Learn Sas Within 7 Weeks: Part1
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Week 7
Introduction to SAS – The Basics Unit 4 SAS for Data Management
Week 7: Introduction to SAS – The Basics Welcome. This reading is an introduction to getting in and out of SAS together with a set of guidelines for navigation, programming, and documentation. Hopefully, it will prove to be a handy reference. Goals of Week 7: Introduction to SAS – The Basics 1. To learn how to enter and exit the SAS program; 2. To learn how to navigate the windows environment in SAS, including the creation of user defined toolbar buttons; 3. To appreciate (and know the principles of writing) code that is organized and clear; 4. To understand the “building block” structure of SAS syntax; 5. To begin a library of programming tips; and 6. To appreciate (and know how to design) a good project indexing system.
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Introduction to SAS – The Basics
Week 7 Outline – Introduction to SAS: The Basics Section Topic
Page
1.
Introduction to the SAS Windowing Environment ……………..
3
2.
How to Issue a SAS Command ………………………………….
7
3.
How to Create Toolbar Buttons for Special Use ……..………....
10
4.
Modes of Running SAS for Windows ………………….……………….
13
5.
How to Write and Execute SAS Code ………………………………….
16
6.
Introduction to the Online Help System ..……………………………….
19
7.
Introduction to Syntax for SAS Programs ………………………….
20
8.
Take Care to Document Your Work ……………………………………
22
9.
General Tips for Programming …………………………………………
26
10.
Archive Your Work ………………………………………………………..
31
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1. Introduction to the SAS Windowing Environment
SAS version 8 operates through a windowing environment that lets you view and work with programming statements, data files, results and file directories in a variety of ways.
How to Start SAS When you first start SAS software: Start Æ Programs Æ The SAS System Æ The SAS System for Windows V8 Alternatively, you may have a shortcut to SAS on your desktop. 5 main SAS windows are opened:
Explorer Results Program Editor Log Output
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Your screen will look as follows. The Results window will be hidden behind the Explorer, and the Output window will be hidden behind the Program editor and log windows. All five windows are seen to be open on the SAS task bar at the bottom of the windows:
SAS Task Bar All the basic tasks for managing data, programs and program output can be accomplished in these windows. Other SAS features will use additional windows. These will be described elsewhere.
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Week 7 Table III:
Introduction to SAS – The Basics Description of 5 main SAS Windows:
Window
Purpose
Explorer
View and manage SAS files; perform most file management tasks such as moving, copying, opening and deleting files.
Program Editor
Enter, edit, and submit SAS programs
Log
Displays messages about SAS session and programs that you submit
Output
Browse output from SAS programs that have been run
Results
Manage output (results) from SAS programs that have been run – view, save and print segments of output.
Following is the basic idea of using the SAS system. • The user “writes” (“codes”) a set of instructions. These are strung together in a program, and executed together in a batch, submitted for processing from the PROGRAM window. • The SAS system then displays Information on the action of the commands (including any error messages) in the LOG window. • Results are output by the SAS system to the OUTPUT window.
Thus, a program in SAS is actually comprised of 3 elements: • The program • The log • The output
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Tip: Save the three elements of a SAS program (program, log, output) as a group as follows. •
Use the same first level name, with extensions to match the contents. For example, the executable program statements can be saved in a file called file1.SAS to indicate that these are SAS program statements. The log and output should be saved in files with the names: file1.LOG and file1.LST to indicate their relationship to the program that created them.
•
The .SAS, .LOG, and .LST extensions will be added automatically when you save files from the program, log and output windows, respectively.
•
The SAS system “looks” for and recognizes these extensions, and has assigned icons to them. For example:
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2. How to Issue a SAS Command There are four ways to issue commands: • Pull down menus: These operate like the pull down menus in MSWord. The particular menus that are available depend upon which is the active window (indicated by the top bar highlighted in blue). • The toolbar: A limited set of common commands are available on the toolbar – again, this changes with the active window. You can program your own buttons to add to the toolbar. • The SAS command bar: You can type SAS commands directly in this bar and hit <enter> to execute the command. Tip: This is generally not recommended, except for commands such as “clear” or “submit”. • Function keys: Commands can also be submit through the function keys. For example, o (pgm) moves you to the program editor window – makes it the active window o
(log) moves you to the log window
o
(keys) brings up the Keys window (shown below), which lists the function key commands that are programmed.
o The keys window can also be found from the pull down menu:
Tools Æ Options Æ Keys.
o You may also program function keys that are unassigned:
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Tools Æ Options Æ Enhanced Editor Keys.
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Pulldown menus
Command Bar
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Toolbar
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You may find it simplest to use the mouse to select, open and save files, and to move around the windows.
Tip: However, some of the commands are handy. • It is useful to know some of the commands so that you can program buttons, or use SAS commands in within SAS programs (e.g., programs that write other programs.) • The CLEAR command clears the contents of the currently active window.
• The SUBMIT submits the contents of the program window for execution.
• Tip: Take care to understand the SAVE command. The SAVE command is executed from either the File menu, the command bar, the button
on the
toolbar, or a function key. It saves the contents of the active window, not your data. You can use this button to save a program, log or output file. Only when you have a data file window open, does the SAVE command or clicking the SAVE icon save your data file.
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3. How to Create Toolbar Buttons for Special Use in SAS Within the SAS system, it is possible to create buttons to add to the toolbar that make working with windows and files easier. The buttons are created using the TOOLS pull down menu.
Example: Creating a button to Clear the LOG and OUTPUT Windows 1. Make your Program Editor the Active Window by clicking inside the Program Window.
2. From the pull down TOOLS menu: •
Select Customize
•
Select the Customize tab
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Click on the ADD TOOL button •
In the Command Box type: o
•
and select BLANK TOOL
log;clear;output;clear;
In the Help Text box type: o
Clear log and output windows
In the Tip Text box type: o
Clear log/out
(The ‘tip text’ is the text that will appear in the rollover box when you move your cursor over the button, but do not click). •
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Click on the Change Icon button:
and select an icon for your button.
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Introduction to SAS – The Basics
With the new button highlighted in the box, click on the up or down arrow buttons toolbar.
to position the button where you would like it to appear on the
•
Click on OK when it is located where you would like.
