Biostatistics II with SPSS and R
Master of Science in Clinical Investigation Program
Date: M- F, February 1 – 28, 2006
Time: 1:30 PM – 4:30 PM
Class Room: Room 412 Light Hall
Instructor:
Ayumi Shintani, PhD, MPH
Department of Biostatistics
Office: MCN S-2323
Phone: (615) 936-1954
Fax: (615) 343-4924
E-mail: Ayumi.shintani@vanderbilt.edu
Class Website: http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/MsciBiostat2
Course Objectives:
1.
Able to analyze data from a complex clinical research project and interpret and
review/critique statistical methods used in published papers.
2.
Know when to use, be able to define and conduct the 30 most commonly used
inferential statistical methods and be able to interpret the statistical software
outputs for those tests.
3.
Understand the fundamental bio-statistical concepts related to univariate analysis
and especially multivariate analysis with a firm understanding between individual
univariate test and corresponding multivariate analysis.
4.
Understand concept of confounding and interaction and how to detect using subgroup analysis and multivariable modeling techniques.
5.
Understand purpose of conducting multivariable models and master proper
strategies for developing reliable multivariable models from complex data and
how to check model assumptions.
6.
Introduce students to a modern area of biostatistics such as non-linear spines for
fitting continuous data, model validation using bootstrap method.
7.
Master the statistical software package SPSS version 13 and develop
complementary skill using R- software.
8.
Able to create publication-quality and statistically meaningful medical graphs.
9.
Able to perform and understand fundamental concept related to sample size and
power computation.
Text Books:
Main text books:
(1) Kirkwood BR, Sterne JAC. Essentials of Medical Statistics. $49.95. Blackwell Sciences,
2nd ed. (2001). ISBN: 0865428719.
(2) Katz MH. Multivariable Analysis: A Practical Guide for Clinicians. $35.00.
Cambridge University Press. (1999). ISBN: 0521596939.
Supplemental text books:
(1) Bernard Rosner. Fundamentals of Biostatistics, Sixth Edition, Duxburry Press, ISBN:
0534418201. List Price (USD) $119.95
(2) Douglas G. Altman. Statistics with Confidence: Confidence Intervals and Statistical
Guidelines. B M J Books. ($31.45)
ISBN: 0727913751; 2nd edition.
(3) SPSS 13.0 Advanced statistical Procedures Companion. Marija J. Norusis ISBN 0-13186540-4
(4) SPSS 13.0 Guide to Data Analysis, Marija J. Norusis ISBN 0-13-186535-8
Hardware: Students are advised to bring a laptop to all sessions.
Software:
1.
SPSS software version 13 (or latest)
2.
R – statistical software. Free download from: http://www.r-project.org
3.
PS sample size software. Free download from:
http://www.mc.vanderbilt.edu/prevmed/ps/index.htm
4.
nQuery Advisor 4.0 (recommended but not required)
Examination and Grading:
Homework
Class attendance
Midterm Exam
Final Exam
40%
10%
10%
40%
Course organization (subject to change):
50 min. Lecture + SPSS tutorials
10 min. Break
50 min. Lecture + SPSS tutorials
10 min. Break
60 min. Homework Presentation
Note: Students will form study groups (each consisting 2-3 members) at the 1st day, all
homework projects are recommended to be discussed in groups before presentation.
Course Schedule
Week 1
Wednesday
Feb 1
Thursday
Feb 2
Friday
Feb 3
Week 2
Wednesday
Feb 6
Thursday
Feb 7
Wednesday
Feb 8
Thursday
Feb 9
Friday
Feb 10
Week 3
Monday
Feb 13
Tuesday
Feb 14
Wednesday
Feb 15
Thursday
Feb 16
Friday
Feb 17
Week 4
Monday
Feb 20
Tuesday
Feb 21
Wednesday
Feb 22
Thursday
Feb 23
Friday
Feb 24
Course Introduction (30 min.)
Chapter 3: Comparing 2 means: Paired t-test, Student’s ttest
Chapter 4: Comparing 3+means: One-way Analysis of
Variances, issues of multiple comparisons
Chapter 5: 2 way ANOVA, Concept of effect modification
(interaction) using means
Book Chapters
Kirkwood Sterne 7
Rosner 8
Kirkwood Sterne 9
Rosner 12
Kirkwood Sterne 9
Rosner 12
Chapter 6: Simple Linear Regression
Pearson Correlation / Spearman Correlation
Chapter 7: Relation between Student’s t-test, One-way
ANOVA, Two-way ANOVA with Linear regressions
Chapter 8: Simple Linear Regression: Transformation,
non-linear association in R
Chapter 9: Multiple Linear Regression: Detecting
confounding and interaction
Chapter 10: Multivariable Regression Strategies:
Kirkwood Sterne 10, 12
Rosner 11
Kirkwood Sterne 11
Rosner 11
Kirkwood Sterne 11.5,
12,13
Kirkwood Sterne 11, 18,
29
Katz (entire book)
Kirkwood Sterne 29
Mid-term Exam
Chapter 10: Multivariable Regression Strategies:
Chapter 11: Comparing Two proportions: Measures of
Association in 2 x 2 tables, Relative risk, Odds ratio, Test for
association: Chi-squares / fisher’s exact test
Comparing 3 + proportions: Test for association for R x C
tables, Chi-squares test for linear trend
Chapter 12: Binary Logistic Regression
Katz (entire book)
Kirkwood Sterne 29
Kirkwood Sterne 14, 15,
16, 17, 21, 36
Rosner 10
Chapter 13:
Multivariable Binary Logistic Regression
Multiple 2 x 2 tables: Confounding, Effect modification,
Testing for homogeneity of odds ratios, Mantel-Haenszel tests
Chapter 14: Analysis of two related categorical variables:
Mcnemar test, Conditional logistic regression
Analysis of categorical variable with more than 2 levels:
Proportional Odds Logistic regression
Kirkwood Sterne 18, 20,
29
Rosner 10
Chapter 15: Survival Analysis (1-1): Introduction to
Survival Analysis
Chapter 16: Survival Analysis (1-2): Kaplan-Meier
estimates, Log-rank test model
Chapter 16: Survival Analysis (2): Cox Proportional Hazard
model
Chapter 17: Analysis of Continuous Repeated measures
(1): Paired t-test, ANCOVA, Response Feature Analysis
Chapter 18: Analysis of Continuous Repeated measures
(2): Linear Mixed model
Kirkwood Sterne 26
Rosner 14
Kirkwood Sterne 26
Rosner 14
Kirkwood Sterne 27
Rosner 14
Kirkwood Sterne 31
Kirkwood Sterne 19
Kirkwood Sterne 21
Kirkwood Sterne 31
Week 5
Monday
Feb 27
Tuesday
Feb 28
Review
Final Exam