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

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

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

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

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

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

Mean

Median

Mode

Standard deviation

Statistical Significance p < .01

Confidence Interval

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

Statistics Online Textbook The Statistics Homepage http://www.statsoftinc.com/textbook/stathome.html

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

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) d c Test is negative b a Test is positive Patients without disease Patients with disease

sensitivity = a / (a+c)

specificity = d / (b+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) d c Test is negative b a Test is positive Patients without disease Patients with disease

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)

Good Resource Sen, Spc, PV An Introduction to Information Mastery http://www.poems.msu.edu/InfoMastery/default.htm Diagnosis Sensitivity and specificity Predictive values Likelihood ratios InfoRetriever Calculators: Epidemiology, Diagnostic test

An Introduction to Information Mastery

http://www.poems.msu.edu/InfoMastery/default.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

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

Fact lookups

Research

Presentations

Social and Policy indicators

Strategies for Finding Health Stats Use Portal Start at Internet site Start with book or article

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/

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

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

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

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

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

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

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

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

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

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

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)

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)

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)

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

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

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

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

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

Utilities Menu

File Info…

Output window

Descriptive Statistics Analyze Menu Descriptive Statistics Frequencies Select Age ► Click Statistic s button In Central Tendency Mean, Median, Mode In Dispersion Standard Deviation, variance In Percentile Values Quartiles Continue OK

Analyze Menu

Descriptive Statistics

Frequencies

Select Age ►

Click Statistic s 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

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

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?

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

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.

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

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

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?