Stats 112/203 - Spring 2013

Stats 112/203: Statistical Methods for Data Analysis III

Spring 2013

Department of Statistics

University of California, Irvine

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Course Syllabus
Instructor and Class Information
R References
Data Sets Used in Class and on Homework
Class Calendar: Material covered, handouts, and homework assignments by day
Homework Solutions

Course Syllabus

Download the course syllabus here.

Grade Dispute Form: You must print and fill out this cover sheet (pdf) and attach the homework/exam in dispute in order for your grade to be reconsidered. Please read the instructions on the cover sheet carefully.

Additional textbook references:

The following books are free to download on link.springer.com if you're accessing it on UCI campus:

Kleinbaum, D.G. and Klein, M. Survival Analysis: A Self-Learning Text, 3rd ed. Springer, 2012.
Pinheiro, J.C. and Bates, D.M. Mixed-Effects Models in S and S-PLUS. Springer, 2000.

Instructor and Class Information

Lecture: Mon/Wed/Fri 2:00-2:50pm ICS 180
Lab: Fri 4:00-4:50pm ICS 180

Instructor

Stacey Hancock, PhD

Office: 2204 DBH

Phone: (949) 824-9795

Email: stacey.hancock_at_uci.edu

Office Hours:
Monday 9-10:30am (Stats 7 students given preference)
Wednesday 9-10:30am (Stats 120C students given preference)
Thursday 2-3:30pm (Stats 112/203 students given preference)
Also available by appointment.

Please email the instructor only for personal questions. Post all questions about course material, homework, exams, etc. on our EEE MessageBoard: https://eee.uci.edu/boards/s13/stats112-203

R References

Download and Install R:
The R Project for Statistical Computing
R for Windows FAQ
R for Mac FAQ

Quick R References:
Jones R Reference Page
Short R Reference Card

Online R Tutorials and Documentation:
R FAQ
R Wiki
An Introduction to R (pdf) (html)
Verzani Simple R Notes

R Books: The following two books are free to download on link.springer.com if you're accessing it on UCI campus:

A Beginner's Guide to R by Alain F. Zuur, Elena N. Ieno, and Erik Meesters; Springer, 2009.
Introductory Statistics with R by Peter Dalgaard; Springer, 2008.

Data Sets

You can download data sets from the textbook here.

Anorexia Data (copy and paste into R) (Lecture 1 Notes)
Twisk Hypothetical Test Score Data (April 5 Lab)
Autism Data, Oti et al., 2006 (Lecture 3 Notes)
AML Study, Embury et al., 1977 (May 17 Lab)
Kidney Transplant Data (Lecture 15 Notes) - Stata format
Depression Data (Final Exam)

Class Calendar

This calendar will be updated after each class. Check back periodically for required reading, additional handouts and references, homework assignments, and lecture notes.

