StudySAS Blog

SDTM Compliance Checks

2011-11-13T00:37:00.001-05:00

Validation checks or tools to check the compliance of SDTM data JANUS is a standard database model which is based on the CDISC’s SDTM standard. JANUS is used by the FDA to store the submitted SDTM clinical data. As a part of data definition file submission pharmaceutical companies have to submit SAS datasets in transport file (.xpt) format along with annotated CRF and Define.xml file. The reason being this is… to properly load the clinical data into JANUS database which is maintained by the FDA. It is very easy for FDA reviewers to review the clinical data once they load the clinical data into their JANUS database. They can even produce ad-hoc reports and perform cross-study review at the same time. FDA runs compliance checks on the data submitted to make sure the data was collected as per the SDTM standard. FDA checks the compliance of data by running the WebSDM™ developed by PhaseForward). WebSDM™ is a SDTM compliance check validation tool performs a set of SDTM compliance...

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How to remove carriage return and linefeed characters within quoted strings.

2011-10-27T16:23:00.003-04:00

HANDLING SPECIAL EMBEDDED CHARACTERS To manage and report data in DBMS that contains very long text fields is not easy. This can be frustrating if the text field has special embedded symbols such as tabs, carriage returns (‘OD’x ), line feeds (‘OA’x) and page breaks. But here is simple SAS code which takes care of those issues. The normal line end for Windows text files is a carriage return character or a line feed character so The syntax for taking out all carriage return ('OD'x) and line feed ('OA'x) characters is comment= Compress(comment,'0D0A'x); or comment= TRANWRD(comment,'0D0A'x,’’); If you just want to take out the Carriage Return, use this code: comment= TRANWRD(comment,'0D'x,''); You could also try this one too.. Comment=compress(Comment, ,"kw");*k is for keep, w is for...

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Counting the number of missing and non-missing values for each variable in a data set.

2011-10-13T10:19:00.000-04:00

/* create sample data */ data one; input a $ b $ c $ d e; cards; a . a 1 3 . b . 2 4 a a a . 5 . . b 3 5 a a a . 6 a a a . 7 a a a 2 8 ; run; /* create a format to group missing and non-missing */ proc format; value $missfmt ' '='missing' other='non-missing'; value missfmt .='missing' other='non-missing'; run; %macro lst(dsn); /** open dataset **/ %let dsid=%sysfunc(open(&dsn)); /** cnt will contain the number of variables in the dataset passed in **/ %let cnt=%sysfunc(attrn(&dsid,nvars)); %do i = 1 %to &cnt; /** create a different macro variable for each variable in dataset **/ %let x&i=%sysfunc(varname(&dsid,&i)); /** list the type of the current variable **/ %let typ&i=%sysfunc(vartype(&dsid,&i)); %end; /** close dataset **/ %let rc=%sysfunc(close(&dsid)); %do i = 1 %to &cnt; /* loop through each variable in PROC FREQ and create */ /* a separate output data set */ proc freq...

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When do I use a WHERE statement instead of an IF statement to subset a data set?

2011-08-17T10:07:00.000-04:00

When programming in SAS, there is almost always more than one way to accomplish a task. Beginning programmers may think that there is no difference between using the WHERE statement and the IF statement to subset your data set. Knowledgeable programmers know that depending on the situation, sometimes one statement is more appropriate than the other. For example, if your subset condition includes automatic variables or new variables created within the DATA step, then you must use the IF statement instead of the WHERE statement. This tip shows you how and when to apply the WHERE and IF statements to get correct and reliable results. It also reviews the similarities as well as the differences between these two SAS programming approaches. Detail differences in program efficiency between the two approaches will not be covered in this tip. For more details refer to http://support.sas.com/kb/24/286.html

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Transporting SAS Files using Proc Copy and or Proc Cport/Proc Cimport

