Analysis Of Medical Data

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  • Analysis Of Medical Data

    1. 1. Analysis of Medical Data Research Perspective Nancy B. Clark. M.Ed. Director of Medical Informatics Education FSU College of Medicine Spring 2004 http://www.med.fsu.edu/informatics
    2. 2. Objectives <ul><li>Review statistical concepts to be on Step 1. </li></ul><ul><li>Determine what data exist relative to a clinical question or formal hypothesis </li></ul><ul><ul><li>use IT to locate existing data sources </li></ul></ul><ul><ul><li>identify and locate existing data sets </li></ul></ul><ul><ul><ul><li>Within institution </li></ul></ul></ul><ul><ul><ul><li>Outside institution </li></ul></ul></ul><ul><li>Analyze, interpret and report findings </li></ul><ul><ul><li>Select and use appropriate computer software: Excel, SPSS </li></ul></ul><ul><ul><li>Use software to perform simple statistical analysis and portray results graphically </li></ul></ul><ul><ul><li>Interpret reports </li></ul></ul>
    3. 3. Prerequisite Skills (Step 1 USMLE) <ul><li>Fundamental concepts of measurement </li></ul><ul><ul><li>Scales of measurement </li></ul></ul><ul><ul><li>Distribution, central tendency, variability, probability </li></ul></ul><ul><ul><li>Disease prevalence and incidence </li></ul></ul><ul><ul><li>Disease outcomes (eg, fatality rates) </li></ul></ul><ul><ul><li>Associations (correlation or covariance) </li></ul></ul><ul><ul><li>Health impact (eg, risk differences and ratios) </li></ul></ul><ul><ul><li>Sensitivity, specificity, predictive values </li></ul></ul>
    4. 4. More Prerequisite Skills (Step 1 USMLE) <ul><li>Fundamental concepts of hypothesis testing and statistical inference </li></ul><ul><ul><li>Confidence intervals </li></ul></ul><ul><ul><li>Statistical significance and type I error </li></ul></ul><ul><ul><li>Statistical power and type II error   </li></ul></ul>
    5. 5. More Step 1 Topics <ul><li>Fundamental concepts of study design </li></ul><ul><ul><li>Types of experimental studies (eg, clinical trials, community intervention trials) </li></ul></ul><ul><ul><li>Types of observational studies (eg, cohort, case-control, cross-sectional, case series, community surveys) </li></ul></ul><ul><ul><li>Sampling and sample size </li></ul></ul><ul><ul><li>Subject selection and exposure allocation (eg, randomization, stratification, self- - selection, systematic assignment) </li></ul></ul><ul><ul><li>Outcome assessment </li></ul></ul><ul><ul><li>Internal and external validity </li></ul></ul>
    6. 6. Scales of Measure <ul><li>Nominal – qualitative classification of equal value: gender, race, color, city </li></ul><ul><li>Ordinal - qualitative classification which can be rank ordered: socioeconomic status of families </li></ul><ul><li>Interval - Numerical or quantitative data: can be rank ordered and sizes compared : temperature </li></ul><ul><li>Ratio - interval data with absolute zero value: time or space </li></ul>
    7. 7. Distribution, Central Tendency… Mean
    8. 8. …Variability, Probability… <ul><li>Mean </li></ul><ul><li>Median </li></ul><ul><li>Mode </li></ul><ul><li>Standard deviation </li></ul><ul><li>Statistical Significance p < .01 </li></ul>
    9. 9. Confidence Interval
    10. 10. Statistical Significance Type I and Type II errors Null Hypothesis = H o Type II error Correct decision Do Not Reject H o Correct decision Type I error Reject H o H o False H o True
    11. 11. Statistics Online Textbook <ul><li>The Statistics Homepage </li></ul><ul><li>http://www.statsoftinc.com/textbook/stathome.html </li></ul>
