5. Software

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Our servers run variants of the Unix operating system. For more information on the Unix operating system, please see the section Basic Unix Commands.

We have a number of software packages installed on RGMiller. Additional software packages are available over the Andrew File System network. Brief descriptions of some important application software follow.

5.1 Online Help
The traditional Unix help is provided by the program man. To find out more about man, type man man at the shell prompt. If you want to search for man pages via a keyword, try man -k <keyword>.

Also note that documentation for most application programs is available under /usr/local/doc.

5.2 Editors
A good editor is an important ingredient of any computing environment. You have a choice of many editors: Emacs, vi, jot, xedit etc. The last assumes use of the X-Window system and is therefore limiting. The best of these without question is Emacs.

There are two variants of Emacs: the Free Software Foundation Emacs and XEmacs. The latter assumes that you are using the X-Window System and so is limiting in that aspect. However, it has nicer looks and it is probably a good idea to start with it. Both editors have extensive documentation online, including a tutorial. A reference card is also available. Learning to use the built-in help system (called Info) is an important skill and will serve you valuably.

5.3 Typesetting Software
We have a comprehensive TeX and LaTeX system installed. You should be able to do everything that you are used to in LaTeX. We run LaTeX2e by default. While LaTeX2e will handle most of the older LaTeX 2.09 constructs, it is not 100% backward compatible. This is something to watch for if you get documents from your collaborators who might have the older LaTeX. (A historical note, in case you are interested: LaTeX2e is now the standard version of LaTeX, and there is no good reason why one should stick to the older LaTeX 2.09 formats.) If you use Emacs or XEmacs to edit your LaTeX files, as you are strongly urged to do, you will be able to use a powerful mode called AucTeX to help you in the document preparation. This mode is automatically invoked whenever you edit a LaTeX file. Life would be a pity without AucTeX. Be sure to check out the menus, etc.

The easiest way to learn LaTeX is to see someone else's document and mimic it.

There are many books now on LaTeX. The first book by Lamport below is the original specification and is now mainly a reference. The last three books are more current.

@book{lamp:1994,
    Publisher = {Addison-Wesley},
    Pages = 256,
    Keywords = {Computing},
    Author = {Leslie Lamport},
    Title = {\LaTeX{} User's Guide and Reference Manual, 2nd ed.},
    Year = 1994
}

@book{goos:mitt:sama:1994,
    Publisher = {Addison-Wesley},
    Pages = 530,
    Author = {Goosens, M., Mittelbach, F. M., Samarin, A.},
    Title = {The \LaTeX{} Companion},
    Year = 1994
}

@book{goos:rahs:mitt:1997,
    Publisher = {Addison-Wesley},
    Pages = 554,
    Author = {Goosens, M., Rahtz, S., Mittelbach, F. M},
    Title = {The \LaTeX{} Graphics Companion},
    Year = 1994
}

@book{kopka:daly:1997,
    Publisher = {Addison-Wesley},
    Author = {Kopka, H., Daly, P.},
    Title = {A Guide to \LaTeX2e{}},
    Year = 1999
}

All of these books are available in our bookstore.

5.4 Web Publishing Software
There are many excellent guides to web publishing. I recommend two resources in particular: The World Wide Web Consortium Web Page and The Netscape Home Page where you can find plenty of tips and guides. Another way to get help in setting up web services is to use the Help menu in Netscape.

For putting documents up on the Web, you'll have to use HTML (Hyper Text Markup Language). Emacs and XEmacs provide at least two modes for editing HTML files: html-helper-mode and PSGML mode. The latter is actually for SGML editing.

For WYSIWYG (What-You-See-Is-What-You-Get) editing, we have SGI's own suite of COSMO tools and Netscape Composer. Both allow you to compose web pages easily and work in a similar fashion. The COSMO suite of software from SGI also includes JAVA and CGI programming tools. These are elaborate pieces of software and come with a set of tutorials and help. See the man pages for cosmocreate, cosmocode, cosmoplayer.

Putting your papers and research on the Web
Under your public_html directory, there is a subdirectory called ftp. If you don't have this directory, you should be able to able to create it as follows.

You should put your technical reports in this area. It is best if you make the technical reports available in two forms at least, compressed PostScript (a file with an extension .ps.gz) and portable document format (PDF, extension .pdf). The following commands show how to go about these steps.

Now make entries in your HTML file to point to both the PostScript and PDF files. See also the Latex FAQ section for some important info on pdf files.

If you follow the procedure above, your paper will be visible via the World Wide Web as well as anonymous ftp. This is a good way of making sure that most of the world, which doesn't have a good connection to the net, can get to your research.