2011-07-04T11:36:00.011-04:00

When moving SAS datasets /catalogs from one type of computer to another, there are several things to be considered, such as the operating systems of the two computers, the versions of SAS and the type of communication link between the computers. The easiest way to move SAS datasets from one system to another system is to: Create a transport file using any SAS version.Move the transport file to the new system. Import the transport file on the new system. Transport datasets are 80-byte length binary files made from SAS datasets. PROC COPY or PROC CPORT can create Transport datasets but they both create different types of transport files. Transport files can be created and read using either PROC COPY or PROC CPORT & PROC CIMPORT, but you cannot mix and match. Transport files created with PROC COPY must be read with PROC COPY; those created by PROC CPORT must be read with PROC CIMPORT. PROC COPY uses an engine (i.e. XPORT) to create a SAS transport file. PROC COPY is used...

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How to generate the month name from a numeric date value

2011-06-14T16:34:00.004-04:00

Task: I have a SAS date and wanted to create a variable with the month name. Here is how to do it...... Using MONNAMEw. format which is simple and easy. MONNAMEw. format is available in SAS 9.X versions. /*Use MONNAMEw. format*/ data month; input date:mmddyy8.; month_name=put(date,monname3.); datalines; 01/15/04 02/29/04 07/04/04 08/18/04 12/31/04;run; proc print; run;

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ERROR: The MS Excel table (worksheetname) has been opened for OUTPUT.

2011-06-14T15:38:00.001-04:00

I happend to stumbleupon a post from SAS support blog regarding the ERROR message in the LOG file when trying to output a SAS dataset in the form of Excel sheet. Direct link: ERROR: The MS Excel table (worksheetname) has been opened for OUTPUT. This table already exists, or there is a name conflict with an existing object. This table will not be replaced. This engine does not support the REPLACE option. ERROR: Export unsuccessful. See SAS Log for details. When you use the EXPORT procedure on an Excel workbook, the workbook might be corrupted and the following error message generated: This problem can occur if a previous EXPORT procedure attempts to export a SAS data set in the workbook that does not contain any observations. The following example illustrates an export procedure on such a data set: %macro blowup; data a; a=1; stop; run; %do i=1 %to 2; proc export data=a outfile="c:\temp\test.xls" dbms=excel2000...

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How to read next record while working on the current record. (LEAD FUNCTION)

2011-02-06T15:08:00.004-05:00

Even though there is no function is available in SAS to do exactly the opposite work of the LAG function (i.e: reading the next record while working on the current one), there are few things you can do to do exactly that. Here are few simple techniques which are proved to work without any problem. *SAMPLE DATASET; data test; input id age grp ; datalines; 1 10 1 2 20 1 3 30 1 4 40 1 5 50 1 1 10 2 2 20 2 3 30 2 4 40 2 5 50 2 ; run; *1) Using the POINT feature along with automatic variable _N_; This solution was suggested by Paul M. Dorfman; data leads; _n_ ++ 1; if _n_ le n then do; set one point=_n_; leadage=age; end; set one nobs=n; run; *OR*; data leads; _n_ ++ _n_ lt n; set one point=_n_; leadage=age; set one nobs=n end=end; if end then leadage=.; run; By using the above techniques, you can jump a bit higher and even look values of two, three or any numbers of observations in advance by advancing the value of...

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STUDY 'DAY' CLCULATION (ONE-LINER)

2011-01-22T13:21:00.003-05:00

Recently I stumbled upon a SUGI-Paper SAS 1-Liners by Stephen Hunt. I liked the way Stephen developed the 1-liner for STUDY DAY calculation. Direct link: One of the most common calculation used across all types of programming is determining a relative 'day' based on 2 date fields. In clinical trials the initial 'Study Day' is generally considered to begin at either randamization or dosing, thus assessments made prior to this starting point require a slight variation in the calculating in order to preserve the typical 'no day 0' concept. SUGI proceedings10/054-2010.pdf When it comes to calculating such, some programmers opt to both with evaluating whether a visit date occurred on or /after randomization. if visdt > randdt >.z then stydy=visdt-randdt; else stydt=visdt-randdt+1; However, this is unnecessary, sine the 1-liner will suffice: if visdt >.z & randdt >.z then stydy=visdt-randdt+(visdt>=randdt); Thanks...

