Computer Hints

Links to Resources

cquest web site
UTORDIAL web site (inexpensive dialup internet access)
Miscellaneous handouts
- Unix
  - unix handout (short version)
  - unix handout (longer version)
- The emacs text editor
  - emacs handout (short version)
  - emacs handout (longer version)
R
- Official R website, including how to obtain a free copy of R to put on your home computer.
- More R Links
- Introduction to R: A very nice 100-page PDF document. Highly recommended if you are going to be using R for serious work.
SAS (Chapter 2 of the online text contains an introductory discussion of the SAS statistical software.)
- SAS Institute website
- Online SAS Documentation.
- Get your own copy of SAS under site license from the U of T information commons. Neither necessary nor recommended for this course, but graduate students who want to use SAS after our course is over will find the transition to SAS/PC an easy one.
Adobe Acrobat Reader: If you are connecting from a computer not located on campus, you may need to download this free software in order to see the handouts and assignments. It's probably already on your computer, though.
Printing files at home
SSH (Secure Shell)
Copy-paste in Putty

SAS on cquest

An important part of this course is use of the SAS statistical software package. SAS is available to students free of charge on U of T's cquest computers. Students in STA429 should go to the cquest web site immediately to set up their accounts. Students in STA1007 will need to fill out a short paper form (available from Jerry); your accounts will be set up manually.

Chapter 2 of the online textbook contains an introduction to SAS, and also to the unix operating system used by cquest. Well, actually cquest uses linux, but for the most part, the differences between linux and unix are just legal, moral and political. That is, they do not matter to most people.

You can use SAS in the cquest labs. There are three labs in the Ramsey Wright building (Rooms 211, 107 and 109), and one in Earth Sciences 1046 (the round building).See the cquest web site for hours of access.

You can also use SAS over the Internet from home or some other remote location. Go to login.cquest.utoronto.ca. This is convenient, but several issues are involved.

For security reasons, you need to connect using software that probably did not come with your computer. The protocol is SSH, which stands for "Secure SHell." When you use SSH, information travels over the Internet in encrypted form, so hackers have trouble intercepting your password and other information. You cna download a free copy of SSH below
At the cquest labs, SAS is easy to find in the menus. Running SAS this way starts up the SAS Display Manager. It's really quite nice once you get used to it, but
- It's much easier to learn how to use the Display Manager if you already know how to use SAS from the command line, the way it will be illustrated in lecture and the online text.
- The display manager does not work over SSH, so if you are running SAS from a remote location you will have to do so from the command line anyway.
So, if you are at a cquest lab, open a terminal window or two (right click on the background area and use the resulting menu), and run SAS from the command line at first. Once you are comfortable with that, it will be easy to move up to the Display Manager (which basically just shows you the various input and output files in separate windows and lets you execute SAS by making a menu choice) when you happen to be in a cquest lab, if you want.
If you are happy running SAS at the command line from home and you try to do it when you are in a cquest lab, you may be prompted for a password when you execute SAS. This annoying problem (and maybe others) problems can be avoided by typing ssh login.cquest at the unix prompt. This uses the Secure SHell protocol to log you onto the application server. That's the machine that has SAS, and you're coming in over the Internet just as you do from home, so the environment is the same
When you run SAS from the command line, either from home or in the lab, there is one unpleasant technical issue that arises. Both the SAS program and the data file must be in your top-level (home) directory.
This is unfortunate, because it is natural to make separate subdirectories for different courses, projects or even assignments. In every other unix environment I have ever seen, when you type SAS filename and press Enter, SAS looks in your current directory for the program file filename.sas, and the name of the data file that you specify in the SAS program implicitly begins with a path to your current directory. I assume that on cquest, SAS is not installed properly, or else there was some other horrible technical problem that was even worse, and the work-around broke this aspect of SAS. Oh well. I suppose we should be thankful we can run SAS from the command line at all, and not complain too much.
When you run SAS from the menus in a cquest lab, your files do not have to be in the top-level directory. SAS can find them. So this a reason to move to running SAS from the menus when you happen to be in a lab. But watch out for different versions of a file with the same name, at different directory levels.
Another advantage of the menu interface is the availability of online help. The manuals may be better, but you probably do not have any SAS manuals. If you are departing from the examples in any substantial way, SAS' online help can be a lifesaver.