    12. 12. Disease Prevalence and Incidence <ul><li>Prevalence </li></ul><ul><ul><li>probability of disease in entire population at any point in time </li></ul></ul><ul><ul><li>2% of the population has diabetes </li></ul></ul><ul><li>Incidence </li></ul><ul><ul><li>probability that patient without disease develops disease during interval </li></ul></ul><ul><ul><li>0.2% or 2 per 1000 new cases per year </li></ul></ul>
    13. 13. Sensitivity, Specificity <ul><li>sensitivity = a / (a+c) </li></ul><ul><li>specificity = d / (b+d) </li></ul>d c Test is negative b a Test is positive Patients without disease Patients with disease
    14. 14. Predictive Value <ul><li>Positive predictive value = a / ( a+b) </li></ul><ul><li>Negative predictive value = d / (c+d) </li></ul><ul><li>Post-test probability of disease given positive test = a / (a+b) </li></ul><ul><li>Post-test probability of disease given negative test = c / (c+d) </li></ul>d c Test is negative b a Test is positive Patients without disease Patients with disease
    15. 15. Good Resource Sen, Spc, PV <ul><li>An Introduction to Information Mastery </li></ul><ul><li>http://www.poems.msu.edu/InfoMastery/default.htm </li></ul><ul><ul><li>Diagnosis </li></ul></ul><ul><ul><ul><li>Sensitivity and specificity </li></ul></ul></ul><ul><ul><ul><li>Predictive values </li></ul></ul></ul><ul><ul><ul><li>Likelihood ratios </li></ul></ul></ul><ul><li>InfoRetriever </li></ul><ul><ul><li>Calculators: Epidemiology, Diagnostic test </li></ul></ul>
    16. 16. Fundamental Concepts of Study Design <ul><li>Good Resource </li></ul><ul><ul><li>Epidemiology for the Uninitiated </li></ul></ul><ul><ul><li>BMJ </li></ul></ul><ul><ul><li>Online Textbook </li></ul></ul><ul><ul><li>http://bmj.com/collections/epidem/epid.shtml </li></ul></ul>
    17. 17. Finding Health Statistics
    18. 18. Types of Health Statistics Questions <ul><li>Fact lookups </li></ul><ul><li>Research </li></ul><ul><li>Presentations </li></ul><ul><li>Social and Policy indicators </li></ul>
    19. 19. Strategies for Finding Health Stats <ul><li>Use Portal </li></ul><ul><li>Start at Internet site </li></ul><ul><li>Start with book or article </li></ul>
    20. 20. Internet Portals of Health Stats <ul><li>Lists of links that provide starting points for browsing or searching </li></ul><ul><ul><li>Keyword search in portal vs Google </li></ul></ul><ul><ul><li>General idea what you want </li></ul></ul><ul><li>The Related Health Services Research Web Sites http://www.nlm.nih.gov/nichsr/hsrsites.html </li></ul><ul><li>The NCHS portal: http://www.cdc.gov/nchs/ </li></ul>
    21. 21. Other Statistical Web Sites <ul><li>CDC Data and Statistics http://www.cdc.gov/scientific.htm </li></ul><ul><li>FedStats Home Page http://www.fedstats.gov/ </li></ul><ul><li>Compare these two </li></ul><ul><li>U Michigan’s Statistical Resources on the WEB – HEALTH </li></ul><ul><li>What type of stats </li></ul>
    22. 22. Lexis-Nexis Statistical Universe <ul><li>Subscription resource </li></ul><ul><li>Searches stat data </li></ul><ul><ul><li>Subject List </li></ul></ul><ul><ul><li>Limit search </li></ul></ul><ul><ul><li>Reports or tables </li></ul></ul><ul><li>http://web.lexis-nexis.com/statuniv?B1=Connect+to+Statistical+Universe </li></ul>
    23. 23. MMWR <ul><li>Morbidity – illness </li></ul><ul><li>Mortality – death </li></ul><ul><li>http://www.cdc.gov/mmwr/ </li></ul><ul><li>Disease Trends </li></ul><ul><li>Tables - searchable </li></ul>