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Easy way to UPCASE variable names of SAS dataset | StudySAS Blog [Digg]

2010-12-06T06:04:37-08:00

Upcasing the Variable names of the SAS dataset

Easy way to UPCASE variable names of SAS dataset

2010-12-05T17:39:00.011-05:00

option VALIDVARNAME=UPCASE; Use trhe above option statement to upcase the variable name of the SAS dataset irrespective of type of variable in the dataset (character or numeric). The following example shows how the option sattement VALIDVARNAME=UPCASE works. proc contents data=sashelp.class out=test; run; Note: Propcase variable names. *Upcasing the variables; option validvarname=upcase; proc sort data=sashelp.class out=test; run; Because of the option statement. Ex: 'Age' becomes 'AGE' and 'Height' becomes 'HEIGHT' etc. See the SAS Language Reference dictionary to get more details. Another way to do this is to use a macro and I call it as UPCASE macro. proc sort data=sashelp.class out=test; by name; run; %macro upcase (lib,dsn); *Create a macro variable with the total number of variable count; data _null_; set sashelp.vtable(where=(libname="&LIB" and...

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MDY Function

2010-11-04T17:42:00.003-04:00

The MDY function converts MONTH, DAY, and YEAR values to a SAS date value. For example, MDY(10,19,1999) returns the SAS date value '19OCT99'D. Syntax: MDY(month,day,year) Arguments month : specifies a numeric expression that represents an integer from 1 through 12. day :specifies a numeric expression that represents an integer from 1 through 31. year :specifies a two-digit or four-digit integer that represents the year. The YEARCUTOFF= system option defines the year value for two-digit dates. If you know month, day, and year values, it’s very easy to derive date variable. You just need to use MDY function (of course, month, day, and year should be numeric). However, if the data is character then the conversion to numeric should occur first and then the conversion to the date value. Example: *When month, day, and year has numeric values; data...

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Overview on CDISC Implementation

2010-10-04T08:36:00.002-04:00

CDISC Advantages CDISC has developed a set of data standards to enhance data collection, management, analysis, and reporting efficiencies, improve safety monitoring, and streamline the review and approval process for investigational treatments. Under the ICH’s electronic Common Technical Document (eCTD) guidance, CDISC Study Data Tabulation Model (SDTM) is the preferred standard for content format and structure of clinical data for all clinical studies. Based on proposed federal regulations, the FDA will mandate that all clinical trial submissions be in electronic format and that the content comply with data standards guidance. Veristat helps our clients by not only implementing these standards on a project or program, but also by providing our clients with an understanding of the CDISC standards. source:veristatinc.com source: http://cro.businessdecision.com/ ('’)

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How to convert the datetime character string to SAS datetime value? (ANYDTDTM and MDYAMPM formats)

2010-09-16T10:35:00.010-04:00

When we have a string like this "9/01/2010 11:52:54 AM" and would like to translate the string to a numeric SAS date time variable, most of the times we use SCAN function to extract the information to get the DATETIME format. This is definitely a tedious job. SAS formats (MDYAMPM, ANTDTDTM) comes to rescue us. Here is how it works. data test; length date $25; date="9/01/2010 11:52:54 AM"; *Convert the character string to SAS datetime value; datetimevar =input(date,mdyampm25.2); datetimevar1 =input(date,anydtdtm20.); *Apply format to the SAS date time value; format datetimevar datetimevar1 datetime19.; run; Result: 01SEP2010:11:52:54 *ANYDTDTM and MDYAMPM informats work together when the datetime value has AM PM specified or day, month, and year components are not ambiguous. The MDYAMPMw. format writes datetime values with separators in the form mm/dd/yy hh:mm AM PM, and requires a space between the date and the time. The ANYDTDTM w. format writes...