•
Click on Yes to SAVE the new version of the toolbar.
Note: The toolbar in the PROGRAM window has been modified in this example. You must repeat the steps if you would like the same button to appear on the toolbar in the LOG or OUTPUT windows -- since these windows have a different toolbar. Start the process with the LOG or OUTPUT window as the active window.
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4. Modes of Running SAS for Windows SAS for Windows can be run in several different modes.
SAS S t AS/Solutions • Analysis • Development and Programming • Reporting • Accessories • ASSIST • Desktop • Application Builder
SAS Programming
SAS Windowing
Batch
Environment
Introduction to the SAS/Solutions Mode •
The SAS System provides a set of ready-to-use solutions, applications, and tools to accomplish specific analysis or data/file management tasks. Most of these tools can be accessed by using the Solutions menu.
•
A user of the solutions mode does not write programs. He or she works through a series of point-and-click menus to select a data file, specific variables and method of analysis.
•
This mode of operation is not the focus in this course, because it does not lend itself as readily to documentation as does programming.
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However, for many of the Solutions applications, Version 8 of SAS does offer the option of saving a program file based upon menu selections. The Solutions menu may become a good way to explore and learn some new applications in SAS, by saving the programming code produced by the application that creates the results you desire.
Introduction to the Programming Mode • SAS programming requires that the user write or edit a series of SAS statements, called a program, to manage data or files and conduct analyses. • In the windowing environment, programs are written or opened and edited in the PROGRAM EDITOR Window, and then submitted for processing from that window. The LOG window displays the executed code and messages, and the OUTPUT window displays the results. • Optionally, results can be written in HTML format to a browser window instead of, or in addition to the standard SAS output window. If you are planning to display results on the web, or if you prefer the table format created for browser output this is a good choice.
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Setting Results Options in SAS From the pull down TOOLS menu select Options Î Preferences and then select the Results tab.
Check “Create HTML” if you wish to have an HTML version of your results written. Note that there is a style box, which allows you to select the format for the results tables. Color and shading are used in various combinations. I recommend the choice “Minimal” to avoid color, shading and font changes. This is easier on printing, and is preferable if you are likely to Xerox results. Additionally, you may select the internal SAS browser or a different web browser for viewing results. By checking/unchecking the “Create Listing” option, you will produce/not produce results in the standard output window. When both options are checked you get 2 versions of your results displayed, one in the output window, and one in a browser window.
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5. How to Write and Execute SAS Code There are a variety of choices for writing and editing SAS code. • Text editor (such as Notepad) • Word processor (be careful how you save your code) tip: If you are using MS Word, it is important that you save your file as a TEXT ONLY type of document and that you name it with the extension “.sas”. TEXT ONLY documents contain only keyboard characters and have no formatting or ASCII control characters or other special characters. SAS does not allow such. • The SAS PROGRAM window
The main advantage to working in a text editor or word processor is that you can write or edit programs on a computer that does not have SAS loaded, and later run the programs when you have access to SAS.
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The SAS PROGRAM EDITOR is a reasonably flexible editor, with cut, copy and paste, as well as find and change commands. • The ENHANCED PROGRAM EDITOR, new in version 8, uses color-coding and dividing lines to help keep track of SAS syntax features and program flow. The new enhanced editor has the potential of reducing programming errors that are a simple matter of a typographical error – a missed quote or semicolon – but which can be very time-consuming to find when proofing and testing programs. I strongly recommend that the new user work with the enhanced program editor. • When SAS is opened from the Start menu, the default active window is the enhanced program editor. A program can be typed in, or a saved program can be opened in the window, using the ‘Open’ button or Open option from the File pull down menu. • Alternatively, SAS and a program can be opened directly from the Windows Explorer by double-clicking on a program file with a .SAS extension. • Programs can also be submitted and run in Batch Mode. When a program has been written and saved with a .SAS extension, the program can be run without opening the SAS windows. To run a program in batch mode: from the Windows Explorer, highlight and right-click on the program to be run. One of the options on the menu is “Batch Submit”. Selecting this will submit the program to the SAS processor. Files with the same first level name and the extensions .LOG and .LST will be written to the same drive and directory as
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the program (.SAS) file. These will contain information on the execution of the program (.LOG) and the program output (.LST).
Using batch mode submission has the advantage of increased speed when working with large data sets, or when working on a machine with the minimum RAM requirement for SAS. Loading the SAS window system itself uses a considerable amount of RAM. This is avoided when submitting programs by batch mode.
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6. Introduction to the Online Help System An online help system is available with SAS and is accessible from the menu bar.
The help feature includes a set of tutorials for learning to use the features of the SAS windowing environment, along with a full reference feature for DATA step and procedure commands and options.
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7. Introduction to Syntax for SAS Programs The SAS system is a structured programming language in which there are two types of “building blocks”, the DATA step and the PROCEDURE (PROC) step. • Each of the steps is limited in scope and has defined input and output. As a result, programs in SAS lend themselves to top-down design with modularization. • Indenting SAS statements in a DATA or PROC step, so as to highlight the modularization, visually enhances this structure. The new Enhanced Editor draws lines between steps in a program as an additional visual aid to distinguish the two (DATA v PROC) types of program steps.
Introduction to the DATA Step SAS DATA steps are used to create SAS data sets, and are used for data manipulation. DATA steps create SAS datasets by giving instructions for reading data into SAS, or for merging, sub-setting or updating existing SAS datasets, along with adding new variables, or modifying existing ones.
Introduction to the PROC Step SAS PROCs (procedures) read SAS datasets and perform specific functions, such as listing the data (PROC PRINT), or producing charts or plots (PROC CHART, PLOT), frequency tables (PROC FREQ), descriptive statistics (PROC MEANS, SUMMARY, UNIVARIATE, TABULATE), and many other specialized functions and analyses.
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SAS procedures produce either results in the OUTPUT and/or browser window, or create new datasets to be used in other procedures or data steps, or both.
There exist some key, NONNEGOTIABLE, syntax requirements • The key syntax requirement is that
ALL SAS STATEMENTS END WITH A SEMI-COLON (;).
