Computer Applications in Epidemiology

1. Computer Applications in Epidemiology Dongmei Li Lecture 26 5/6/2009

2. Outline • Fixing programs that don’t work • Data step debugger • SAS truncates a character variable • SAS stops in the middle of the job • SAS runs out of memory or Disk Space

3. 1. Fixing programs that don’t work • Read the SAS log • SAS log has three types of messages about your program: errors, warnings, and notes. • Start at the beginning when you read SAS log. • Look for common mistakes first. • Check your syntax. • Searching for missing semicolon • Most common errors in SAS. • SAS usually give nonsense message when you miss semicolon. • Use DATASTMTCHK system option • EX: Options DATASTMTCHK=ALLKEYWORDS;

4. Note: Input statement reached past the end of the line • If you see the note ‘SAS went to a new line when Input statement reached past the end of the line’, it usually means there is a problem. • It means SAS was reading your data, it got to the end of the data line before it read values for all the variables in your Input statement. • Possible causes: blank lines in your data file, use list input without a space between every value, some data lines are shorter than the rest and you are using column or formatted input. • Use Proc Print or Viewtable to check your SAS data set.

5. Note: Lost Card • A lost card means that SAS are expecting another line of data and did not find it. • Printing the SAS data set as well as careful proofreading of the data file can be helpful in identifying problem areas.

6. Note: Invalid Data • Common reasons for invalid data: • Character values in a field that should be numeric • Forgetting to specify that a variable is character • Incorrect column specifications producing embedded spaces in numeric data • List-style input with two periods in a row and no space in between • Missing data not marked with a period for list-style input causing SAS to read the next data value. • Special characters such as tab in numeric data • Using the wrong informat such as MMDDYY instead of DDMMYY. • Invalid dates (Sep. 31) read with a date informat.

7. Note: Numeric values have been converted to character • When you accidentally mix numeric and character variables, SAS tries to fix your program by converting variables from numeric to character or vice versa. • Converting variables • Character to Numeric • Newvar=Input (oldvar, informat); • EX: newscore2=input(score2, 2.); • Numeric to Character • Newvar=PUT(oldvar, format); • NewID=PUT(studentID, 3.);

8. Data step produces wrong results but no error message • Use the Put and Putlog statements to debug. • Put and Putlog statement: • Putlog _ALL_; or • Putlog variable-1= variable-2= … variable-n=; • Ex: Data lowscore; • infile ‘c:\class.dat’; • Input name $ score1 score2 score3 Homework; • Homework=Homework*2; • averagescore=mean(score1+score2+score3+Homework); • Putlog name= score1= score2= score3= Homework= averagescore=; • If averagescore < 70; • Run;

9. 2. Data step debugger • Starting the debugger (class.dat data set) • Data lowscore/debug; • infile ‘c:\class.dat’; • Input name $ score1 score2 score3 Homework; • Homework=Homework*2; • averagescore=mean(score1+score2+score3+Homework); • Putlog name= score1= score2= score3= Homework= averagescore=; • If averagescore < 70; • Run;

10. Data step debugger (cont’d) • Executing debugger commands • Command Results • <return> Execute one statement • Step n Execute n statements • Examine variable-list Prints the values of variables • Set variable=expression Assigns a value to a specified variable for the current observation • Go Finishes executing the Data Step • Quit closes the debugger • Ex: Examine _All_

11. Possible causes for invalid options and statements • A misspelled key words • A missing semicolon • A Data step statement in a Proc step (or vice versa) • A Run statement in the middle of a DATA or Proc Step • The correct option with the wrong statement • An unmatched quotation mark • An unmatched comment.

12. Possible causes for “Variable not found” • Misspelling a variable name • Using a variable that was dropped at some earlier time • Using the wrong data set • Committing a logic error, such as using a variable before it is created.

13. 3. SAS truncates a character variable • The length of character variables are determined by the following methods: • Input statement • Ex: Input Food $; length: 8 • Input Food $1-10; length: 10 • Input Food $15.; length: 15 • Assignment statement • Ex: data summer; • set temps; • If Temperature > 100 then Status=‘Hot’; • else Status=‘Cold’;

14. SAS truncates a character variable (cont’d) • Length statement in Data step • Ex: Length Status $4 Food $15; • Attrib statement in Data step • Ex: Attrib Status Length=$4 Label=‘Hot or Cold’; • Data carsurvey; • infile'D:\Cars.dat'; • input age sex income color$; • length agegroup $6; • if age < 20then agegroup='Teen'; • elseif age < 65then agegroup='Adult'; • else agegroup='Senior'; • procprintdata=carsurvey; • title'Car color survey results'; • run;

15. 4. SAS stops in the middle of a job • Possible causes: • An unmatched quotation mark • Submit ‘; run; • An unmatched comment • Submit */; run; • No Run statement at the end of a program • Submit run; • Not sure what the problem is? • Submit *’; *”; */; run; • Out of time • Batch system may have time limit, talk to systems programmer or other SAS user at your site. • /* in the first column

16. 5. SAS runs out of memory or disk space • Memory and disk space • Decrease the number of bytes needed to store the data to help decrease disk storage. • Default is eight bytes for both numeric and character variables, can decrease it using input, length or attrib statement • EX: length Answer $1; • length Tigers 4; • Subset your data or decrease the number of variables • Clear the SAS log and output often. • Compress SAS data set (might increase the size of your data set sometime) • Ex: Data comzoo (Compress=YES); set zoo;