Analysis of Medical DataResearch 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 SignificanceType I and Type II errors

Ho True Ho False

Reject Ho Type I error Correct decision

Do Not Reject Ho Correct decision Type II error

Null Hypothesis = Ho

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 = a / (a+c)

specificity = d / (b+d)

Patients with disease

Patients without disease

Test is positive a bTest is negative c d

Predictive Value

Positive predictive value = a / ( a+b)

Negative predictive value = d / (c+d)

Post-test probability of disease given positive test = a / (a+b)

Post-test probability of disease given negative test = c / (c+d)

Patients with disease

Patients without disease

Test is positive a bTest is 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

Numerical (interval or ratio) data

Sums Averages Standard deviations Simple charts and graphs

Statistical Software 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 Histogram

Central tendency Mean Median mode

Dispersion Range Standard deviation Variance

N 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 SoftwareIntro 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 Descriptive Statistics Frequencies Select Age ► Click Statistics button In Central Tendency

Mean, Median, Mode In Dispersion

Standard Deviation, variance

In Percentile Values Quartiles

Continue OK

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, dBase, etc.

Variable names first row

File Menu, Open Data…

Files of Type Excel

Tutorial, Samples Demo.exe

Type in Labels Pick Type of variable Enter Value Labels Etc.

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?