• Several short SAS statements may be written on the same line, with program statements separated by semi-colons. Alternatively, a single statement may span several lines, where a semi-colon indicates the end of the statement. • SAS program statements can be typed in CAPITAL LETTERS or lower case letters – these are equivalent. That is, capitalization of programming statements is ignored. TIP: This is not true for data, which is case sensitive.
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8. Take Care to Document Your Work There are three self-documentation features of the SAS system: comments, titles, and footnotes. Introduction to Comments •
Comments can be placed in SAS programs to help explain the code or identify modules. Comments appear in the LOG, but do not appear in the output. The syntax for comments can take two forms:
* comment ;
< first character in the statement is an asterisk (*). Comment must end with a semicolon (;). In this form, the comment is a SAS statement>
/* comment */
< comment is surrounded by /* */. In this form the comment can appear within a SAS statement >
• In the Enhanced Program editor, comments appear in green. If you forget the end semi-colon or */, the statements following the comment will still appear in green. •
When the comment is in the first form (as a SAS statement), statements immediately following the semi-colon will be read and executed. The second form of comment can surround a block of SAS statements that include semicolons, but statements will not be executed until after the concluding */. This can be useful when rerunning a program, when some section of the program does not need to be rerun. Surrounding a section of code that is to be skipped by /* and */ is called “commenting out” a section of code.
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• Comments should appear liberally to help clarify the programming steps. This can be a tremendous aid in later proofreading, or in copying and using code for another application at a later date.
Introduction to TITLES • TITLES and FOOTNOTES are special SAS statements that print a title with results, following the step containing the title statement. The syntax for title statements is illustrated below. You are allowed up to 10 titles. • The title that will be printed on each page of your results is contained in the single or double quotes that follows the TITLE instruction. •
Following is an example
TITLE1 'Listing of Outliers'; TITLE2 'Pilot Data'; TITLE3 “Columbia's Data” ;
< First title > < Second title > < Third title in double quotes>
Note: Double quotes must be used when the title itself contains a question mark. • A useful feature of the new enhanced editor is that: ‘All information within quotes appears in purple.’ If you neglect to close a quote, the SAS processor assumes the next lines are part of the quote – even semi-colons are ignored. If several lines appear in purple – you may have a problem with unbalanced quotes. This is a very common programming error. • Capitalization appears on the output just as you typed it within the quotes. Several titles can be specified, with the order of the titles indicated by the title number. Titles stay in effect for all output until you write a new title statement. • To get rid of all previous titles you can simply use the line TITLE1; • To keep the same first 2 title lines and replace the third use TITLE3 ‘New Third Title’;
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• To replace an early title and keep subsequent ones, you must copy and repeat all titles with higher numbers. •
The first title (Title1) will appear in the RESULTS window next to the procedure name used to produce the output, as well as in the OUTPUT window. The first title, therefore, can be a useful aid in navigating through your output.
First titles used in program
Introduction to FOOTNOTES • Footnotes are similar to titles except that they will be printed on the bottom of the output page. Footnotes have a similar syntax to titles as illustrated below: FOOTNOTE1 'DATA were collected from 6/89-8/89'; FOOTNOTE2 'All values out of range were set to missing values'; •
One useful practice is to reserve the first title or first footnote for the program name, for easy reference to the program that produced the output. For example, at the beginning of your SAS program, you could include a line:
Footnote1 ‘Program:
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HW01a.sas’;
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• This would appear beneath all subsequent output, as long as you don’t replace it with a new footnote1 statement. This can be a tremendous aid in documentation – linking a data table or graph directly to the program that produced it.
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9. General tips for programming Key among these – take time to plan. When writing programs, take time to write a detailed step-by-step outline of what you want to accomplish first. You can always revise as you go, but it helps save time wasted from missing important steps and results in fewer errors. Other tips:
1. Don't compose on the computer. Using your outline, write your program in SAS language on paper first. Initially, and even as you become more proficient, it is hard to keep track of the editing commands and at the same time focus well on writing a program.
2. Use comments, blank lines, and indenting so as to make it easier to follow the flow and logic of your program. This is a tremendous aid in proofreading and editing for errors, as well as in making modifications in the program, or adapting a program for use in another setting at a later date. “Talk to yourself” with comments as you go. Make your programs user-friendly.
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3. Use a program header to keep track of when, where, and why the program was written, what data sets were used, and what data sets were created. A program header is merely a block of comments at the start of the program that contains documentation information. In addition, use titles and footnotes to label your results. To reiterate, reserving the first title or footnote for the program filename helps link results to the program that produced them.
Example Program Header: *_______________________________________________________________ * * Corinne Jurgens 2003 * * code: p02.sas * path: z:\bigelow\consulting\jurgens 2003\sascode * prog: carol bigelow * date: February 15, 2003 * * input: z:\bigelow\consulting\jurgents 2003\sasdata\jurgens.sas7bdat * output: none * * title: * What is the relationship between symptom awareness (HFSAS vars) * and delay in care seeking (ACUTESXS, DOEDUR, DYSPDUR, * ACUTEDYS,ORTHPDUR,PNDDUR,COUGHDUR,FATIGDUR,WTGAIN,EDEMA,ABDGIRTH, * TACHYDUR,CPDUR,NAUSEA) * * summary: * 1. For all 14 Y=delay in care variables, the distribution * of Y is compared across strata defined by HFSASTOT * Strata define quintiles of HFSASTOT, approx. * * 2. For the 6 Y=delay in care variables that are essential * a Kruskal Wallis nonparametric anova is performed to * see if Y=delay in care varies appreciably by * HFSASTOT quintile * * The 6 delay in care seeking Y variables are ACUTESXS, * DYSPDUR, ORTHDUR, ACUTEDYS, PNDDUR, and DOEDUR *
*_________________________________________________________________;
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A header need not be this elaborate, but the essential information should be available.
4. Use the OPTIONS Statement at the start of each program to control the format of your resulting output. The SAS defaults for line size and page size are designed to fit on a computer screen, rather than a page of paper. Printing this way wastes paper as well as breaking up tables and lists unnecessarily. To set output for 8.5 X 11 inch paper, use values in the range of 55 to 60 for pagesize, and 78 to 128 for linesize.