Course Web Pages
We highly recommend that course pages be prepared for use in teaching classes. There are several templates that one can use for organizing information. The department web page lists courses offered each quarter along with links to the actual pages if present. For getting information on setting up course web pages and for reserving space on the server, please see the Leland Server Web Page. In the same place, you will also find examples of course web pages we've used in the past.

Beware that it takes time to set up these resources and one should prepare at least a week ahead of the class starting date.

Course Notes Online
The following is a verbatim copy of a message that was relayed to us by Helen Tombropoulos, our department secretary.

We have received a memo from Adrienne Arden, Head of Meyer Reserves, informing the department that Meyer Library will be piloting electronic reserves this year. ``As of Fall Quarter, all exams, problem and solution sets, and lecture notes will be scanned into the Libraries' web space and mounted as graphic images. Students will be able to locate these materials as they traditionally have (by searching the reserves catalog) but once the appropriate citation has been found they will be able to view the image online or print it out as complete documents.''

Helen, our secretary, phoned Adrienne (5-2191) and asked if current teaching material could be included in this electronic data base. She said that if two copies of lectures notes, reading material, etc. are brought to the reserve office on the first floor of Meyer, within 24 hours one copy would be scanned into the system and the other paper copy would be put on reserve.

Lecture notes, answer keys, course syllabi and/or outlines would be kept for a year; exams would be kept for 3 years.

Adrienne also informed Helen that faculty can go on line to place books on reserve; if, however, there is only a personal copy of the text, that must be brought in.

She said many departments have already sent in material that they will be using in their fall courses.

If you have any questions about this call Adrienne Arden, Head of Meyer Reserves at 5-2191; or let Helen know and she'll forward your concerns on to her.

5.5 Statistical Computing Software
RGMiller has compilers for C, C++, and Fortran. See the man pages for cc, CC, and f77 for example. For most statistical computing, we use an interactive statistical environment like Splus. I list several such programs below.

Splus

is widely used here. It is documented in several books; here are some that are widely used.

@book{beck:cham:wilk:1988,
    Publisher = {Wadsworth},
    Pages = 720,
    Author = {Becker, Richard A. and Chambers, John M. and 
             Wilks, Allan R.},
    Title = {The New {S} Language: {A} Programming 
             Environment for Data Analysis and Graphics},
    Year = 1988
}
@book{cham:hast:1991,
    Publisher = {Wadsworth},
    Pages = 608,
    Keywords = {Computing},
    Author = {Chambers, John M. and Hastie, Trevor J. (Ed)},
    Title = {Statistical Models in {S}},
    Year = 1991
}
@book{vena:ripl:1997,
    Publisher = {Springer Verlag},
    Author = {Venables, W. N., and Ripley, Brian D.},
    Title = {Modern Applied Statistics with S-Plus 
             (Second Edition)},
    Year = 1994
}

There are many resources for Splus. Just point your browser at The Insightful Splus Page, where you can find answers to Frequently Asked Questions about S and Emacs S mode, among other things. We have many useful libraries already installed on our machine.

R

is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.

The design of R has been heavily influenced by two existing languages: Becker, Chambers and Wilks' S (see question What is S?) and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme.

R is free software. More information on R can be found at R FAQ.

CART

is software for doing Classification and Regression Trees. Currently, we have a version that runs only on Girshick and so one has to log into Girshick to use it. The documentation for the implementation is non-existent but the ideas are discussed in the book

@book{brei:frie:olsh:ston:1984,
    Publisher = {Wadsworth},
    Pages = 358,
    Keywords = {Computing},
    Author = {Leo Breiman , Jerome H. Friedman, Richard A. 
             Olshen, Charles J. S tone},
    Title = {Classification and Regression Trees},
    Year = 1984
}

Matlab

is a solid piece of software for doing matrix computations. We also have many toolboxes available for use with Matlab, including a Statistics toolbox. The Mathworks Home Page has an extensive set of resources for Matlab. Matlab 5 is available on our systems. Typing matlab5 invokes Matlab 5.1.

XlispStat

is a nifty object-oriented statistical computing environment. It is free and runs on X11, Windows and Macs. For more information see the Xlisp-Stat Web Page

BUGS

stands for Bayesian inference Using Gibbs Sampling. This software is only available on Girshick, and the Leland Systems. However it is free and comes with an extensive tutorial. For more information see the Bugs Home Page.

MCSim

on MCSim is a set of C programs that allow you to run Markov Chains and integrate coupled differential equations. It has a good amount of documentation but is still not too useful to statisticians.

Others

SAS, SPSS, GAUSS, etc. The department does not have a license for many products. However, all the above mentioned software as well as a few others are available on the Leland system. For more information on this, see the Statistical Applications Consultants' Home Page.

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