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07-22-2015 09:31 AM

How to calculate the sensitivity,specificity and Youden index for 18 factors,and its combination (6 factors in each) with an outcome measure.

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Solution

07-27-2015
09:58 AM

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07-27-2015 09:58 AM

Read this SAS support note: 24170 - Estimating sensitivity, specificity, positive and negative predictive values, and other stat...

Run that code first, this code can inform you about obtaining sensitivity and specificity as values.

**PROC TABULATE**

**DATA**=WORK.FATCOMP

OUT =WORK.STABSummaryTablesFATCOMP(LABEL="Summary Tables for WORK.FATCOMP");

CLASS Test / ORDER=UNFORMATTED DESCENDING MISSING;

CLASS Response / ORDER=UNFORMATTED DESCENDING MISSING;

TABLE Test*ColPctN,Response;

FREQ Count;**RUN**;**data** numbers (Keep=sensitivity specificity);

do until (eof);

set **&syslast** end=eof;

if Test=**1** and Response=**1** then sensitivity=PctN_01;

if Test=**0** and Response=**0** then specificity=PctN_01;

end;

putlog "NOTE: " sensitivity= specificity=;

output;

stop;**run**;

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07-22-2015 04:57 PM

PROC MEANS/SUMMARY can be used to calculate a confusion matrix.

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07-22-2015 04:58 PM

We can communicate a solution more effectively if you give us a sample of your data. Then we can speak in terms of your data's variables names.

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07-22-2015 09:58 PM

Thank you for your kind reply.I have added sample of my data.Here 'malnut'(malnutrition) is the outcome measure and others like chew,weilos......cc are the independent variables.I want to get the sensitivity,specificity and youden index of each of these variables and their combination having 6 factors(A+B+C+D+E+F) like 'chew,weilos,mobil,stress,dement,bmi' with the outcome measure.

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07-23-2015 09:43 AM

So you want sensitivity and specificity with respect to what predictive model? Is 'MALNUT' the result of your predictive model, or is it the known state of the patient? If you have established a predictive model then its outcome would be compared with the clinical data, this is how I know this type of statistics. I can refer you to https://en.wikipedia.org/wiki/Confusion_matrix. I don't know anything in SAS_STATS that will do this, but perhaps this question should be posed in that forum: https://communities.sas.com/community/support-communities/sas_statistical_procedures .

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07-23-2015 11:24 AM

Thank you for your consistent support. Ya 'Malnut' is the known state of the patient,which indicates malnutrition.Here we wish to find the sensitivity and specificity of each factor and 'Malnut' status 0=not malnourished & 1=malnourished.Thanks for your directions.

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07-23-2015 01:01 PM

Run a proc freq between each set of variables. That will create your cross tabs and you can get the number from there to calculate your specificity/sensitivity.

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07-25-2015 12:10 AM

Definitely i will do so :smileycool:

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07-23-2015 01:07 PM

Actually PROC MEANS is what I've used and it involved another step, but PROC TABULATE can be used using one step.

My question about predictive models is still relevant: I believe you need to choose dichotomous values to represent your independent variables to do this correctly. If both MALNUT and another variable, _x_ are dichotomous then this code will produce a dataset with up to four rows, each corresponding to a cell of the confusion matrix. Sensitivity, specificity and Youden's index can be calculated from these values.

**PROC TABULATE** **DATA**=Given_DS

OUT=Want_X_vs_Malnut ;

CLASS _x_ ;

CLASS Malnut ;

TABLE _x_,Malnut * N ;

;**RUN**;

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07-23-2015 10:02 PM

Thank you very much, Phil for your extremely valuable SAS codes.In my data set i have coded the independent and dependent variable(s) as dichotomous ones; 0=no & 1=yes.I have 190 rows of 18 independent dichotomous variables and 1 dependent dichotomous variable.

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07-24-2015 01:00 AM

If you have your answer please mark the question answered

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07-24-2015 08:45 AM

Well we * technically* did not answer the question pertaining to the combinations of factors... so... what can we do?

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07-25-2015 12:04 AM

Thank you for the support offered !.I just wanted to get sensitivity and specificity.proc freq procedure produces that but its mixed with other values,is there any way to cull out only those 2 items from that table.

Solution

07-27-2015
09:58 AM

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07-27-2015 09:58 AM

Read this SAS support note: 24170 - Estimating sensitivity, specificity, positive and negative predictive values, and other stat...

Run that code first, this code can inform you about obtaining sensitivity and specificity as values.

**PROC TABULATE**

**DATA**=WORK.FATCOMP

OUT =WORK.STABSummaryTablesFATCOMP(LABEL="Summary Tables for WORK.FATCOMP");

CLASS Test / ORDER=UNFORMATTED DESCENDING MISSING;

CLASS Response / ORDER=UNFORMATTED DESCENDING MISSING;

TABLE Test*ColPctN,Response;

FREQ Count;**RUN**;**data** numbers (Keep=sensitivity specificity);

do until (eof);

set **&syslast** end=eof;

if Test=**1** and Response=**1** then sensitivity=PctN_01;

if Test=**0** and Response=**0** then specificity=PctN_01;

end;

putlog "NOTE: " sensitivity= specificity=;

output;

stop;**run**;

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07-28-2015 05:52 AM

Thank you for SAS codes,Is there any provision(code) to find the Youden Index(sensitivity+specificity-1).