If you select a larger number for linesize, you will need to print output
in “landscape” format or else select a small size font when printing. This saves paper, as well as enabling more variables to be listed across a page. For example:
OPTIONS LINESIZE=128 PAGESIZE=55;
can be used for most programming. The OPTIONS statement also gives you control over printing of page numbers (NONUMBER turns numbering off), or dates (NODATE turns date off). These and other options can be reset during the program with subsequent OPTIONS statements. By default, SAS puts page numbers on output, starting the numbering within a SAS session, not within a program. Typically the numbers are irrelevant to a report. In addition, the date is printed on the first title line, and output is always centered (side-to-side) on the
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page. I prefer to turn off these features, so a commonly used options line at the start of a program is:
OPTIONS LINESIZE=110 PAGESIZE=55 NODATE NONUMBER NOCENTER;
5. It is good practice to always save your program before you run (submit) it, when working in the SAS windows. If you find you need to make changes in your program after reviewing the log and output, first clear the log and output windows, return to the program window, edit, and again save the revised version before resubmitting. The enhanced editor has a nice feature: if you have modified the contents of the program editor, but not saved it, an asterisk (*) appears next to the program name in the task bar, as a reminder to save the program. If you fail to clear the log and output windows, the new version will be appended to the old. You will have a lot of garbage to deal with in the results window, as you try to figure out which is the old and which the new version. You can easily save the contents of the log and output windows from the final version, without a lot of other junk, as long as you keep clearing the windows before resubmitting.
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6. Always review your log before looking at the output. Check for error messages, other notes and messages on how the program ran, including the number of observations in the data sets read and created. Sometimes a mistake in your program won't produce an error message – the program may be valid, but it just doesn't do what you want it to do. Often, this kind of error can be picked up by a careful reading of the log, especially checking for the number of variables and observations in a data set, when the problem might be missed if you look only at the output. SO READ YOUR LOG!
7. Last but not least, as always, make back-up copies of your programs and data sets. Log and output files can be easily reproduced by re-running a program on the same data, so keep track of you programs and data.
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Week 7 10.
Introduction to SAS – The Basics
Archiving your work
It is easy to lose track of all the data management and analysis activities associated with even a small-scale study. Therefore, it is important to develop, ahead of time, an easy system for documenting, indexing and filing your work. The following are suggestions only -- you need to develop a system of your own, one that you like and will actually use.
1.
Use Internal Documentation. Use program headers, and make generous use of comments within your programs. If you have a copy of the program, you will then have (detailed) information on its purpose, and when and where the program was used.
2.
Use Back-up Disks Spending an extra $1 per disk can be cheap compared to the time and effort needed to replace lost data or analyses. For each project you should keep on separate disks (2 copies each): -
Grant proposal Study protocols, forms Data and associated files (e.g. .rec, .chk, .qes files in EpiInfo) SAS program files (*.sas files) SAS data sets (*.sas7bdat files in SAS V8) Reports and memos Manuscripts or presentation files (include final analysis data set)
Always save SAS data files and SAS program files on disk. You may choose to save log and output files on disk, and/or to print hard copies. The log and output can be recreated as long as you have the data and SAS code.
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Disks can be named or labeled. In the Windows Explorer, under the File Menu ÆProperties, a label can be assigned to a disk.
Disk label
This label should then be written on the stick-on disk label, in addition to your name and any other information you deem pertinent. In your documentation, keep track of which disk you use to store which files!
Be sure to label all your disks with your name, and perhaps phone and/or office number. The chances are great that at some point in your career here you will leave a disk behind in one of the computer labs.
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Name Your Files According to a System Always use the .SAS extension for SAS program files, .LOG for the associated log and .LST for the associated output. The SAS system recognizes these files extensions, and enables options such as batch submission of programs, and use of the SAS Viewer to review log and output files from the Windows Explorer.
Icons for SAS files: program (.sas) log (.log) output
Choose a naming convention for the first part of the filename that is easy for you to understand. Since the number of programs that can be developed on a project can grow astronomically, a simple name with a numbering system is recommended. For example for the Warm/Cold Cardiac Surgery Pilot study, the prefix WCP was used and programs were and then numbered sequentially. The first program was WCP01.sas, followed by WCP02.sas, etc. If programs were modified or rerun, this was always noted in the header. If the program was significantly modified, a new version was named: WCP01a.sas. week 07
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(.lst)
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Choose names that allow you this flexibility. Another suggestion is that programmers on a study use their own set of names (so that two programmers don’t produce two different files having the same name). One suggestion is to use programmer’s initials in the name, e.g. for the Warm/Cold study, one set of files were WCP*.sas, one student used WCS*.sas, another WCM*.sas, etc, based on the user’s initial.
4.
Index Your Work Create an index of all management and analysis activities. This index should describe the name and location (name of disk, where stored) of every data set; the name, purpose and location (name of disk and notebook or file drawer) of every program file. This index should be updated on a regular basis. For example, make it standard practice to reserve an hour every Friday to update your project index.
Example Project Index Date 2-6-03 2-13-03 2-15-03 2-22-03 2-23-03 2-23-03 2-25-03 2-27-03 2-28-03 2-28-03 2-28-03 3-2-03 3-2-03 3-2-03 3-2-03 3-13-03
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Program Formats.sas P01.sas P02.sas P03.sas P04.sas P05.sas P06.sas P07.sas P08.sas P09.sas P10.sas P11.sas P12.sas P13.sas P14.sas P15.sas
Description Code book Defines formats Proc contents and descriptives (alphabetic) Delay in care seeking – by quintile of HFSASTOT Delay in care seeking – by quintile of HFSFACT1 Delay in care seeking – by quintile of MSPQTOT Delay in care seeking – by quintile of MUISTOT Delay in care seeking – by quintile of AGE Delay in care seeking – by hx of previous heart failure Regression analysis of ACUTESXS Regression analysis of DYSPDUR Regression analysis of ORTHPDUR Regression analysis of PNDDUR Regression analysis of DOEDUR Regression analysis of ACUTEDYS Six Sets of ONE Predictor Models Wilcoxon Rank Sum Tests of Gender Differences in Awareness
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Introduction to SAS – The Basics Unit 4 SAS for Data Management
Week 7: Introduction to SAS – The Basics Welcome. This reading is an introduction to getting in and out of SAS together with a set of guidelines for navigation, programming, and documentation. Hopefully, it will prove to be a handy reference. Goals of Week 7: Introduction to SAS – The Basics 1. To learn how to enter and exit the SAS program; 2. To learn how to navigate the windows environment in SAS, including the creation of user defined toolbar buttons; 3. To appreciate (and know the principles of writing) code that is organized and clear; 4. To understand the “building block” structure of SAS syntax; 5. To begin a library of programming tips; and 6. To appreciate (and know how to design) a good project indexing system.