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SAS Keyboard Shortcuts

2010-09-12T08:04:00.002-04:00

Here are the few shortcuts you need to know to speed up the code writing. These work in both EPG (Enterprise Guide) and SAS Enhanced Editor. Shortcuts and their descriptions: Remember that the keyboard shortcuts listed here are default. Selection Operations:1) Comment the section with line comments (/): press CTL + / 2) Undo the comment: press CTL + SHIFT + / 3) Convert selected text to lowercase: press CTL + SHIFT + L 4) Convert selected text to uppercase: press CTL + SHIFT + U Shortcuts (pre-defined) CTRL+Shift+L or +U (only for the enhanced editor), which convert all selected text into lowercase or uppercase respectively. These become very handy when we insert the text by copy+paste. 5) Indent selected section: press TAB 6) Un-indent selected section: press SHIFT + TAB 7) To move curser to the matching DO/END statement: press ALT + [ or ALT + { or ALT+]...

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How to create Global or Local macro variables: (%Global / %Local)

2010-09-10T09:34:00.002-04:00

Global Macro Variables:The global macro variable gets created during the initialization of a SAS session and its get deleted at the end of the session. Global macro variable cane be created with 􀀀 a %LET statement (used outside a macro definition) 􀀀 a DATA step that contains a SYMPUT routine 􀀀 a DATA step that contains a SYMPUTX routine (New with SAS 9) 􀀀 a SELECT statement that contains an INTO clause in PROC SQL 􀀀 a %GLOBAL statement. Global macro variables include the following: *all automatic macro variables except SYSPBUFF. See Automatic Macro Variables for more information about SYSPBUFF and other automatic macro variables. *macro variables created outside of any macro. *macro variables created in %GLOBAL statements. See Creating Global Macro Variables for more information about the %GLOBAL statement. *most macro variables created by the CALL SYMPUT routine. See Special Cases of Scope with the CALL SYMPUT Routine for more information about...

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How to get the details of formats from the format libraries:

2010-08-26T15:56:00.003-04:00

If you are like me wanted to get the details of formats stored in the format library, here are two easy ways ….Proc catalog or Proc format Proc Catalog: Proc catalog will give us the details about name and type (numeric or character) of formats Syntax: proc catalog catalog = frmtdir.formats; contents; run; *FORMATS, is the name of the folder where all permanent formats are stored inside the library FRMTDIR. *If you want to get the details of temporary formats use WORK in place of frmtdir.formats; Proc Format: Use either SELECT or EXCLUDE statements to choose the formats for which you want to get the details. Syntax: proc format library = frmtdir.formats; select locfmt; run; This code will provide the details of LOCFMT in the FRMTDIR library. Below code gives complte information about what's stored in your format catalogs. libname frmtdir 'c:\saswork'; proc format library=frmtdir.formats cntlout = formats; run; Look at the...

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Converting SAS datasets to SPSS

2010-07-19T19:27:00.001-04:00

If you want to view SAS dataset in SPSS you can use GET SAS command of SPSS. Here is the syntax; get sas data='C:\data\class.sas7bdat'. For conversion of SAS to SPSS we need to see if any formats assigned to variables in the dataset or not. If there are no formats then we just follow following steps to convert SAS dataset to SPSS. **STEP1: Creating .xpt file of a SAS dataset using Proc COPY.** libname SAS 'c:\sas\data\'; libname SPSS xport 'c:\sas\data\class.xpt'; proc copy in=sas out=spss; select class; run; **STEP2: Use SPSS command to convert the transport format SAS file to SPSS;** You should use following commands to convert transport format file to SPSS data. get sas data='c:\sas\data\class.xpt'. execute. *******************************************************************************************; If there are formats then we need to convert the formats catalog to a SAS data set before converting the SAS dataset into a .XPT file. This has...