If you want to connect from home but you do not already have an Internet Service Provider, U of T provides good inexpensive dialup access through UTORDIAL.

There is a PC version of SAS, and you can get a copy and run it on your own computer if you wish. The SAS Institute makes a lot of money selling its software to big corporations as well as universities, research institutes and so on; SAS is expensive! But U of T has paid them a lot of money for a site license, and you can get your own copy of SAS that locks up on July 1st for $110 a year.

Printing files at home

A convenient way to get a file to your home computer for printing is to email it to yourself. Try
mail yourname@yourisp.com < fname
where yourname@yourisp.com is your email address and fname is the name of the file, like hw3.lst.

SSH (Secure Shell)

With an Internet connection, SSH applications give you a text-only connection to cquest and other unix machines from your home computer. From cquest's prompt, you can run programs such as SAS, R and emacs. SSH is secure because what you type and see on your screen is encrypted at one end and decrypted at the other end. This prevents hackers from stealing your password as you log on, and also prevents nosy people from spying on the highly sensitive and confidential work you do in your Statistics courses.

Different SSH programs are recommended, depending on the operating system that you are using. To use these programs, you must be connected to the Internet, say with a broadband connnnection or via PPP over your phone line.

Linux: SSH is built in. Suppose your login name on cquest is botulism. At the linux prompt, type
ssh -l botulism login.cquest.toronto.edu
That -l is a lower case L. If your login name on your linux machine is also botulism, you can omit the "-l botulism" part.
Mac OS X: SSH is built in. Suppose your login name on cquest is botulism. Start up the terminal application on your Mac. At the prompt, type
ssh -l botulism login.cquest.toronto.edu
That -l is a lower case L. If your login name on your Mac is also botulism, you can omit the "-l botulism" part.
Mac OS 7, 8 or 9: A number of free SSH programs are available. Mac SSH is nice.
- Local Download
- Download from an official site
To connect, note that the Host Name is login.cquest.toronto.edu.
MS Windows: A number of free SSH programs are available. PuTTY is nice.
- Local Download
  - Download the bare bones version (all you really need). This version is so compact that you can copy it onto a floppy disk and run it directly from from the floppy on just about any PC without installing it. This is handy on friends' computers.
  - Download a fuller version: Includes a number of helper programs, including one for sftp (Secure File Transfer Protocol).
- Download from an official site
To connect, note that for cquest's IP address (or Host Name), you can put login.cquest.toronto.edu.

In any of these SSH programs, the first time you connect to a host, you will be told that the program can't verify that this host is really what it appears to be. Do you want to trust it? SSH is just being sanely paraniod. Say yes.

Copy-paste in Putty

Suppose you want to transfer fairly small amounts of text between the unix machine and your PC. In a normal Windows application like Explorer or Word, the edit menu has Copy and Paste items -- or you can use control-C and control-V. But PuTTY has no menus, and Control-C and control-V don't do what you might expect, especially if emacs is running. But you can still copy-paste; here's how:

When you select a block of text in PuTTY, it's automatically copied into a buffer; you don't need to do anything extra to copy it. So to copy from unix to your PC, select in PuTTY, click over on a Word document or whatever, and then choose Paste from the edit menu.
In PuTTY, you paste by clicking on the right mouse button. So, to get text from Word into emacs, have emacs running in a PuTTY window. In Word, select the text and choose Copy from the edit menu. Click on the PuTTY window (left click). Then right click, and the text will be pasted in.