Chapter 6: Single group studies using SPSS

1. Open the file.
1. From the File menu choose Open > Data....
2. Find the file chlamydia.sav and open it.

For this to work with your own data, be sure that your variable is coded as 0 and 1 with the event of interest coded as 1.

2. Do the analysis.
1. From the Analyze menu choose Generalized Linear Models > Generalized Linear Models....
2. Click on Reset (at the bottom of the window).
3. Click on Type of Model (at the top of the window).
4. Click Custom (near the bottom of the window).
5. Click OK.
6. Click on Response (at the top of the window).
7. Drag noChlamydia to the Dependent Variable: box.
8. Click OK.
9. When you are warned that "No effects have been specified," Click OK.

SPSS does not have an automatic way to calculate sensitivity and specificity with confidence intervals. However, there is custom code on their website which can be found if you click here. The code, modified to use our data, is below.

1. Create a new SPSS program.
1. From the File menu choose New > Syntax....
2. Enter the program into an SPSS syntax editing window.

	
DATA LIST LIST / Predicted Actual Count.
BEGIN DATA.
1 1 13
1 2 9
2 1 3
2 2 39
END DATA.
FORMATS ALL (F8.0).
WEIGHT BY Count.

*Positive Predictive Value (Estimate for Intercept in GENLIN output).
TEMPORARY.
SELECT IF Predicted=1.
GENLIN Actual (REFERENCE=LAST)
/MODEL DISTRIBUTION=BINOMIAL LINK=IDENTITY
/CRITERIA CITYPE=PROFILE 
/PRINT SOLUTION.

*Negative Predictive Value (Estimate for Intercept in GENLIN output).
TEMPORARY.
SELECT IF Predicted=2.
GENLIN Actual (REFERENCE=FIRST)
/MODEL DISTRIBUTION=BINOMIAL LINK=IDENTITY
/CRITERIA CITYPE=PROFILE 
/PRINT SOLUTION.

*Sensitivity (Estimate for Intercept in GENLIN output).
TEMPORARY.
SELECT IF Actual=1.
GENLIN Predicted (REFERENCE=LAST)
/MODEL DISTRIBUTION=BINOMIAL LINK=IDENTITY
/CRITERIA CITYPE=PROFILE 
/PRINT SOLUTION.

*Specificity (Estimate for Intercept in GENLIN output).
TEMPORARY.
SELECT IF Actual=2.
GENLIN Predicted (REFERENCE=FIRST)
/MODEL DISTRIBUTION=BINOMIAL LINK=IDENTITY
/CRITERIA CITYPE=PROFILE 
/PRINT SOLUTION.

*LR+ & LR- as cohort risk estimates. Use file with cells b & c flipped.
*LR+ is estimate for cohort Actual = 1. LR- is estimate for Actual = 2.
DO IF Predicted <> Actual.
RECODE Predicted Actual (1=2) (2=1).
END IF.
CROSSTABS
/TABLES=Predicted BY Actual
/FORMAT=AVALUE NOTABLES
/STATISTICS=RISK.

*Return original codings (flip cells b & c back to original values).
DO IF Predicted <> Actual.
RECODE Predicted Actual (1=2) (2=1).
END IF.
EXECUTE

3. Run the program.
1. From the Run menu choose All.