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Week 7 Outline – Introduction to SAS: The Basics Section Topic
Page
1.
Introduction to the SAS Windowing Environment ……………..
3
2.
How to Issue a SAS Command ………………………………….
7
3.
How to Create Toolbar Buttons for Special Use ……..………....
10
4.
Modes of Running SAS for Windows ………………….……………….
13
5.
How to Write and Execute SAS Code ………………………………….
16
6.
Introduction to the Online Help System ..……………………………….
19
7.
Introduction to Syntax for SAS Programs ………………………….
20
8.
Take Care to Document Your Work ……………………………………
22
9.
General Tips for Programming …………………………………………
26
10.
Archive Your Work ………………………………………………………..
31
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Introduction to SAS – The Basics
1. Introduction to the SAS Windowing Environment
SAS version 8 operates through a windowing environment that lets you view and work with programming statements, data files, results and file directories in a variety of ways.
How to Start SAS When you first start SAS software: Start Æ Programs Æ The SAS System Æ The SAS System for Windows V8 Alternatively, you may have a shortcut to SAS on your desktop. 5 main SAS windows are opened:
Explorer Results Program Editor Log Output
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Introduction to SAS – The Basics
Your screen will look as follows. The Results window will be hidden behind the Explorer, and the Output window will be hidden behind the Program editor and log windows. All five windows are seen to be open on the SAS task bar at the bottom of the windows:
SAS Task Bar All the basic tasks for managing data, programs and program output can be accomplished in these windows. Other SAS features will use additional windows. These will be described elsewhere.
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Week 7 Table III:
Introduction to SAS – The Basics Description of 5 main SAS Windows:
Window
Purpose
Explorer
View and manage SAS files; perform most file management tasks such as moving, copying, opening and deleting files.
Program Editor
Enter, edit, and submit SAS programs
Log
Displays messages about SAS session and programs that you submit
Output
Browse output from SAS programs that have been run
Results
Manage output (results) from SAS programs that have been run – view, save and print segments of output.
Following is the basic idea of using the SAS system. • The user “writes” (“codes”) a set of instructions. These are strung together in a program, and executed together in a batch, submitted for processing from the PROGRAM window. • The SAS system then displays Information on the action of the commands (including any error messages) in the LOG window. • Results are output by the SAS system to the OUTPUT window.
Thus, a program in SAS is actually comprised of 3 elements: • The program • The log • The output
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Tip: Save the three elements of a SAS program (program, log, output) as a group as follows. •
Use the same first level name, with extensions to match the contents. For example, the executable program statements can be saved in a file called file1.SAS to indicate that these are SAS program statements. The log and output should be saved in files with the names: file1.LOG and file1.LST to indicate their relationship to the program that created them.
•
The .SAS, .LOG, and .LST extensions will be added automatically when you save files from the program, log and output windows, respectively.
•
The SAS system “looks” for and recognizes these extensions, and has assigned icons to them. For example:
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7.6
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Introduction to SAS – The Basics
2. How to Issue a SAS Command There are four ways to issue commands: • Pull down menus: These operate like the pull down menus in MSWord. The particular menus that are available depend upon which is the active window (indicated by the top bar highlighted in blue). • The toolbar: A limited set of common commands are available on the toolbar – again, this changes with the active window. You can program your own buttons to add to the toolbar. • The SAS command bar: You can type SAS commands directly in this bar and hit <enter> to execute the command. Tip: This is generally not recommended, except for commands such as “clear” or “submit”. • Function keys: Commands can also be submit through the function keys. For example, o
o
o The keys window can also be found from the pull down menu:
Tools Æ Options Æ Keys.
o You may also program function keys that are unassigned:
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Tools Æ Options Æ Enhanced Editor Keys.
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Week 7
Introduction to SAS – The Basics
Pulldown menus
Command Bar
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Toolbar
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Introduction to SAS – The Basics
You may find it simplest to use the mouse to select, open and save files, and to move around the windows.
Tip: However, some of the commands are handy. • It is useful to know some of the commands so that you can program buttons, or use SAS commands in within SAS programs (e.g., programs that write other programs.) • The CLEAR command clears the contents of the currently active window.
• The SUBMIT submits the contents of the program window for execution.
• Tip: Take care to understand the SAVE command. The SAVE command is executed from either the File menu, the command bar, the button
on the
toolbar, or a function key. It saves the contents of the active window, not your data. You can use this button to save a program, log or output file. Only when you have a data file window open, does the SAVE command or clicking the SAVE icon save your data file.
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Introduction to SAS – The Basics
3. How to Create Toolbar Buttons for Special Use in SAS Within the SAS system, it is possible to create buttons to add to the toolbar that make working with windows and files easier. The buttons are created using the TOOLS pull down menu.
Example: Creating a button to Clear the LOG and OUTPUT Windows 1. Make your Program Editor the Active Window by clicking inside the Program Window.
2. From the pull down TOOLS menu: •
Select Customize
•
Select the Customize tab
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7.10
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Introduction to SAS – The Basics
Click on the ADD TOOL button •
In the Command Box type: o
•
and select BLANK TOOL
log;clear;output;clear;
In the Help Text box type: o
Clear log and output windows
In the Tip Text box type: o
Clear log/out
(The ‘tip text’ is the text that will appear in the rollover box when you move your cursor over the button, but do not click). •
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Click on the Change Icon button:
and select an icon for your button.
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Introduction to SAS – The Basics
With the new button highlighted in the box, click on the up or down arrow buttons toolbar.
to position the button where you would like it to appear on the
•
Click on OK when it is located where you would like.
•
Click on Yes to SAVE the new version of the toolbar.
Note: The toolbar in the PROGRAM window has been modified in this example. You must repeat the steps if you would like the same button to appear on the toolbar in the LOG or OUTPUT windows -- since these windows have a different toolbar. Start the process with the LOG or OUTPUT window as the active window.
