Biostatistical Methods II: Regression Analysis (Biometry 701)
Spring 2010
Description: This is a one-semester course intended for graduate students pursuing degrees in biostatistics and related fields such as epidemiology and bioinformatics. Topics covered will include linear, logistic, poisson, and Cox regression. Estimation, interpretation, and diagnostic approaches will be discussed. Software instruction will be provided in class in R. Students will be evaluated via homeworks (55%), two exams (35%) and class participation (10%). This is a four credit course.
Textbooks:
(1) Introduction to Linear Regression Analysis (4th Edition). Montgomery, Peck and Vining. Wiley; New York, 2006.
(2) Regression with Modeling Strategies: With Applications to Linear Models, Logistic Regression, and Survival Analysis. Frank E. Harrell, Jr. Springer; New York, 2001.
Prerequisites: Biometry 700
Course Objectives: Upon successful completion of the course, the student will be able to
1. Apply, interpret and diagnose linear regression models
2. Apply, interpret and diagnose logistic, poisson and Cox regresssion models
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Instructor: |
Elizabeth Garrett-Mayer |
| Website: | http://people.musc.edu/~elg26/teaching/methods2.2009/methods2.2010.htm |
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Contact Info: |
Hollings Cancer Center, Rm 118G |
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garrettm@musc.edu (preferred mode of contact is email) |
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792-7764 |
| Time: | Mondays and Wednesdays, 1:30-3:30 |
| Location: | Cannon 301, Room 305V |
| Office Hours: | Thursdays 10:30-Noon |
Lectures:
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Date |
Topic |
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Computing | Readings |
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W Jan 6 |
Introduction to regression; simple linear regression (SLR) |
R code | MPV 1, 2.1-2.2; Harrell 1 | |
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M Jan 11 |
Linear model properties; software tutorial |
Harrell 6; R-intro.pdf (supplemental) | ||
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W Jan 13 |
Inferences and assumption checking in SLR |
R code | MPV 2.2, 2.3, 2.5; Harrell 9 | |
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M Jan 18 |
no class! MLK Jr. Day |
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W Jan 20 |
SLR Diagnostics |
R code | MPV 2.4, 2.5, 4.1, 4.2 | |
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M Jan 25 |
Diagnostics (continued);Correlation; Intro to Multiple Linear Regression | lect5.ppt | R code | MPV 3.1, 4.4, 5 |
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W Jan 27 |
Hypothesis testing in MLR | lect6.ppt | R code | MPV 4.2.4; Harrell 2.1-2.2 |
| M Feb 1 | MLR | (lect6 continued) | ||
| W Feb 3 | Forms for predictors | lect7.ppt | R code | MPV 7, 8; Harrell 2.3-2.4 |
| M Feb 8 | interactions | lect8.ppt | R code | Harrell 2.3 |
| W Feb 10 | F-tests and ANOVA | lect9.ppt | R code | MPV 2.3.3, 4.5; Harrell 2.7 |
| M Feb 15 | F-tests and Coefficients of Determination | lect10.ppt | R code | MPV 3.3, 2.6 |
| W Feb 17 | Multicollinearity | lect11.ppt | R code | MPV 11 |
| M Feb 22 | MLR Model Building | lect12.ppt | R code | MPV 9, 10; Harrell 4 |
| W Feb 24 | MLR: continued | lect13.ppt | R code | MPV 4.2.4, 6 |
| M Mar 1 | MLR: example (Harrell Ch 7) | Harrell 7 | ||
| W Mar 3 | Exam 1 | |||
| M Mar 8 | NO CLASSES: SPRING BREAK! | |||
| W Mar 10 | NO CLASSES: SPRING BREAK! | |||
| M Mar 15 | MLR validation, bootstrap | |||
| W Mar 17 | Introduction to logistic regression; link functions | lect14.ppt | R code | MPV 14.1-14.2; Harrell 10.1 |
| M Mar 22 | Likelihood ratio tests and deviance | lect15.ppt | R code | Harrell 10.2-10.4 |
| W Mar 24 | Goodness of fit, Information criteria, ROC analysis | lect16.ppt | R code, Stata do | Harrell 10.3-10.9 |
| M Mar 29 | Logistic regression for case control studies | lect17.ppt | ||
| W Mar 31 | Logistic regression example | Harrell 11 or 12 | ||
| M Apr 5 | Ordinal logistic regression | Harrell 13.1-13.3 | ||
| W Apr 7 | Introduction to survival data | lect18.ppt | Harrell 16.1, 16.2 http://jslhr.asha.org/cgi/reprint/42/2/432 http://www.walkerbioscience.com/pdfs/Survival%20analysis.pdf | |
| M Apr 12 | Survival analysis | lect19.ppt | Harrell 16.5 | |
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W Apr 14 |
Cox regression | lect20.ppt | R code | Harrell 17.2 |
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M Apr 19 |
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| W Apr 21 | ||||
| M Apr 26 |
Datasets:
Ischemic Heart Disease: IschemicHeartDisease.csv
Prostate Cancer Dataset: Prostate.csv (codebook: prostate.txt)
ICU dataset: icu.csv (codebook: icu.txt)
Kidney Dialysis: kidneydialysis.csv
Homeworks:
Homework 1.pdf Due Mon 01/26/09
Homework2.doc Due Wed 02/04/09
homework3.doc Due Wed 02/18/09
homework4.doc Due Fri 03/06/09
homework5.doc Due Wed 04/08/09
homework6.doc Due Mon 04/20/09
homework7.doc Due Wed 04/29/09
EXAMS:
exam1.doc Due Mon 03/09/09
Articles:
gillison.pdf: Case control study of HPV16 and Oropharyngeal Cancer
hanley&mcneill.pdf: Comparing AUCs for ROC curves based on the same data
chaves.pdf: Nomograms for mobility disability
Computing:
R website: http://cran.r-project.org/
R tutorial: R-intro.pdf
Stata website: http://www.stata.com/