SPSS Instructions for Introduction to Biostatistics Larry Winner

SPSS Instructions for Introduction to Biostatistics Larry Winner Department of Statistics University of Florida

SPSS Windows • Data View – Used to display data – Columns represent variables – Rows represent individual units or groups of units that share common values of variables • Variable View – – – Used to display information on variables in dataset TYPE: Allows for various styles of displaying LABEL: Allows for longer description of variable name VALUES: Allows for longer description of variable levels MEASURE: Allows choice of measurement scale • Output View – Displays Results of analyses/graphs

Data Entry Tips I • For variables that are not identifiers (such as name, county, school, etc), use numeric values for levels and use the VALUES option in VARIABLE VIEW to give their levels. Some procedures require numeric labels for levels. SPSS will print the VALUES on output • For large datasets, use a spreadsheet such as EXCEL which is more flexible for data entry, and import the file into SPSS • Give descriptive LABEL to variable names in the VARIABLE VIEW • Keep in mind that Columns are Variables, you don’t want multiple columns with the same variable

Data Entry/Analysis Tips II • When re-analyzing previously published data, it is often possible to have only a few outcomes (especially with categorical data), with many individuals sharing the same outcomes (as in contingency tables) • For ease of data entry: – Create one line for each combination of factor levels – Create a new variable representing a COUNT of the number of individuals sharing this “outcome” • When analyzing data Click on: – DATA WEIGHT CASES BY – Click on the variable representing COUNT – All subsequent analyses treat that outcome as if it occurred COUNT times

Example 1. 3 - Grapefruit Juice Study To import an EXCEL file, click on: FILE OPEN DATA then change FILES OF TYPE to EXCEL (. xls) To import a TEXT or DATA file, click on: FILE OPEN DATA then change FILES OF TYPE to TEXT (. txt) or DATA (. dat) You will be prompted through a series of dialog boxes to import dataset

Descriptive Statistics-Numeric Data • After Importing your dataset, and providing names to variables, click on: • ANALYZE DESCRIPTIVE STATISTICS DESCRIPTIVES • Choose any variables to be analyzed and place them in box on right • Options include:

Example 1. 3 - Grapefruit Juice Study

Descriptive Statistics-General Data • After Importing your dataset, and providing names to variables, click on: • ANALYZE DESCRIPTIVE STATISTICS FREQUENCIES • Choose any variables to be analyzed and place them in box on right • Options include (For Categorical Variables): – Frequency Tables – Pie Charts, Bar Charts • Options include (For Numeric Variables) – Frequency Tables (Useful for discrete data) – Measures of Central Tendency, Dispersion, Percentiles – Pie Charts, Histograms

Example 1. 4 - Smoking Status

Vertical Bar Charts and Pie Charts • After Importing your dataset, and providing names to variables, click on: • GRAPHS BAR… SIMPLE (Summaries for Groups of Cases) DEFINE • Bars Represent N of Cases (or % of Cases) • Put the variable of interest as the CATEGORY AXIS • GRAPHS PIE… (Summaries for Groups of Cases) DEFINE • Slices Represent N of Cases (or % of Cases) • Put the variable of interest as the DEFINE SLICES BY

Example 1. 5 - Antibiotic Study

Histograms • After Importing your dataset, and providing names to variables, click on: • GRAPHS HISTOGRAM • Select Variable to be plotted • Click on DISPLAY NORMAL CURVE if you want a normal curve superimposed (see Chapter 3).