Date	Material Covered and Required Reading (Tentative schedule; may be updated after each class)	Date HW Due	Assignment
Week 1:
Mon. Apr. 1	Lecture 1 Notes Lecture 1 PPT Slides Review syllabus; Overview of longitudinal data. FLW: Chapters 1 & 2, Appendix A R Code for Anorexia data
Wed. Apr. 3	Lecture 2 Notes More on covariance/correlation, repeated measures ANOVA, multivariate normal distribution. FLW: Chapter 3, Sections 3.1-3.2, 3.6 (rANOVA section)
Fri. Apr. 5	Finish Lecture 2 notes.	Mon. Apr. 15	Homework #1
Discussion	Introduction to longitudinal data manipulation in R FLW: Chapter 3, Section 3.3
Week 2:
Mon. Apr. 8	Lecture 3 Notes Ordinary and generalized least squares, maximum likelihood and restricted maximum likelihood estimation, statistical inference, modeling the mean and covariance. FLW: Chapter 4, Sections 4.1-4.2, 4.4-4.5; Brief overview of Chapters 5-6.
Wed. Apr. 10	Finish Lecture 3 notes. R Code for fitting mean models to Autism data
Fri. Apr. 12	Lecture 4 Notes Variance structures; start linear mixed models. FLW: Brief overview of Chapter 7. Start Chapter 8.
Discussion	No discussion this week.
Week 3:
Mon. Apr. 15	Lecture 5 Notes Linear mixed models. FLW: Chapter 8, Sections 8.1-8.3 and 8.5-8.8.	Tue. Apr. 22	Homework #2 FLW Problem 8.1
Wed. Apr. 17	Finish Lecture 5 Notes with dental data example. Lecture 6 Notes R Code for Pinheiro and Bates dental data
Fri. Apr. 19	Finish Lecture 5 and Lecture 6 Notes.
Discussion	More with the nlme R library and the lme function. R Code for fitting LMEs to Autism data R Session from discussion
Week 4:
Mon. Apr. 22	Finish Lecture 6 Notes. Lecture 7 Notes Residual diagnostics for mixed effects models. FLW: Chapter 10, Sections 10.1-10.3 and 10.5-10.7. R Code for MIT Growth and Development Study (updated Apr. 24)
Wed. Apr. 24	Continue Lecture 7 Notes. R Session from lecture
Fri. Apr. 26	Finish Lecture 7 notes on residuals diagnostics. R Session from lecture	Fri. May 3	Homework #3 FLW Problems 8.2 and 10.1
Discussion	No discussion this week. Prof. Hancock will have office hours during discussion time.
Week 5:
Mon. Apr. 29	Lecture 8 Notes Start generalized linear mixed effects models (GLMMs). FLW: Chapter 14, Sections 14.1-14.2. How to deal with convergence issues with lme function in R
Wed. May 1	Lecture 9 Notes Lecture 9 Slides Interpreting GLMM coefficients. FLW: 14.3, 14.7. R code for Epilepsy Case Study (p. 421-427) R session from lecture
Fri. May 3	Lecture 10 Notes Lecture 10 Slides Marginal models and generalized estimating equations (GEEs). R code for Epilepsy study with GEEs	Wed. May 8	Homework #4 FLW Problem 14.1
Discussion	Fitting GLMMs and GEEs in R.
Week 6:
Mon. May 6	Finish Lecture 10 notes and slides on GEEs.
Wed. May 8	Lecture 11 Notes (Revised May 8) Start survival data analysis - change to Collett book! Collett: Chapter 1; Chapter 2, Section 2.1 Additional References for survival analysis in R: David Diez: Survival Analysis in R Chapter 14 of Dalgaard's Introductory Statistics with R (download for free if on UCI network) Comprehensive summary of R packages for survival analysis
Fri. May 10	Midterm Exam (SOLUTIONS) Midterm Exam Practice Problems (Solutions)
Discussion	No discussion this week.
Week 7:
Mon. May 13	Continue Lecture 11 Notes.
Wed. May 15	Finish Lecture 11 Notes. Lecture 12 Notes (updated May 17) Lecture 12 Slides Collett: Chapter 2, Sections 2.2, 2.4-2.5 R example with Life Tables	Wed. May 22	Homework #5
Fri. May 17	Life Table example from Lecture 12 Notes Lecture 13 Notes Collett: Chapter 2, Sections 2.6-2.8
Discussion	Survival Analysis in R
Week 8:
Mon. May 20	Finish Lecture 13 Notes. Lecture 14 Notes Collett: Chapter 3, Sections 3.1-3.3
Wed. May 22	Finish Lecture 14 Notes. Lecture 15 Notes Collett: Chapter 3, Sections 3.4-3.5 R code for Kidney Transplant example	Wed. May 29	Homework #6
Fri. May 24	Finish Kidney Transplant example from Lecture 15 Lecture 16 Notes Lecture 16 Slides Collett: Chapter 2, Section 2.3; Chapter 3, Sections 3.6-3.8; Chapter 4, Section 4.4
Discussion	Make-up Week 10 Lecture
Week 9:
Mon. May 27	Memorial Day Holiday: No class or office hours
Wed. May 29	Lecture 17 Slides Lecture 17 Notes Collett: Chapter 5 R code for parametric model with Kidney data
Fri. May 31	Lecture 18 Notes Lecture 18 Slides Collett: Chapter 5; Chapter 11, Sections 11.1-11.2 R code for limitations of log-cumulative hazard plots		Take-home final exam handed out at the end of lecture.
Discussion	Make-up Week 10 Lecture
Week 10:	Prof. Hancock will be in Vietnam all of Week 10
Mon. June 3	No class.
Wed. June 5	No class.
Fri. June 7	No class.
Discussion	No discussion.
Final Exam: Due Mon. June 10 by 12pm	The final exam is take-home and comprehensive, due by 12:00pm on Monday, June 10. Final Exam Solutions

Homework Solutions

Homework solutions will be posted the evening homework is due (or early the next morning).

Homework Assignment	Solutions
Homework #1	Homework #1 Solutions
Homework #2	Homework #2 Solutions
Homework #3	Homework #3 Solutions
Homework #4	Homework #4 Solutions
Homework #5	Homework #5 Solutions
Homework #6	Homework #6 Solutions