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
Objectives
 Review statistical concepts to be on Step 1.
 Determine what data exist relative to a clinical
question or formal hypothesis
 use IT to locate existing data sources
 identify and locate existing data sets
 Within institution
 Outside institution
 Analyze, interpret and report findings
 Select and use appropriate computer software: Excel, SPSS
 Use software to perform simple statistical analysis and
portray results graphically
 Interpret reports
Prerequisite Skills
(Step 1 USMLE)
• Fundamental concepts of measurement
• Scales of measurement
• Distribution, central tendency, variability,
probability
• Disease prevalence and incidence
• Disease outcomes (eg, fatality rates)
• Associations (correlation or covariance)
• Health impact (eg, risk differences and ratios)
• Sensitivity, specificity, predictive values
More Prerequisite Skills
(Step 1 USMLE)

 Fundamental concepts of hypothesis testing

and statistical inference
 Confidence intervals
 Statistical significance and type I error
 Statistical power and type II error  
More Step 1 Topics
 Fundamental concepts of study design
 Types of experimental studies (eg, clinical trials,
community intervention trials)
 Types of observational studies (eg, cohort, case-
control, cross-sectional, case series, community
surveys)
 Sampling and sample size
 Subject selection and exposure allocation (eg,
randomization, stratification, self- - selection,
systematic assignment)
 Outcome assessment
 Internal and external validity
Scales of Measure
 Nominal – qualitative classification of equal
value: gender, race, color, city
 Ordinal - qualitative classification which
can be rank ordered: socioeconomic status
of families
 Interval - Numerical or quantitative data:
can be rank ordered and sizes compared :
temperature
 Ratio - interval data with absolute zero
value: time or space
Distribution, Central Tendency…
Mean
…Variability, Probability…

 Mean
 Median
 Mode
 Standard deviation
 Statistical Significance p < .01
Confidence Interval
Statistical Significance
Type I and Type II errors
Null Hypothesis = Ho

Ho True Ho False

Reject Ho Type I error Correct decision

Do Not Reject Ho Correct decision Type II error

Statistics Online Textbook

 The Statistics Homepage

 http://www.statsoftinc.com/textbook/stathome
.html
Disease Prevalence and Incidence

 Prevalence
 probability of disease in entire population at any
point in time
 2% of the population has diabetes
 Incidence
 probability that patient without disease develops
disease during interval
 0.2% or 2 per 1000 new cases per year
Sensitivity, Specificity
 sensitivity = Patients Patients
a / (a+c) with without
disease disease
 specificity =
d / (b+d) Test is
positive
a b
Test is
negative
c d
Predictive Value
 Positive predictive Patients Patients
value = a / ( a+b) with without
 Negative predictive disease disease
value = d / (c+d)
 Post-test probability of
disease given positive Test is


test = a / (a+b)
Post-test probability of
positive
a b
disease given negative Test is
test = c / (c+d)
negative
c d
Good Resource Sen, Spc, PV

 An Introduction to Information Mastery

 http://www.poems.msu.edu/InfoMastery/defa
ult.htm

 Diagnosis
 Sensitivity and specificity
 Predictive values
 Likelihood ratios
 InfoRetriever
 Calculators: Epidemiology, Diagnostic test
Fundamental Concepts of Study Design

 Good Resource
 Epidemiology for the Uninitiated
 BMJ
 Online Textbook
 http://bmj.com/collections/epidem/epid.shtml
Finding Health Statistics
Types of Health Statistics Questions

 Fact lookups
 Research
 Presentations
 Social and Policy indicators
Strategies for Finding Health Stats

 Use Portal
 Start at Internet site
 Start with book or article
Internet Portals of Health Stats

 Lists of links that provide starting points for

browsing or searching
 Keyword search in portal vs Google
 General idea what you want
 The Related Health Services Research Web
Sites
http://www.nlm.nih.gov/nichsr/hsrsites.html
 The NCHS portal: http://www.cdc.gov/nchs/
Other Statistical Web Sites

 CDC Data and Statistics

http://www.cdc.gov/scientific.htm
 FedStats Home Page
http://www.fedstats.gov/
 Compare these two
 U Michigan’s Statistical Resources on the
WEB – HEALTH
 What type of stats
Lexis-Nexis Statistical Universe

 Subscription resource
 Searches stat data
 Subject List
 Limit search
 Reports or tables
 http://web.lexis-nexis.com/statuniv?
B1=Connect+to+Statistical+Universe
MMWR

 Morbidity – illness
 Mortality – death
 http://www.cdc.gov/mmwr/
 Disease Trends
 Tables - searchable
Health Care Data