Example 1. 6 - Drug Approval Times

Side-by-Side Bar Charts • After Importing your dataset, and providing names to variables, click on: • GRAPHS BAR… Clustered (Summaries for Groups of Cases) DEFINE • Bars Represent N of Cases (or % of Cases) • CATEGORY AXIS: Variable that represents groups to be compared (independent variable) • DEFINE CLUSTERS BY: Variable that represents outcomes of interest (dependent variable)

Example 1. 7 - Streptomycin Study

Scatterplots • After Importing your dataset, and providing names to variables, click on: • GRAPHS SCATTER SIMPLE DEFINE • For Y-AXIS, choose the Dependent (Response) Variable • For X-AXIS, choose the Independent (Explanatory) Variable

Example 1. 8 - Theophylline Clearance

Scatterplots with 2 Independent Variables • After Importing your dataset, and providing names to variables, click on: • GRAPHS SCATTER SIMPLE DEFINE • For Y-AXIS, choose the Dependent Variable • For X-AXIS, choose the Independent Variable with the most levels • For SET MARKERS BY, choose the Independent Variable with the fewest levels

Example 1. 8 - Theophylline Clearance

Contingency Tables for Conditional Probabilities • After Importing your dataset, and providing names to variables, click on: • ANALYZE DESCRIPTIVE STATISTICS CROSSTABS • For ROWS, select the variable you are conditioning on (Independent Variable) • For COLUMNS, select the variable you are finding the conditional probability of (Dependent Variable) • Click on CELLS • Click on ROW Percentages

Example 1. 10 - Alcohol & Mortality

Independent Sample t-Test • After Importing your dataset, and providing names to variables, click on: • ANALYZE COMPARE MEANS INDEPENDENT SAMPLES T-TEST • For TEST VARIABLE, Select the dependent (response) variable(s) • For GROUPING VARIABLE, Select the independent variable. Then define the names of the 2 levels to be compared (this can be used even when the full dataset has more than 2 levels for independent variable).

Example 3. 5 - Levocabastine in Renal Patients

Wilcoxon Rank-Sum/Mann-Whitney Tests • After Importing your dataset, and providing names to variables, click on: • ANALYZE NONPARAMETRIC TESTS 2 INDEPENDENT SAMPLES • For TEST VARIABLE, Select the dependent (response) variable(s) • For GROUPING VARIABLE, Select the independent variable. Then define the names of the 2 levels to be compared (this can be used even when the full dataset has more than 2 levels for independent variable). • Click on MANN-WHITNEY U

Example 3. 6 - Levocabastine in Renal Patients

Paired t-test • After Importing your dataset, and providing names to variables, click on: • ANALYZE COMPARE MEANS PAIRED SAMPLES T-TEST • For PAIRED VARIABLES, Select the two dependent (response) variables (the analysis will be based on first variable minus second variable)

Example 3. 7 - Cmax in SRC&IRC Codeine

Wilcoxon Signed-Rank Test • After Importing your dataset, and providing names to variables, click on: • ANALYZE NONPARAMETRIC TESTS 2 RELATED SAMPLES • For PAIRED VARIABLES, Select the two dependent (response) variables (be careful in determining which order the differences are being obtained, it will be clear on output) • Click on WILCOXON Option

Example 3. 8 - t 1/2 SS in SRC&IRC Codeine

Relative Risks and Odds Ratios • After Importing your dataset, and providing names to variables, click on: • • • ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select the Independent Variable For COLUMNS, Select the Dependent Variable Under STATISTICS, Click on RISK Under CELLS, Click on OBSERVED and ROW PERCENTAGES NOTE: You will want to code the data so that the outcome present (Success) category has the lower value (e. g. 1) and the outcome absent (Failure) category has the higher value (e. g. 2). Similar for Exposure present category (e. g. 1) and exposure absent (e. g. 2). Use Value Labels to keep output straight.