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Introduction to SAS – The Basics
4. Modes of Running SAS for Windows SAS for Windows can be run in several different modes.
SAS S t AS/Solutions • Analysis • Development and Programming • Reporting • Accessories • ASSIST • Desktop • Application Builder
SAS Programming
SAS Windowing
Batch
Environment
Introduction to the SAS/Solutions Mode •
The SAS System provides a set of ready-to-use solutions, applications, and tools to accomplish specific analysis or data/file management tasks. Most of these tools can be accessed by using the Solutions menu.
•
A user of the solutions mode does not write programs. He or she works through a series of point-and-click menus to select a data file, specific variables and method of analysis.
•
This mode of operation is not the focus in this course, because it does not lend itself as readily to documentation as does programming.
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Introduction to SAS – The Basics
However, for many of the Solutions applications, Version 8 of SAS does offer the option of saving a program file based upon menu selections. The Solutions menu may become a good way to explore and learn some new applications in SAS, by saving the programming code produced by the application that creates the results you desire.
Introduction to the Programming Mode • SAS programming requires that the user write or edit a series of SAS statements, called a program, to manage data or files and conduct analyses. • In the windowing environment, programs are written or opened and edited in the PROGRAM EDITOR Window, and then submitted for processing from that window. The LOG window displays the executed code and messages, and the OUTPUT window displays the results. • Optionally, results can be written in HTML format to a browser window instead of, or in addition to the standard SAS output window. If you are planning to display results on the web, or if you prefer the table format created for browser output this is a good choice.
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Introduction to SAS – The Basics
Setting Results Options in SAS From the pull down TOOLS menu select Options Î Preferences and then select the Results tab.
Check “Create HTML” if you wish to have an HTML version of your results written. Note that there is a style box, which allows you to select the format for the results tables. Color and shading are used in various combinations. I recommend the choice “Minimal” to avoid color, shading and font changes. This is easier on printing, and is preferable if you are likely to Xerox results. Additionally, you may select the internal SAS browser or a different web browser for viewing results. By checking/unchecking the “Create Listing” option, you will produce/not produce results in the standard output window. When both options are checked you get 2 versions of your results displayed, one in the output window, and one in a browser window.
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Introduction to SAS – The Basics
5. How to Write and Execute SAS Code There are a variety of choices for writing and editing SAS code. • Text editor (such as Notepad) • Word processor (be careful how you save your code) tip: If you are using MS Word, it is important that you save your file as a TEXT ONLY type of document and that you name it with the extension “.sas”. TEXT ONLY documents contain only keyboard characters and have no formatting or ASCII control characters or other special characters. SAS does not allow such. • The SAS PROGRAM window
The main advantage to working in a text editor or word processor is that you can write or edit programs on a computer that does not have SAS loaded, and later run the programs when you have access to SAS.
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Introduction to SAS – The Basics
The SAS PROGRAM EDITOR is a reasonably flexible editor, with cut, copy and paste, as well as find and change commands. • The ENHANCED PROGRAM EDITOR, new in version 8, uses color-coding and dividing lines to help keep track of SAS syntax features and program flow. The new enhanced editor has the potential of reducing programming errors that are a simple matter of a typographical error – a missed quote or semicolon – but which can be very time-consuming to find when proofing and testing programs. I strongly recommend that the new user work with the enhanced program editor. • When SAS is opened from the Start menu, the default active window is the enhanced program editor. A program can be typed in, or a saved program can be opened in the window, using the ‘Open’ button or Open option from the File pull down menu. • Alternatively, SAS and a program can be opened directly from the Windows Explorer by double-clicking on a program file with a .SAS extension. • Programs can also be submitted and run in Batch Mode. When a program has been written and saved with a .SAS extension, the program can be run without opening the SAS windows. To run a program in batch mode: from the Windows Explorer, highlight and right-click on the program to be run. One of the options on the menu is “Batch Submit”. Selecting this will submit the program to the SAS processor. Files with the same first level name and the extensions .LOG and .LST will be written to the same drive and directory as
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Introduction to SAS – The Basics
the program (.SAS) file. These will contain information on the execution of the program (.LOG) and the program output (.LST).
Using batch mode submission has the advantage of increased speed when working with large data sets, or when working on a machine with the minimum RAM requirement for SAS. Loading the SAS window system itself uses a considerable amount of RAM. This is avoided when submitting programs by batch mode.
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Introduction to SAS – The Basics
6. Introduction to the Online Help System An online help system is available with SAS and is accessible from the menu bar.
The help feature includes a set of tutorials for learning to use the features of the SAS windowing environment, along with a full reference feature for DATA step and procedure commands and options.
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Introduction to SAS – The Basics
7. Introduction to Syntax for SAS Programs The SAS system is a structured programming language in which there are two types of “building blocks”, the DATA step and the PROCEDURE (PROC) step. • Each of the steps is limited in scope and has defined input and output. As a result, programs in SAS lend themselves to top-down design with modularization. • Indenting SAS statements in a DATA or PROC step, so as to highlight the modularization, visually enhances this structure. The new Enhanced Editor draws lines between steps in a program as an additional visual aid to distinguish the two (DATA v PROC) types of program steps.
Introduction to the DATA Step SAS DATA steps are used to create SAS data sets, and are used for data manipulation. DATA steps create SAS datasets by giving instructions for reading data into SAS, or for merging, sub-setting or updating existing SAS datasets, along with adding new variables, or modifying existing ones.
Introduction to the PROC Step SAS PROCs (procedures) read SAS datasets and perform specific functions, such as listing the data (PROC PRINT), or producing charts or plots (PROC CHART, PLOT), frequency tables (PROC FREQ), descriptive statistics (PROC MEANS, SUMMARY, UNIVARIATE, TABULATE), and many other specialized functions and analyses.
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Introduction to SAS – The Basics
SAS procedures produce either results in the OUTPUT and/or browser window, or create new datasets to be used in other procedures or data steps, or both.
There exist some key, NONNEGOTIABLE, syntax requirements • The key syntax requirement is that
ALL SAS STATEMENTS END WITH A SEMI-COLON (;).
