Local Software

1  Statistical

• SAS is the most widely used statistical package in biostatistics. PC version can be accessed on Microlab computers and Unix version on ``hsph''. Students/faculty can obtain the PC version of SAS for an annual fee of about $120. Call 617-496-SITE for Harvard University Information Systems.
• S-plus software was developed by Statistical Sciences and it is available on hsph and in the Microlab. Splus is a superset of S, developed by folks at Bell Labs to meet their statistical needs. It advocates and supports the use of Exploratory Data Analysis (EDA) and encourages the user to look at their data through sophisticated data display and plotting capabilities. It also supports standard descriptive and predictive statistics. "Modern Applied Statistics with Splus" (MASS) by Venables and Ripley is an excellent text covering most of anybody would ever want to know about Splus.
• R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. On hsph, R (version 1.8.1) can be run using command R. R is also available for free download at R. The most current Windows version (version 2.6.0) is available on all lab machines in room 414.
• "stata" is available on "hsph". Documentation is available in the computing lab. The HSPH ICF office (Rm LL19) sells Stata to students for Mac and PC/Windows.

2  Mathematical

All mathematical programs mentioned below (Matlab, Mathematica and Maple) are available for download from the FAS download page. You will need your student ID number in order to obtain the software.

• Matlab is a numerical math program. Its development started in 1984 with mainly technical aims. Currently, it is one of the most widely used scientific programs. There is a very good archive of Matlab routines. Matlab documentation and several other books are available in the biostats computing lab.
• Mathematica handles complex symbolic calculations that often involve hundreds of thousands or millions of terms. It can solve equations, differential equations, and minimization problems numerically or symbolically. Mathematica is also doing numerical modeling and simulations. Wolfram supports an archive. Mathematica documentation and several other books are available in the biostats computing lab.
• Maple features include a comprehensive suite of mathematical solvers, mathematical visualization, and a rich document-processing environment. Maple supports an archive with applications and packages. Maple documentation and several other books are available in the biostats computing lab.

3  Text editors

• Emacs and XEmacs are highly customizable open source text editors. XEmacs runs on Linux/Unix and Windows 2000/XP.
• Vi is mode-based (Tutorial) It has a straightforward but non-mnemonic command set, and it is not fully configurable (i.e. you can't make vi look like emacs). VIM (VI IMproved) is a Vi clone. VIM can operate in a text based environment but there is a version known as gVim which operates in a GUI environment.
• For new users who are unfamiliar with either "vi/gvim" or "emacs/Xemacs", we recommend that they learn "XEmacs", if only because it features a built-in online tutorial and extensive help.
• Also available on the public machines is WinEdt, which an editor and shell for MS Windows. WinEdt is often used as a front-end for TeX. On the public machines, it is used in conjunction with MikTeX.

4  Formatting packages

The main system for text formatting is L^AT_EX (recommended). Users considering using L^AT_EX should get their hands on the L^AT_EX Users Guide, by Les Lamport or any other good L^AT_EX book (check the computing lab). There is also a growing guide called The Not So Short Introduction to L^AT_EX These documents lay out how to run these formatters and previewers that are supported. Currently installed commands on hsph are:

latex - command to format documents into dvi format

pdflatex - command to format documents into pdf format

bibtex - bibliography support

dvips - dvi to postscript (printing)

ppower4 - PowerPoint-like presentations

xdvi - dvi previewer

There is more information (with examples) on the main Computing webpage. With increasing popularity of PC-Windows machines many students use Windows-versions of L^AT_EX. One of the most popular implementations is MikTeX.

5  Programming languages

• C compilers
  The biostatistics department currently supports the standard c compiler on all machines ("cc") as well as "gcc" (GNU cc). "gcc" is ansi-compliant and the stock compilers ("cc") generally aren't.

This page is maintained by The User Assistants

Last updated: 11-13-2007