Example 5. 1 - Pamidronate Study

Example 5. 2 - Lip Cancer

Fisher’s Exact Test • After Importing your dataset, and providing names to variables, click on: ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select the Independent Variable For COLUMNS, Select the Dependent Variable Under STATISTICS, Click on CHI-SQUARE Under CELLS, Click on OBSERVED and ROW PERCENTAGES • NOTE: You will want to code the data so that the outcome present (Success) category has the lower value (e. g. 1) and the outcome absent (Failure) category has the higher value (e. g. 2). Similar for Exposure present category (e. g. 1) and exposure absent (e. g. 2). Use Value Labels to keep output straight. • • •

Example 5. 5 - Antiseptic Experiment

Mc. Nemar’s Test • After Importing your dataset, and providing names to variables, click on: ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select the outcome for condition/time 1 For COLUMNS, Select the outcome for condition/time 2 Under STATISTICS, Click on MCNEMAR Under CELLS, Click on OBSERVED and TOTAL PERCENTAGES • NOTE: You will want to code the data so that the outcome present (Success) category has the lower value (e. g. 1) and the outcome absent (Failure) category has the higher value (e. g. 2). Similar for Exposure present category (e. g. 1) and exposure absent (e. g. 2). Use Value Labels to keep output straight. • • •

Example 5. 6 - Report of Implant Leak P-value

Cochran Mantel-Haenszel Test • After Importing your dataset, and providing names to variables, click on: ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select the Independent Variable For COLUMNS, Select the Dependent Variable For LAYERS, Select the Strata Variable Under STATISTICS, Click on COCHRAN’S AND MANTELHAENSZEL STATISTICS • NOTE: You will want to code the data so that the outcome present (Success) category has the lower value (e. g. 1) and the outcome absent (Failure) category has the higher value (e. g. 2). Similar for Exposure present category (e. g. 1) and exposure absent (e. g. 2). Use Value Labels to keep output straight. • • •

Example 5. 7 Smoking/Death by Age

Chi-Square Test • After Importing your dataset, and providing names to variables, click on: • • • ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select the Independent Variable For COLUMNS, Select the Dependent Variable Under STATISTICS, Click on CHI-SQUARE Under CELLS, Click on OBSERVED, EXPECTED, ROW PERCENTAGES, and ADJUSTED STANDARDIZED RESIDUALS • NOTE: Large ADJUSTED STANDARDIZED RESIDUALS (in absolute value) show which cells are inconsistent with null hypothesis of independence. A common rule of thumb is seeing which if any cells have values >3 in absolute value

Example 5. 8 - Marital Status & Cancer

Goodman & Kruskal’s g / Kendall’s tb • After Importing your dataset, and providing names to variables, click on: • ANALYZE DESCRIPTIVE STATISTICS CROSSTABS • For ROWS, Select the Independent Variable • For COLUMNS, Select the Dependent Variable • Under STATISTICS, Click on GAMMA and KENDALL’S tb

Examples 5. 9, 10 - Nicotine Patch/Exhaustion

Kruskal-Wallis Test • After Importing your dataset, and providing names to variables, click on: • ANALYZE NONPARAMETRIC TESTS k INDEPENDENT SAMPLES • For TEST VARIABLE, Select Dependent Variable • For GROUPING VARIABLE, Select Independent Variable, then define range of levels of variable (Minimum and Maximum) • Click on KRUSKAL-WALLIS H

Example 5. 11 - Antibiotic Delivery Note: This statistic makes the adjustment for ties. See Hollander and Wolfe (1973), p. 140.

Cohen’s k • After Importing your dataset, and providing names to variables, click on: • • • ANALYZE DESCRIPTIVE STATISTICS CROSSTABS For ROWS, Select Rater 1 For COLUMNS, Select Rater 2 Under STATISTICS, Click on KAPPA Under CELLS, Click on TOTAL Percentages to get the observed percentages in each cell (the first number under observed count in Table 5. 17).