• Several short SAS statements may be written on the same line, with program statements separated by semi-colons. Alternatively, a single statement may span several lines, where a semi-colon indicates the end of the statement. • SAS program statements can be typed in CAPITAL LETTERS or lower case letters – these are equivalent. That is, capitalization of programming statements is ignored. TIP: This is not true for data, which is case sensitive.
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Introduction to SAS – The Basics
8. Take Care to Document Your Work There are three self-documentation features of the SAS system: comments, titles, and footnotes. Introduction to Comments •
Comments can be placed in SAS programs to help explain the code or identify modules. Comments appear in the LOG, but do not appear in the output. The syntax for comments can take two forms:
* comment ;
< first character in the statement is an asterisk (*). Comment must end with a semicolon (;). In this form, the comment is a SAS statement>
/* comment */
< comment is surrounded by /* */. In this form the comment can appear within a SAS statement >
• In the Enhanced Program editor, comments appear in green. If you forget the end semi-colon or */, the statements following the comment will still appear in green. •
When the comment is in the first form (as a SAS statement), statements immediately following the semi-colon will be read and executed. The second form of comment can surround a block of SAS statements that include semicolons, but statements will not be executed until after the concluding */. This can be useful when rerunning a program, when some section of the program does not need to be rerun. Surrounding a section of code that is to be skipped by /* and */ is called “commenting out” a section of code.
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• Comments should appear liberally to help clarify the programming steps. This can be a tremendous aid in later proofreading, or in copying and using code for another application at a later date.
Introduction to TITLES • TITLES and FOOTNOTES are special SAS statements that print a title with results, following the step containing the title statement. The syntax for title statements is illustrated below. You are allowed up to 10 titles. • The title that will be printed on each page of your results is contained in the single or double quotes that follows the TITLE instruction. •
Following is an example
TITLE1 'Listing of Outliers'; TITLE2 'Pilot Data'; TITLE3 “Columbia's Data” ;
< First title > < Second title > < Third title in double quotes>
Note: Double quotes must be used when the title itself contains a question mark. • A useful feature of the new enhanced editor is that: ‘All information within quotes appears in purple.’ If you neglect to close a quote, the SAS processor assumes the next lines are part of the quote – even semi-colons are ignored. If several lines appear in purple – you may have a problem with unbalanced quotes. This is a very common programming error. • Capitalization appears on the output just as you typed it within the quotes. Several titles can be specified, with the order of the titles indicated by the title number. Titles stay in effect for all output until you write a new title statement. • To get rid of all previous titles you can simply use the line TITLE1; • To keep the same first 2 title lines and replace the third use TITLE3 ‘New Third Title’;
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Introduction to SAS – The Basics
• To replace an early title and keep subsequent ones, you must copy and repeat all titles with higher numbers. •
The first title (Title1) will appear in the RESULTS window next to the procedure name used to produce the output, as well as in the OUTPUT window. The first title, therefore, can be a useful aid in navigating through your output.
First titles used in program
Introduction to FOOTNOTES • Footnotes are similar to titles except that they will be printed on the bottom of the output page. Footnotes have a similar syntax to titles as illustrated below: FOOTNOTE1 'DATA were collected from 6/89-8/89'; FOOTNOTE2 'All values out of range were set to missing values'; •
One useful practice is to reserve the first title or first footnote for the program name, for easy reference to the program that produced the output. For example, at the beginning of your SAS program, you could include a line:
Footnote1 ‘Program:
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HW01a.sas’;
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Introduction to SAS – The Basics
• This would appear beneath all subsequent output, as long as you don’t replace it with a new footnote1 statement. This can be a tremendous aid in documentation – linking a data table or graph directly to the program that produced it.
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Introduction to SAS – The Basics
9. General tips for programming Key among these – take time to plan. When writing programs, take time to write a detailed step-by-step outline of what you want to accomplish first. You can always revise as you go, but it helps save time wasted from missing important steps and results in fewer errors. Other tips:
1. Don't compose on the computer. Using your outline, write your program in SAS language on paper first. Initially, and even as you become more proficient, it is hard to keep track of the editing commands and at the same time focus well on writing a program.
2. Use comments, blank lines, and indenting so as to make it easier to follow the flow and logic of your program. This is a tremendous aid in proofreading and editing for errors, as well as in making modifications in the program, or adapting a program for use in another setting at a later date. “Talk to yourself” with comments as you go. Make your programs user-friendly.
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3. Use a program header to keep track of when, where, and why the program was written, what data sets were used, and what data sets were created. A program header is merely a block of comments at the start of the program that contains documentation information. In addition, use titles and footnotes to label your results. To reiterate, reserving the first title or footnote for the program filename helps link results to the program that produced them.
Example Program Header: *_______________________________________________________________ * * Corinne Jurgens 2003 * * code: p02.sas * path: z:\bigelow\consulting\jurgens 2003\sascode * prog: carol bigelow * date: February 15, 2003 * * input: z:\bigelow\consulting\jurgents 2003\sasdata\jurgens.sas7bdat * output: none * * title: * What is the relationship between symptom awareness (HFSAS vars) * and delay in care seeking (ACUTESXS, DOEDUR, DYSPDUR, * ACUTEDYS,ORTHPDUR,PNDDUR,COUGHDUR,FATIGDUR,WTGAIN,EDEMA,ABDGIRTH, * TACHYDUR,CPDUR,NAUSEA) * * summary: * 1. For all 14 Y=delay in care variables, the distribution * of Y is compared across strata defined by HFSASTOT * Strata define quintiles of HFSASTOT, approx. * * 2. For the 6 Y=delay in care variables that are essential * a Kruskal Wallis nonparametric anova is performed to * see if Y=delay in care varies appreciably by * HFSASTOT quintile * * The 6 delay in care seeking Y variables are ACUTESXS, * DYSPDUR, ORTHDUR, ACUTEDYS, PNDDUR, and DOEDUR *
*_________________________________________________________________;
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A header need not be this elaborate, but the essential information should be available.
4. Use the OPTIONS Statement at the start of each program to control the format of your resulting output. The SAS defaults for line size and page size are designed to fit on a computer screen, rather than a page of paper. Printing this way wastes paper as well as breaking up tables and lists unnecessarily. To set output for 8.5 X 11 inch paper, use values in the range of 55 to 60 for pagesize, and 78 to 128 for linesize.
