Proc Tabulate SAS code to automate a report

[sdwhite1989]

Hello, I am working on creating a SAS code that will automate a report on Tuberculosis cases and contacts. I have some sample code that I have been working on but it is not looking how I the report looks. I have attached report that I am trying to create. I have also attached my SAS code so far. I can attach the dataset if someone needs it. 

options center ps=60 ls=120;

/**************************************************************	*/
/*File: 	AutoCode to convert Excel Data to SAS data set		*/
/*Date:		01/21/2016											*/
/*Data:		Data from C:\Users\Shaquina\	 */
*/			AutoCode.xlsx										*/
*/Create:	C:\Users\Shaquina\AutoCode.sas7bdat					*/
/****************************************************************/
;


* First: Import data using the import wizard
	1. Save file to be imported as a CSV(MS-DOS) file.
	2. In SAS, click on File, Import Data...
	3. From the drop down menu, click on Comma Separated Values (*.csv).
	4. Choose the file destination and click next.
	5. Choose library and name the new sas file and click next.
	6. Click finish.
	7. Proc print data= XX.XXX (obs=5) *This will confirm you successfully uploaded the file**;
******************************************************************************************************;

libname Danielle 'C:\Users\Shaquina\';


Title color=	black "Tuberculosis Control Program-Arkansas";
title2 color= black  "Preliminary";
title3 color = black "Aggregate Reports for Tuberculosis Program Evaluation:";
title4 color = black "Follow-up and Treatment for Contacts to Tuberculosis Cases";
title5 color = black "Reporting Area AR0000";
title6 color = black "Cohort Year: 2014";
title7 color = black "Closure Date for Follow-up: 08/15/2015";
title8 color = black "Total TB Cases Reported: 93";

run; 
footnote ' ';

*merging the data;

PROC PRINT data = Danielle.AutoCode1 (obs=5);
run; 

proc print data = Danielle.AutoCode_2 (obs=5); run; 

proc sort data=Danielle.Autocode1;
by StateCaseNo;
run;

proc sort data= Danielle.Autocode_2;
by StateCaseNo;
run; 

data Danielle.AutoCodeAll_;
merge Danielle.AutoCode1 Danielle.AutoCode_2;
by StateCaseNo;
run; 


proc print data = Danielle.AutoCodeAll (obs=5); run;
Data Danielle.NewAutoCode_1;
set Danielle.AutocodeAll;
if Sputum_Smear_Result= 'Positive' or Sputum_Smear_Result= 'Negative';
if Therapy_Stop_Reason = 'Completed Therapy';
run;

 proc contents data = Danielle.NewAutoCode_1; run; 

 *Part 1. Cases and Contacts;


proc tabulate data =Danielle.NewAutoCode_1 missing;
TITLE9 "Types of Cases for Investigation" ;
table 	DispositionClass_Desc="Cases For Investigation"  Therapy_Stop_Reason, 
		Sputum_Smear_Result="Sputum Smear";
Class  Sputum_Smear_Result DispositionClass_Desc Therapy_Stop_Reason;

run; 






*Reasons Treatment Not Completed; 
title '';
data Danielle.NewAutoCode_2;
set Danielle.AutoCodeAll;
if Sputum_Smear_Result='Positive' or Sputum_Smear_Result='Negative';
run;
proc tabulate data = Danielle.NewAutoCode_2;

table Therapy_Stop_Reason='Reason Treatment Not Completed:', Sputum_Smear_Result='Sputum Smear';	
Class Sputum_Smear_Result Therapy_Stop_Reason;
run; 

Footnote ' Public reporting burden for this collection of information is estimated to average 3 hours per manual by data clerks; 30 minutes per hour
manual response by program managers; 30 minutes per electronic response by data clers and program managers, including the time for reviewing instructions,
searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. An agency may
not conduct or sponsor, and a person is not required to respond to a collection of information unless it displays a currently valid OMB control 
number. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this
burden to CDC/ASTDR Information Collection Review Office, 1600 Clfton Road, MS-D-24 Atlanta, GA 30333, ATTN: PRA(0920-0457). Do not send the completed form to this address.';
run;

[paulnevinthomas]

In principle, you can't create this type of output as a default part of the TABULATE function; in essence, you are asking for two different table definitions. Anything you do with the SAS syntax will basically amount to adding more dimensions to the table, but it won't fix your core problem.