Example 5. 12 - Siskel & Ebert

1 -Factor ANOVA - Independent Samples (Parallel Groups) • After Importing your dataset, and providing names to variables, click on: • • ANALYZE COMPARE MEANS ONE-WAY ANOVA For DEPENDENT LIST, Click on the Dependent Variable For FACTOR, Click on the Independent Variable To obtain Pairwise Comparisons of Treatment Means: – Click on POST HOC – Then TUKEY and BONFERRONI (among many other choices)

Examples 6. 1, 2 - HIV Clinical Trial

Kruskal-Wallis Test • After Importing your dataset, and providing names to variables, click on: • ANALYZE NONPARAMETRIC TESTS k INDEPENDENT SAMPLES • For TEST VARIABLE, Select Dependent Variable • For GROUPING VARIABLE, Select Independent Variable, then define range of levels of variable (Minimum and Maximum) • Click on KRUSKAL-WALLIS H

Example 6. 2(a) - Thalidomide and HIV-1

Randomized Block Design - F-test • After Importing your dataset, and providing names to variables, click on: ANALYZE GENERAL LINEAR MODEL UNIVARIATE Assign the DEPENDENT VARIABLE Assign the TREATMENT variable as a FIXED FACTOR Assign the BLOCK variable as a RANDOM FACTOR Click on MODEL, then CUSTOM, under BUILD TERMS choose MAIN EFFECTS, move both factors to MODEL list • Click on POST HOC and select the TREATMENT factor for POST HOC TESTS and BONFERRONI and TUKEY (among many choices) • For PLOTS, Select the BLOCK factor for HORIZONTAL AXIS and the TREATMENT factor for SEPARATE LINES, click ADD • • •

Example 6. 3 - Theophylline Clearance

Randomized Block Design - Friedman’s test • After Importing your dataset, and providing names to variables, click on: • ANALYZE NONPARAMETRIC TESTS k RELATED SAMPLES • For TEST VARIABLES, select the variables representing the treatments (each line is a subject/block) • Click on FRIEDMAN

Example 6. 4 - Absorption of Valproate Depakote Note: This makes an adjustment for ties, see Hollander and Wolfe (1973), p. 140.

2 -Way ANOVA • After Importing your dataset, and providing names to variables, click on: ANALYZE GENERAL LINEAR MODEL UNIVARIATE Assign the DEPENDENT VARIABLE Assign the FACTOR A variable as a FIXED FACTOR Assign the FACTOR B variable as a FIXED FACTOR Click on MODEL, then CUSTOM, select FULL FACTORIAL Click on POST HOC and select the both factors for POST HOC TESTS and BONFERRONI and TUKEY (among many choices) • For PLOTS, Select FACTOR B for HORIZONTAL AXIS and FACTOR A for SEPARATE LINES, click ADD • • •

Example 6. 5 - Nortriptyline Clearance

Linear Regression • After Importing your dataset, and providing names to variables, click on: ANALYZE REGRESSION LINEAR Select the DEPENDENT VARIABLE Select the INDEPENDENT VARAIABLE(S) Click on STATISTICS, then ESTIMATES, CONFIDENCE INTERVALS, MODEL FIT • For histogram of residuals, click on PLOTS, and HISTOGRAM under STANDARDIZED RESIDUAL PLOTS • •

Examples 7. 1 -7. 6 - Gemfibrozil Clearance

Example 7. 8 - TB/Thalidomide in HIV

Useful Regression Plots • Scatterplot with Fitted (Least Squares) Line – – – GRAPHS INTERACTIVE SCATTERPLOT Select DEPENDENT VARIABLE for UP/DOWN AXIS Select INDEPENDENT VARIABLE for RIGHT/LEFT AXIS Click on FIT Tab, then REGRESSION for METHOD NOTE: Be certain both variables are SCALE in VARIABLE VIEW under MEASURE • Partial Regression Plots (Multiple Regression) to observe association of each Independent Variable with Y, controlling for all others – Fit REGRESSION model with all Independent Variables – Click PLOTS, then PRODUCE ALL PARTIAL PLOTS

Example 7. 1 - Gemfibrozil Scatterplot

Logistic Regression • After Importing your dataset, and providing names to variables, click on: • ANALYZE REGRESSION BINARY LOGISTIC • Select the DEPENDENT VARIABLE • Select the INDEPENDENT VARAIABLE(S) as COVARIATES • For a 95% CI for the odds ratio, click on OPTIONS, then CI for exp(B) • Declare any CATEGORICAL COVARIATES (Independent variables whose levels are categorical, not numeric)