If you select a larger number for linesize, you will need to print output
in “landscape” format or else select a small size font when printing. This saves paper, as well as enabling more variables to be listed across a page. For example:
OPTIONS LINESIZE=128 PAGESIZE=55;
can be used for most programming. The OPTIONS statement also gives you control over printing of page numbers (NONUMBER turns numbering off), or dates (NODATE turns date off). These and other options can be reset during the program with subsequent OPTIONS statements. By default, SAS puts page numbers on output, starting the numbering within a SAS session, not within a program. Typically the numbers are irrelevant to a report. In addition, the date is printed on the first title line, and output is always centered (side-to-side) on the
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page. I prefer to turn off these features, so a commonly used options line at the start of a program is:
OPTIONS LINESIZE=110 PAGESIZE=55 NODATE NONUMBER NOCENTER;
5. It is good practice to always save your program before you run (submit) it, when working in the SAS windows. If you find you need to make changes in your program after reviewing the log and output, first clear the log and output windows, return to the program window, edit, and again save the revised version before resubmitting. The enhanced editor has a nice feature: if you have modified the contents of the program editor, but not saved it, an asterisk (*) appears next to the program name in the task bar, as a reminder to save the program. If you fail to clear the log and output windows, the new version will be appended to the old. You will have a lot of garbage to deal with in the results window, as you try to figure out which is the old and which the new version. You can easily save the contents of the log and output windows from the final version, without a lot of other junk, as long as you keep clearing the windows before resubmitting.
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6. Always review your log before looking at the output. Check for error messages, other notes and messages on how the program ran, including the number of observations in the data sets read and created. Sometimes a mistake in your program won't produce an error message – the program may be valid, but it just doesn't do what you want it to do. Often, this kind of error can be picked up by a careful reading of the log, especially checking for the number of variables and observations in a data set, when the problem might be missed if you look only at the output. SO READ YOUR LOG!
7. Last but not least, as always, make back-up copies of your programs and data sets. Log and output files can be easily reproduced by re-running a program on the same data, so keep track of you programs and data.
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Week 7 10.
Introduction to SAS – The Basics
Archiving your work
It is easy to lose track of all the data management and analysis activities associated with even a small-scale study. Therefore, it is important to develop, ahead of time, an easy system for documenting, indexing and filing your work. The following are suggestions only -- you need to develop a system of your own, one that you like and will actually use.
1.
Use Internal Documentation. Use program headers, and make generous use of comments within your programs. If you have a copy of the program, you will then have (detailed) information on its purpose, and when and where the program was used.
2.
Use Back-up Disks Spending an extra $1 per disk can be cheap compared to the time and effort needed to replace lost data or analyses. For each project you should keep on separate disks (2 copies each): -
Grant proposal Study protocols, forms Data and associated files (e.g. .rec, .chk, .qes files in EpiInfo) SAS program files (*.sas files) SAS data sets (*.sas7bdat files in SAS V8) Reports and memos Manuscripts or presentation files (include final analysis data set)
Always save SAS data files and SAS program files on disk. You may choose to save log and output files on disk, and/or to print hard copies. The log and output can be recreated as long as you have the data and SAS code.
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Disks can be named or labeled. In the Windows Explorer, under the File Menu ÆProperties, a label can be assigned to a disk.
Disk label
This label should then be written on the stick-on disk label, in addition to your name and any other information you deem pertinent. In your documentation, keep track of which disk you use to store which files!
Be sure to label all your disks with your name, and perhaps phone and/or office number. The chances are great that at some point in your career here you will leave a disk behind in one of the computer labs.
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Week 7 3.
Introduction to SAS – The Basics
Name Your Files According to a System Always use the .SAS extension for SAS program files, .LOG for the associated log and .LST for the associated output. The SAS system recognizes these files extensions, and enables options such as batch submission of programs, and use of the SAS Viewer to review log and output files from the Windows Explorer.
Icons for SAS files: program (.sas) log (.log) output
Choose a naming convention for the first part of the filename that is easy for you to understand. Since the number of programs that can be developed on a project can grow astronomically, a simple name with a numbering system is recommended. For example for the Warm/Cold Cardiac Surgery Pilot study, the prefix WCP was used and programs were and then numbered sequentially. The first program was WCP01.sas, followed by WCP02.sas, etc. If programs were modified or rerun, this was always noted in the header. If the program was significantly modified, a new version was named: WCP01a.sas. week 07
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(.lst)
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Introduction to SAS – The Basics
Choose names that allow you this flexibility. Another suggestion is that programmers on a study use their own set of names (so that two programmers don’t produce two different files having the same name). One suggestion is to use programmer’s initials in the name, e.g. for the Warm/Cold study, one set of files were WCP*.sas, one student used WCS*.sas, another WCM*.sas, etc, based on the user’s initial.
4.
Index Your Work Create an index of all management and analysis activities. This index should describe the name and location (name of disk, where stored) of every data set; the name, purpose and location (name of disk and notebook or file drawer) of every program file. This index should be updated on a regular basis. For example, make it standard practice to reserve an hour every Friday to update your project index.
Example Project Index Date 2-6-03 2-13-03 2-15-03 2-22-03 2-23-03 2-23-03 2-25-03 2-27-03 2-28-03 2-28-03 2-28-03 3-2-03 3-2-03 3-2-03 3-2-03 3-13-03
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Program Formats.sas P01.sas P02.sas P03.sas P04.sas P05.sas P06.sas P07.sas P08.sas P09.sas P10.sas P11.sas P12.sas P13.sas P14.sas P15.sas
Description Code book Defines formats Proc contents and descriptives (alphabetic) Delay in care seeking – by quintile of HFSASTOT Delay in care seeking – by quintile of HFSFACT1 Delay in care seeking – by quintile of MSPQTOT Delay in care seeking – by quintile of MUISTOT Delay in care seeking – by quintile of AGE Delay in care seeking – by hx of previous heart failure Regression analysis of ACUTESXS Regression analysis of DYSPDUR Regression analysis of ORTHPDUR Regression analysis of PNDDUR Regression analysis of DOEDUR Regression analysis of ACUTEDYS Six Sets of ONE Predictor Models Wilcoxon Rank Sum Tests of Gender Differences in Awareness
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