 Healthcare Cost and Utilization Project

 HCUPnet
 Hospital discharges
 Ambulatory service
 Costs
 Amount of care
 By diagnosis and procedure
 Surveys of hosp, physicians, nursing homes
Health Consequences

 Costs to society, individuals

 Cost from care
 Costs of illness
 Impact on infrastructure
 HCFA=>CMS Health Accounts
 http://www.cms.hhs.gov/statistics/nhe/default.
asp
State and International Data

 Floridahealthstat.com - Where Florida Health

Data Resides
 DOH Epidemiology
 KFF State Health Facts Online
 United Nations Statistics Division
 World Health Organization Research Tools
Individual Datasets

 EMR
 Billing
 CDCS
 Customized data collection tools
Data Analysis
Selecting the Appropriate Software
 Spreadsheet  Statistical Software
 Numerical (interval or
ratio) data
 Sums
 Averages
 Standard deviations
 Simple charts and graphs
 Nominal or Ordinal data
 Comparisons of two+
groups
 Frequency tables
 Complicated charts and
graphs
 Normal curves
 Class intervals
 Statistical significance
Spreadsheets

 Excel
 Pocket Excel
Data Tables

 Field names at top

 Each row is a record (sample)
 Sorting whole table
 By one column
 By more than one column
 Sorting individual sections
Descriptive Statistics
 Distribution
 frequency distribution
 Dispersion
 Histogram
 Range
 Standard deviation
 Central tendency
 Variance
 Mean
 Median
 N
 mode  Not P (inferential
stats)
Central Tendency
 Mean
 =AVERAGE(b2:b1500)
 Median
 =MEDIAN(A2:A7)
 Mode
 =MODE(A2:A7)
 N
 =COUNT(A2:A1500)
 =COUNTBLANK(A2:B5)
Dispersion

 Range
 =MAX(A2:A60)- MIN(A2:A60)
 Standard deviation
 =STDEV(A2:A110)
 Variance
 =VAR(A2:A110)
Distribution

 Frequency distribution
 Not easy – use SPSS
 FREQUENCY(data_array,bins_array)
 Use help
 Histogram
 Bar chart of frequency table
Hands on experience

 Analyze data in examples2.xls

Statistical Software
Intro to SPSS
Statistical Software

 SPSS
 Provided by request/justification
 Lab Computers
 Start => Programs => SPSS for Windows =>
SPSS 11.0 for Windows
Start Screen
 Don’t show this dialog
in the future.
 OK
Open Breast Cancer Survival

Data View
Views

Variables
View
File Information
 Utilities Menu
 File Info…
 Output window
Descriptive Statistics
 Analyze Menu  In Percentile Values
 Descriptive Statistics  Quartiles
 Frequencies  Continue
 Select Age ►  OK
 Click Statistics button
 In Central Tendency
 Mean, Median, Mode
 In Dispersion
 Standard Deviation,
variance
Graphing
 Graphs Menu
 Pie…
 Summary for Groups of
cases
 Lymph Nodes ►
 OK
Histogram with Normal Curve
 Graphs Menu
 Histogram..
 Select Age ►
 Check Display Normal
Curve
 OK
Simple Correlation Analysis
 Age and Tumor Size
 Analyze Menu
 Correlate…
 Bivariate
 Select Age ►
 Select Pathological Tumor Size ►
 Check Pearson and Spearman – Two tailed
 OK
 Is there a correlation? Negative or Positive?
 Is it statistically significant?
Save Output

 Save on All Users drive

 Under Nancy.clark
 SPSS Output Files
 Name it your name: ie, KerryBachista.spo
Importing Data
 From Excel, SAS,  Type in Labels
dBase, etc.  Pick Type of variable
 Variable names first  Enter Value Labels
row  Etc.
 File Menu, Open
 Data…
 Files of Type
 Excel
 Tutorial, Samples
 Demo.exe
SPSS Tutorials

 In the Help Menu

 On Informatics Web page
 Books:
 Statistics for Social & Health Research (Sage)
 Argyrous, George
 Statistics Applied to Clinical Trials (Klawer
Academic Publishers)
 Cleophas, Ton J., et al
Objectives
 Determine what data exist relative to a clinical
question or formal hypothesis
 use IT to locate existing data sources
 identify and locate existing data sets
 Within institution
 Outside institution
 Analyze, interpret and report findings
 Select appropriate computer software: Excel, SPSS
 Use software to perform simple statistical analysis and
portray results graphically
 Interpret reports
Questions?