Example 8. 1 - Navelbine Toxicity Omnibus test for all regression coefficients (like F in linear regression)

Example 8. 2 - CHD, BP, Cholesterol

Nonlinear Regression • After Importing your dataset, and providing names to variables, click on: • ANALYZE REGRESSION NONLINEAR • Select the DEPENDENT VARIABLE • Define the MODEL EXPRESSION as a function of the INDEPENDENT VARIABLE(s) and unknown PARAMETERS • Define the PARAMETERS and give them STARTING VALUES (this may take several attempts)

Example 8. 3 - MK-639 in AIDS Patients Nonlinear Regression Summary Statistics Source DF Dependent Variable RNACHNG Sum of Squares Regression Residual Uncorrected Total 3 2 5 24. 97099. 02783 24. 99881 (Corrected Total) 4 10. 83973 Mean Square R squared = 1 - Residual SS / Corrected SS = Parameter A B C Estimate Asymptotic Std. Error 8. 32366. 01391 . 99743 Asymptotic 95 % Confidence Interval Lower Upper 3. 521788512. 121466117 2. 999161991 4. 044415032 35. 598069675 7. 532265897 3. 189345253 68. 006794097 18374. 392967 82. 899219276 18017. 706415 18731. 079519

Survival Analysis -Kaplan-Meier Estimates and Log-Rank Test • After Importing your dataset, and providing names to variables, click on: • ANALYZE SURVIVAL KAPLAN-MEIER • Select the variable representing the survival TIME of individual • Select the variable representing the STATUS of individual (whether or not event has occured). NOTE: If the variable is an indicator that the observation was CENSORED, then a value of 0 for that variable will mean the event has occured. • Select the variable representing the FACTOR containing the groups to be compared • Click on COMPARE FACTOR, select LOG-RANK, and POOL ACROSS STRATA

Examples 9. 1 -2 - Navelbine and Taxol in Mice Survival Analysis for TIME Factor REGIMEN = 1 Time Status 6 8 22 32 32 35 41 46 54 Cumulative Survival 0 0 0 0 0 Standard Error Cumulative Events Number Remaining . 9796. 9592. 9388 . 0202. 0283. 0342 . 8980. 8776. 8571. 8367. 8163 . 0432. 0468. 0500. 0528. 0553 1 2 3 4 5 6 7 8 9 48 47 46 45 44 43 42 41 40 Standard Error Cumulative Events Number Remaining . 0644. 0878. 1033. 1142. 1217. 1265. 1288. 1265 1 2 3 4 5 6 7 8 9 14 13 12 11 10 9 8 7 6 Factor REGIMEN = 2 Time Status 8 10 27 31 34 35 39 47 57 Cumulative Survival 0 0 0 0 0 . 9333. 8667. 8000. 7333. 6667. 6000. 5333. 4667. 4000

Examples 9. 1 -2 - Navelbine and Taxol in Mice Test Statistics for Equality of Survival Distributions for REGIMEN Statistic df Significance Log Rank 10. 93 1. 0009 This is the square of the Z-statistic in text, and is a chi-square statistic

Relative Risk Regression (Cox Model) • After Importing your dataset, and providing names to variables, click on: • ANALYZE SURVIVAL COX REGRESSION • Select the variable representing the survival TIME of individual • Select the variable representing the STATUS of individual (whether or not event has occured). NOTE: If the variable is an indicator that the observation was CENSORED, then a value of 0 for that variable will mean the event has occured. • Select the variable(s) representing the COVARIATES (Independent Variables in Model) • Identify any CATEGORICAL COVARIATES including Dummy/Indicator variables • K-M PLOTS can be obtained, with separate SURVIVAL curves by categories

Example 9. 3 - 6 MP vs Placebo