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Delete observations from a SAS data set when all or most of variables has missing data

2010-07-19T13:41:00.000-04:00

/* Sample data set */ data missing; input n1 n2 n3 n4 n5 n6 n7 n8 c1 $ c2 $ c3 $ c4 $; datalines; 1 . 1 . 1 . 1 4 a . c . 1 1 . . 2 . . 5 e . g h 1 . 1 . 3 . . 6 . . k i 1 . . . . . . . . . . . 1 . . . . . . . c . . . . . . . . . . . . . . . ; run; *If you want to delete observation if the data for every variable is missing then use the following code; *Approach 1: Using the coalesce option inside the datastep; data drop_misobs; set missing; if missing(coalesce(of _numeric_)) and missing(coalesce(of _character_)) then delete; run; Pros: *Simple code Cons; *This code doesn't work if we want to delete observation based on specific variables and not all of them. *Approach 2:Using N/NMISS option inside the datastep; data drop_missing; set missing; *Checks the Non missing values using ; if n(n1, n2, n3, n4, n5, n6, n7, n8, c1, c2, c3, c4)=0 then delete; run; data drop_missing; set missing; *Checks the missing...

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Diffrence Between RUN and QUIT statements

2010-07-10T16:08:00.002-04:00

Folkes, Here is the answer from Andrew Karp..... Direct link ****************************************************************************************************;Allow me to weigh in on this topic. It comes up alot when I give SAS training classes. First, RUN and QUIT are both "explicit step boundaries" in the SAS Programming Language. PROC and DATA are "implied step boundaries." Example 1: Two explicit step boundaries. DATA NEW; SET OLD: C = A + B;RUN; PROC PRINT DATA=NEW; RUN; In this example, both the data and the proc steps are explicitly "ended" by their respective RUN statements. Example 2: No explicit step boundaries. DATA NEW; SET OLD;C = A + B; PROC PRINT DATA=NEW; In this example, the data step is implicitly terminated by the PROC statement. But, there is no step boundary for the PROC PRINT step/task, so it will not terminate unless/until the SAS supervisor "receives" a step boundary. Some PROCS support what is called RUN group processing. These include...

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Sending the LOG and OUTPUT from PC SAS to a seperate file

2010-05-18T12:57:00.002-04:00

Here is how to direct the SAS LOG file and or SAS Output to a seperate file. Approach 1: Using Display Manager Statements; filename log 'C:\temp\logfile.log'; filename out 'C:\temp\output.lst'; *Select only male students and age less than 16; proc sql; create table males as select age, height, weight from sashelp.class where sex='M' and age lt 16 order by age; quit; *Get the descriptive statistics for height variable by age; proc means data=males ; by age; var height; output out=htstats mean=mean n=n std=sd median=med min=min max=max; run; DM 'OUT;FILE OUT REP;'; DM 'LOG;FILE LOG REP;'; Information about Display Manager Commands: DEXPORT and DIMPORT: DISPLAY MANAGER commands used to IMPORT and EXPORT the Tab delimited (Excel and .CSV) files; SAS Display Manager Commands Approach 2: Using Proc PRINTTO procedure; Refer: How to save the log file or what is PROC PRINTTO procedure ('’)

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Random Sample Selection

2010-05-09T08:49:00.002-04:00

Last week my manager asked me to randomly pick 10%observations from a large data set and then create a listing so that the Data management programmers can QC the data. I want to share some thoughts here … how easy and simple to do random sampling. Approach 1: Data step Approach: In this approach, the observations are shuffled using the RANUNI function which assigns a random number to each observation. Step1: Generating the Random Vector (shuffling) using the RANUNI function; The RANUNI function generates a random number from a continuous uniform distribution (the interval (0, 1). Step2: After assigning a random number to each record, the records can then be sorted in ascending or descending order of the random numbers.; data randsamp ;input patno @@; random=RANUNI(-1);* RANUNI function to assign a random number to each record.;* Here the seed is negative integer (-1) so the results are not replicable.;cards; 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23...

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WARNING: You may have unbalanced quotation marks.