    24. 24. Health Care Data <ul><li>Healthcare Cost and Utilization Project </li></ul><ul><li>HCUPnet </li></ul><ul><li>Hospital discharges </li></ul><ul><li>Ambulatory service </li></ul><ul><li>Costs </li></ul><ul><li>Amount of care </li></ul><ul><li>By diagnosis and procedure </li></ul><ul><li>Surveys of hosp, physicians, nursing homes </li></ul>
    25. 25. Health Consequences <ul><li>Costs to society, individuals </li></ul><ul><li>Cost from care </li></ul><ul><li>Costs of illness </li></ul><ul><li>Impact on infrastructure </li></ul><ul><li>HCFA=>CMS Health Accounts </li></ul><ul><li>http://www.cms.hhs.gov/statistics/nhe/default.asp </li></ul>
    26. 26. State and International Data <ul><li>Floridahealthstat.com - Where Florida Health Data Resides </li></ul><ul><li>DOH Epidemiology </li></ul><ul><li>KFF State Health Facts Online </li></ul><ul><li>United Nations Statistics Division </li></ul><ul><li>World Health Organization Research Tools </li></ul>
    27. 27. Individual Datasets <ul><li>EMR </li></ul><ul><li>Billing </li></ul><ul><li>CDCS </li></ul><ul><li>Customized data collection tools </li></ul>
    28. 28. Data Analysis
    29. 29. Selecting the Appropriate Software <ul><li>Spreadsheet </li></ul><ul><ul><li>Numerical (interval or ratio) data </li></ul></ul><ul><ul><li>Sums </li></ul></ul><ul><ul><li>Averages </li></ul></ul><ul><ul><li>Standard deviations </li></ul></ul><ul><ul><li>Simple charts and graphs </li></ul></ul><ul><li>Statistical Software </li></ul><ul><ul><li>Nominal or Ordinal data </li></ul></ul><ul><ul><li>Comparisons of two+ groups </li></ul></ul><ul><ul><li>Frequency tables </li></ul></ul><ul><ul><li>Complicated charts and graphs </li></ul></ul><ul><ul><li>Normal curves </li></ul></ul><ul><ul><li>Class intervals </li></ul></ul><ul><ul><li>Statistical significance </li></ul></ul>
    30. 30. Spreadsheets <ul><li>Excel </li></ul><ul><li>Pocket Excel </li></ul>
    31. 31. Data Tables <ul><li>Field names at top </li></ul><ul><li>Each row is a record (sample) </li></ul><ul><li>Sorting whole table </li></ul><ul><ul><li>By one column </li></ul></ul><ul><ul><li>By more than one column </li></ul></ul><ul><li>Sorting individual sections </li></ul>
    32. 32. Descriptive Statistics <ul><li>Distribution </li></ul><ul><ul><li>frequency distribution </li></ul></ul><ul><ul><li>Histogram </li></ul></ul><ul><li>Central tendency </li></ul><ul><ul><li>Mean </li></ul></ul><ul><ul><li>Median </li></ul></ul><ul><ul><li>mode </li></ul></ul><ul><li>Dispersion </li></ul><ul><ul><li>Range </li></ul></ul><ul><ul><li>Standard deviation </li></ul></ul><ul><ul><li>Variance </li></ul></ul><ul><li>N </li></ul><ul><li>Not P (inferential stats) </li></ul>
    33. 33. Central Tendency <ul><li>Mean </li></ul><ul><ul><li>=AVERAGE(b2:b1500) </li></ul></ul><ul><li>Median </li></ul><ul><ul><li>=MEDIAN(A2:A7) </li></ul></ul><ul><li>Mode </li></ul><ul><ul><li>=MODE(A2:A7) </li></ul></ul><ul><li>N </li></ul><ul><ul><li>=COUNT(A2:A1500) </li></ul></ul><ul><ul><li>=COUNTBLANK(A2:B5) </li></ul></ul>
    34. 34. Dispersion <ul><li>Range </li></ul><ul><ul><li>=MAX(A2:A60)- MIN(A2:A60) </li></ul></ul><ul><li>Standard deviation </li></ul><ul><ul><li>=STDEV(A2:A110) </li></ul></ul><ul><li>Variance </li></ul><ul><ul><li>=VAR(A2:A110) </li></ul></ul>
    35. 35. Distribution <ul><li>Frequency distribution </li></ul><ul><ul><li>Not easy – use SPSS </li></ul></ul><ul><ul><li>FREQUENCY(data_array,bins_array) </li></ul></ul><ul><ul><li>Use help </li></ul></ul><ul><li>Histogram </li></ul><ul><ul><li>Bar chart of frequency table </li></ul></ul>
    36. 36. Hands on experience <ul><li>Analyze data in examples2.xls </li></ul>
    37. 37. Statistical Software Intro to SPSS