You can use this code to get the tables you want, but they're still different tables:

PROC TABULATE DATA=want NOSEPS;
VAR stake winnings margin;
TABLE (stake winnings),(N SUM MEAN MEDIAN STDDEV MIN MAX);
TABLE (margin),(N MEAN MEDIAN STDDEV MIN MAX);
RUN;
There are some guides out there on hacking ODS to do what you want (namely, create "stacked tables" where several child tables are assembled into a single table. Check out here for an example. If you Google "SAS stack tables" you'll find more examples.

I've done this in HTML by creating a new tagset - basically, a special ODS destination that removes spaces between tables, etc. I don't have the code that I used anymore, unfortunately; I moved to R to do automated reporting.

[jklaverstijn]

I advise you to be specific in what you want from the forum. If you ask an actual question you stand a better chance of getting feedback.

Reg's Jan

[ballardw]

Please be explicit about which part(s) "is not looking how the report looks".

Without actual data it will be next to impossible to say what may be needed to generate your report. If you provide some data please make in in the form of a data step which reads datalines. If we have to "import" an excel file the results may be different.

Also anything appearing in the body of a report is likely to need a variable of some sort. So the parenthetical elements such as (a1) may be difficult to incorporate.

Also does the final result have to be in Excel? There can be major headaches getting some strickly appearance options such as the dot leaders ( ......... ) to appear as desired.

And a not about repeated processes:

First: Import data using the import wizard
	1. Save file to be imported as a CSV(MS-DOS) file.
	2. In SAS, click on File, Import Data...
	3. From the drop down menu, click on Comma Separated Values (*.csv).
	4. Choose the file destination and click next.
	5. Choose library and name the new sas file and click next.
	6. Click finish.
	7. Proc print data= XX.XXX (obs=5) *This will confirm you successfully uploaded the file**;

If you are going to do this with multiple files, either different data sources or over time, with the same layout do 1 through 5 one time.

The log will have data step code that you can extract and save as a program file and then you only have to change the source file, output set and possible the library. You control informats and especially length of character variables and whether a variable is numeric or character as well as setting variable labels formats, add some data checking for ranges or such and possibly calculating additional needed variables. If you keep using proc import I am willing to make a small wager that eventually something doesn't come in as expected because one of your data sources provides unexpected values an a variable that was defaulting to numeric suddenly becomes character. Which may mean a failure later on.

Whether you could hope to make such tables in a single pass through Proc tabulate depends on your data and many definitions. I've had multiple go-arounds with CDC over what the appropriate numerator and denominators may be for percentages. Often they lead to serious preprocessing before getting to actually preparing the tables.

[sdwhite1989]

To clarify my question:

The final result does not have to be in EXCEL. I attached the excel dataset, rather than datalines, because that it what we will always be using to create the report. When I stated it is not looking how the report looks, I was referring to the table values. I am not certain how to pull only values from a variable that I need. A little more about the dataset. All TB "contacts" are listed by the StateCaseNo. Repeated StateCaseNo means that is the same contact for one TB case. The purpose of the report is to use the contact's datasheet, which I have attached, to make a report showing how many contacts, how many cases, how many contacts got the disease (disease status is listed in the DispositionClass_Desc variable; blanks indicate not infected), how many contact got the infection (once again, it's listed in DispositionClass_Desc), how many started treatment (I'm assuming we could tell this by looking a started treatment date variable), and how many completed treatment (i used the therapy_stop_reason variable). The "others" variable on the report are referring to kids ages 2 and under. I do not know how to get the table to format like the report I attached on my initial post. I was going to use the Therapy_Stop_Reason variable for the middle table of the report. The last table calculates rates using the same variables from the 1st table. This is the part where I have no idea what to do. The (b1/a1),% next to the numbers in the table I am not concerned about. I am really just wanting the calculation rates. Please let me know if I cleared this up a little or if it is still vague. I have copied and pasted the first few lines of the dataset below. The enitre dataset is attached. Thank you!