2010-04-26T20:25:00.003-04:00

SAS can allow the strings up to 32,767 characters long but some times SAS will write a Warning message ‘WARNING: The quoted string currently being processed has become more than 262 characters long. You may have unbalanced quotation marks.’, when you try to keep a character string longer than 262 characters to a variable. It is hard to look back at the SAS code to search for unbalanced quotes. To make it more clearly I am going to show an example. I want to add a 263 characters long name to a variable (longvar) and to do that I will simply use a data step… and when I do that I will see the WARNING message in Log. data TEST; x="(SEE DOCTOR'S LETTER)3RD ADMINISTRATION OF MTX WAS DELAYED BY 14 DAYS AND WAS REDUCED TO 1G/M2 INSTEAD OF 5G/M2, PROBLEMS, E.COLI SEPSIS WITH HEART INSUFFICIENCY WITH SINUS TACHYCARDY, PARALYTIC ILEUS, TACHYPNEA , PATIENT DIED ON 21.04.98 FROM MULTIORGAN FAILURE."; y=length(x); put x; run; LOG FILE: There is a SAS option (NOQUOTELENMAX)...

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CALL EXECUTE: Easy way to print or sort multiple files.

2010-04-17T08:45:00.007-04:00

When printing multiple files, or sorting multiple datasets, the traditional method is to write multiple steps as below. Proc print data=libref.ae; var _all_; run; Proc print data=libref.conmed; var _all_; run; Proc print data=libref.demog; var _all_; run; Proc print data=libref.lab; var _all_; run; Proc print data=libref.medhist; var _all_; run; If you are like me who likes to simplify the traditional SAS code here is the tip. CALL EXECUTE comes to rescue here. *Using Disctionary Tables and Call Execute; proc sql; create table dsn as select distinct memname from dictionary.tables where libname="LIBREF" and memtype="DATA"; quit; *Sorts all the datasets using Call Execute; data _null_; set dsn; call execute ("proc sort data=final.||'memname||';by usubjid; run;"); run; *Prints all the datasets using Call Execute; data _null_; set dsn; call execute ("proc print data=final.||'trim(memname)||';var _all_; run;"); run; *Using Proc Contents and Call...

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Write a Letter using SAS/ Emailing with SAS

2010-04-10T13:08:00.004-04:00

SAS can do many things which most of us don’t have a clue. Here is one example…. Writing a letter: filename formltr 'C:\Documents and Settings\sreddy\Desktop\formltr.rtf'; data address; infile datalines; input @ 1 stno @ 6 lane $12. @19 aptno $7. @27 city $9. @37 state $2. @40 zip ; datalines; 2550 Augusta Blvd Apt#203 Fairfield OH 45014 ; run; data _null_; retain lm 5; set address; file formltr;* print notitles; put _page_; adr1 = trim(stno) ' ' trim(lane); put @lm adr1; adr2 = trim(aptno); put @lm adr2; adr3 = trim(city) ||', '|| trim(state) ||' '|| trim(zip); put @lm adr3; adr4 = trim('Dear')|| ' ' ||trim('SAS') || ' ' || trim('Users,'); put / @lm adr4; put / @lm 'StudySAS Blog offers a lot of information regarding tips and tutorials on various topics ' ; put @lm 'in SAS. It covers basics to get started to more in-depth topics like Macros and Proc SQL.'; put @lm 'It is a great site to browse to help broaden and deepen your SAS knowledge...

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Special Missing Values in SAS

2010-04-03T08:46:00.003-04:00

Definition: Special missing value is a type of numeric missing value that enables you to represent different categories of missing data by using the letters A-Z or an underscore. Ref: SAS 9.1.3 language reference: concepts page no: 102 The symbol usually used to represent a missing value for a numerical variable is the period or dot. Aside from the dot, there are 27 special missing values SAS can store in numerical variables. They are the dot-underscore (._), and dot-letter (.A thru .Z). Note that these special values are case insensitive. That is, .A=.a .B=.b .C=.c etc. If you do not begin a special numeric missing value with a period, SAS identifies it as a variable name. Therefore, to use a special numeric missing value in a SAS expression or assignment statement, you must begin the value with a period, followed by the letter or underscore, as in the following example: x=.d; When SAS prints a special missing value, it prints only the letter. When data values contain characters...

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