    38. 38. Statistical Software <ul><li>SPSS </li></ul><ul><li>Provided by request/justification </li></ul><ul><li>Lab Computers </li></ul><ul><li>Start => Programs => SPSS for Windows => SPSS 11.0 for Windows </li></ul>
    39. 39. Start Screen <ul><li>Don’t show this dialog in the future. </li></ul><ul><li>OK </li></ul>
    40. 40. Open Breast Cancer Survival Data View
    41. 41. Views Variables View
    42. 42. File Information <ul><li>Utilities Menu </li></ul><ul><li>File Info… </li></ul><ul><li>Output window </li></ul>
    43. 43. Descriptive Statistics <ul><li>Analyze Menu </li></ul><ul><li>Descriptive Statistics </li></ul><ul><li>Frequencies </li></ul><ul><li>Select Age ► </li></ul><ul><li>Click Statistic s button </li></ul><ul><li>In Central Tendency </li></ul><ul><ul><li>Mean, Median, Mode </li></ul></ul><ul><li>In Dispersion </li></ul><ul><ul><li>Standard Deviation, variance </li></ul></ul><ul><li>In Percentile Values </li></ul><ul><ul><li>Quartiles </li></ul></ul><ul><li>Continue </li></ul><ul><li>OK </li></ul>
    44. 44. Graphing <ul><li>Graphs Menu </li></ul><ul><ul><li>Pie… </li></ul></ul><ul><li>Summary for Groups of cases </li></ul><ul><li>Lymph Nodes ► </li></ul><ul><li>OK </li></ul>
    45. 45. Histogram with Normal Curve <ul><li>Graphs Menu </li></ul><ul><ul><li>Histogram.. </li></ul></ul><ul><li>Select Age ► </li></ul><ul><li>Check Display Normal Curve </li></ul><ul><li>OK </li></ul>
    46. 46. Simple Correlation Analysis <ul><li>Age and Tumor Size </li></ul><ul><li>Analyze Menu </li></ul><ul><ul><li>Correlate… </li></ul></ul><ul><ul><ul><li>Bivariate </li></ul></ul></ul><ul><li>Select Age ► </li></ul><ul><li>Select Pathological Tumor Size ► </li></ul><ul><li>Check Pearson and Spearman – Two tailed </li></ul><ul><li>OK </li></ul><ul><li>Is there a correlation? Negative or Positive? </li></ul><ul><li>Is it statistically significant? </li></ul>
    47. 47. Save Output <ul><li>Save on All Users drive </li></ul><ul><li>Under Nancy.clark </li></ul><ul><li>SPSS Output Files </li></ul><ul><li>Name it your name: ie, KerryBachista.spo </li></ul>
    48. 48. Importing Data <ul><li>From Excel, SAS, dBase, etc. </li></ul><ul><li>Variable names first row </li></ul><ul><li>File Menu, Open </li></ul><ul><ul><li>Data… </li></ul></ul><ul><li>Files of Type </li></ul><ul><ul><li>Excel </li></ul></ul><ul><li>Tutorial, Samples </li></ul><ul><ul><li>Demo.exe </li></ul></ul><ul><li>Type in Labels </li></ul><ul><li>Pick Type of variable </li></ul><ul><li>Enter Value Labels </li></ul><ul><li>Etc. </li></ul>
    49. 49. SPSS Tutorials <ul><li>In the Help Menu </li></ul><ul><li>On Informatics Web page </li></ul><ul><li>Books: </li></ul><ul><ul><li>Statistics for Social & Health Research (Sage) </li></ul></ul><ul><ul><ul><li>Argyrous, George </li></ul></ul></ul><ul><ul><li>Statistics Applied to Clinical Trials (Klawer Academic Publishers) </li></ul></ul><ul><ul><ul><li>Cleophas, Ton J., et al </li></ul></ul></ul>
    50. 50. Objectives <ul><li>Determine what data exist relative to a clinical question or formal hypothesis </li></ul><ul><ul><li>use IT to locate existing data sources </li></ul></ul><ul><ul><li>identify and locate existing data sets </li></ul></ul><ul><ul><ul><li>Within institution </li></ul></ul></ul><ul><ul><ul><li>Outside institution </li></ul></ul></ul><ul><li>Analyze, interpret and report findings </li></ul><ul><ul><li>Select appropriate computer software: Excel, SPSS </li></ul></ul><ul><ul><li>Use software to perform simple statistical analysis and portray results graphically </li></ul></ul><ul><ul><li>Interpret reports </li></ul></ul>
    51. 51. Questions?

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