StateCaseNo

CaseCount

SPUTUM_CULTURE_RESULT

SPUTUM_SMEAR_RESULT

CASE_VERIFICATION

SPUTUM_SMEAR_COLLECT_DATE

INIT_REGIMEN_START_DATE

CASE_STATUS

SPUTUM_CULT_COLLECT_DATE

CALC_DISEASE_SITE

AGE_REPORTED

CHEST_XRAY_CAVITY_EVIDENCE

CHEST_XRAY_MILIARY_EVIDENCE

CHEST_XRAY_RESULT

CONFIRMATION_DATE

COUNTRY_OF_VERIFIED_CASE

COUNT_DATE

COUNT_STATUS

DATE_ARRIVED_IN_US

DATE_REPORTED

DATE_SUBMITTED

DISEASE_SITE_1

FINAL_ISOLATE_COLLECT_DATE

FINAL_ISOLATE_IS_SPUTUM_IND

HOMELESS_IND

INIT_SUSCEPT_ETHAMBUTOL

INIT_SUSCEPT_ISONIAZID

INIT_SUSCEPT_PYRAZINAMIDE

INIT_SUSCEPT_RIFAMPIN

INIT_SUSCEPT_STREPTOMYCIN

OCCUPATION_RISK

PATIENT_BIRTH_SEX

PATIENT_BIRTH_COUNTRY

PATIENT_ETHNICITY

PATIENT_DOB

PATIENT_ZIP

PATIENT_WITHIN_CITY_LIMITS

PREVIOUS_DIAGNOSIS_IND

RACE_CALCULATED

SMR_EXAM_TY_1

STATUS_AT_DIAGNOSIS

TST_MM_INDURATION

TST_RESULT

PATIENT_COUNTY

HIV_STATUS

THERAPY_STOP_DATE

THERAPY_STOP_REASON

THERAPY_STOP_CAUSE_OF_DEATH

THERAPY_EXTEND_GT_12_OTHER

INIT_REGIMEN_ETHAMBUTOL

INIT_REGIMEN_ISONIAZID

INIT_REGIMEN_PYRAZINAMIDE

INIT_REGIMEN_RIFABUTIN

INIT_REGIMEN_RIFAMPIN

INIT_REGIMEN_STREPTOMYCIN

CORRECTIONAL_FACIL_RESIDENT

CORRECTIONAL_FACIL_TY

CT_SCAN_CAVITY_EVIDENCE

CT_SCAN_RESULT

CULT_TISSUE_RESULT

CULT_TISSUE_RESULT_RPT_DATE

CULT_TISSUE_RESULT_RPT_LAB_TY

CULT_TISSUE_SITE

EXCESS_ALCOHOL_USE_PAST_YEAR

IGRA_RESULT

NAA_RESULT

NONINJECT_DRUG_USE_PAST_YEAR

PATIENT_CITY

PATIENT_COUNTRY

PATIENT_STREET_ADDRESS_1

PATIENT_STREET_ADDRESS_2

PREGNANT

PREVIOUS_DIAGNOSIS_YEAR

RACE_ASIAN_ALL

RACE_NAT_HI_ALL

SMR_EXAM_TY_ALL

SMR_PATH_CYTO_RESULT

TB_SPUTUM_CULTURE_NEGATIVE_DAT

US_BORN_IND

Relationship_Desc

NaturalBornUSCitizen

ContactCity

ContactCounty

ContactState

ContactZip

ContactBirthCountry

ContactRace

Ethnicity

ContactGender

ContactCountryofOrigin

ContactArrivedUS

InformantCase

InformantContact

InformantThirdParty

InformantPersonalObservation

Exposure

TheTime

FirstExposureDate

ContactBrokenDate

Impression

Ventilation

TheSize

Place

RelevantTSTDate

RelevantTSTResult

RelevantTSTInduration

RelevantIGRADate

RelevantIGRAResult

RelevantIGRAType

RelevantIGRAValue

DispositionClass_Desc

DispositionClassDate

2014ARAR1400001

1

Positive

Positive

1 Positive Culture

12JAN14:00:00:00

13JAN14:00:00:00

Confirmed

19JAN14:00:00:00

Pulmonary

25

No

No

Abnormal

17JAN14:00:00:00

Count as a TB Case

.

17JAN14:00:00:00

17JAN14:00:00:00

Pulmonary

04JUN14:00:00:00

Yes

No

Susceptible

Susceptible

Susceptible

Susceptible

Susceptible

Unemployed

Male

UNITED STATES

Not Hispanic or Latino

28JUN88:00:00:00

71801

Y

No

Black or African American

Alive

18

Positive

Hempstead County

Positive

27JAN15:00:00:00

Completed Therapy

Yes

Yes

Yes

No

Yes

No

No

Not Done

Not Done

.

No

Not Done

Positive

Yes

Hope

United States

903 North Walker

Not Done

18JUN14:00:00:00

Yes

Household

No

AR

.

UNITED STATES

Black

Non-Hispanic

Male

No

No

No

No

Close

House

Household

.

.

4-Mar-14

Positive

T-Spot

.

2014ARAR1400001

Positive

Positive

1 Positive Culture

12JAN14:00:00:00

13JAN14:00:00:00

Confirmed

19JAN14:00:00:00

Pulmonary

25

No

No

Abnormal

17JAN14:00:00:00

Count as a TB