |
Generates shades of gray at different levels. |
grey.colors |
Generates gamma-corrected shades of gray. |
heat.colors |
Creates color sets suitable for image palettes. |
hsl |
Converts HSL color specification to RGB. |
hsv |
Converts HSV color specification to RGB. |
image.palette |
Sets or gets the default palette and image palette RGB values. |
palette |
Sets or gets default palette and image palette RGB values. |
rainbow |
Creates a color set based on a sequence in HSV color space. |
rgb |
Creates an RGB value from numeric RGB intensities. |
rgb2hsl |
Creates an HSL value from numeric RGB intensities. |
rgb2hsv |
Creates an HSV value from numeric RGB intensities. |
terrain.colors |
Creates color sets suitable for image palettes. |
topo.colors |
Creates color sets suitable for image palettes. |
use.device.palette |
Use a device-specific palette or a global palette. |
use.legacy.graphics |
Uses legacy graphics internal code. |
| Function name | Description |
dQuote |
Puts single or double quotation marks around text. |
delimMatch |
Matches delimited substrings in a character vector, with proper nesting. |
format.char |
Formats using C-style formats. |
formatC |
Formats using C-style formats. |
gettext |
Translates text messages. |
gettextf |
Uses the C sprintf function to combine numbers and
strings into a formatted string. |
make.unique |
Makes character strings unique. |
ngettext |
Translates text messages. |
sprintf |
Uses the C sprintf function to combine numbers and strings into a formatted string. |
sQuote, dQuote |
Puts single or double quotation marks, respectively, around text. |
strsplit |
Splits strings into pieces based on regular expression. |
tolower |
Translates letters in a vector of character strings or a
bdCharacter to all lower case. |
toupper |
Translates letters in a vector of character strings or a
bdCharacter to all upper case. |
| Function name(s) | Description |
%w/o% |
operator version of setdiff. |
bquote |
Returns a quoted expression, where parts of the expression wrapped in
".()" are evaluated in the environment specified by the
where argument. |
colnames, colnames<- |
specifies column names. See colIds. |
complete.cases |
which cases have no missing values. |
cov2cor |
convert a covariance matrix into a correlation matrix. |
data |
just checks if data object is available. |
download.file |
get a file from the Internet. |
expm1, log1p |
accurate exp(x) - 1, log(x+1). |
getOption |
same as options(arg)[[1]]. |
head, tail |
look at start or end of an object. |
igroupAlls, igroupAnys, |
fast group summaries. |
is.R |
FALSE in S‑PLUS. |
is.symbol |
same as is.name, for compatibility with R. |
log2 |
log base 2. |
model.offset, model.response, |
like model.extract but for specific model
components. |
NCOL, NROW |
like ncol, nrow, but works with vectors. |
nlevels |
shortcut for length(levels(x)). |
optim |
optim function from MASS library section now part of
S‑PLUS. |
perl |
call Perl from inside of S‑PLUS. |
quote |
like Quote. |
rownames, rownames<- |
specifies row names. See rowIds. |
sd |
like colStdevs. |
setwd |
set working directory. |
stopifnot |
for writing tests. |
subscript2d, subscript2d<- |
subscripting rectangular data objects. |
Sys.getenv |
like getenv. |
Sys.getpid |
like process.id()[[1]]. |
Sys.putenv |
set an environment variable. |
Sys.sleep |
like sleep. |
upper.tri |
upper version of lower.tri. |
which.max, which.min |
index for max and min. |
| Function name(s) | Description |
checkExample, checkExamples |
runs example code from help files. |
getSversion |
version object for packages. |
install.pkgutils |
installs pkgutils library section. |
installFromDataFiles, |
install S code from files. |
read.dcf |
reads a package DESCRIPTION file. Required. |
set.parse.mode |
set S‑PLUS or R parsing mode. |
unresolvedGlobalReferences |
look for undefined functions and data in source files. Useful for
porting packages from R. |
| Function name(s) | Description |
basename |
basename of a file path. |
dir |
lists files in a directory. |
dir.create |
makes a directory. |
dirname |
the directory part of a file path. |
file.access |
checks file access permission. |
file.append |
appends to a file. |
file.copy |
copies a file. |
file.create |
creates a file. |
file.info |
gets information about a file. |
file.remove |
removes a file. |
file.rename |
renames a file. |
file.show |
displays a file. |
file.splitpath |
splits a full path name into individual components. |
is.symlink |
checks if a file is a symbolic link. |
list.files |
lists files. |
path.expand |
expands a file path. |
system.file |
finds full names of files in packages. |
| Data set name | Description |
css.colors |
Named vector describing the 147 named colors from the CSS3 Color Module specification. |
r.default.colors |
Named character vector containing the RGB hex string values for the 8
colors in the default R global color palette. |
r.default.image.colors |
Named character vector containing the RGB hex string values for the 12
colors that R uses by default in its image function. |
splus.default.colors |
Named character vector containing the RGB hex string values for the 16
colors in the default S‑PLUS global color palette. |
splus.default.image.colors |
Unnamed vector containing the RGB hex string values for the 256 colors
in the default S‑PLUS global image color palette. |
x11.colors |
Named vector with the 657 named colors in the standard X11 color
specification, after removing spaces and normalizing to lowercase names. |
| Function name(s) | Description |
iris.df |
iris data as a data frame. |