Biostatistical Methods II: Regression Analysis (Biometry 701)
Spring 2009
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 and Stata. Students will be evaluated via homeworks (55%), two in-class exams (35%) and class participation (10%). This is a four credit course.
Textbook: Applied Linear Statistical Models. Kutner, Nachtsheim, Neter and Li. McGraw-Hill, Fifth Edition
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/methods2.2009.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 |
Lectures:
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Date |
Topic |
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Computing | Reading Assignment |
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W Jan 7 |
Introduction to regression; simple linear regression (SLR) |
R code | Ch 1 | |
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M Jan 12 |
no class! Instructor at workshop in MD |
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W Jan 14 |
Linear model properties; software tutorial |
R-intro.pdf (supplemental) | ||
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M Jan 19 |
no class! MLK Jr. Day |
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W Jan 21 |
Linear model properties; software tutorial |
(see Jan 14) |
Ch 2 | |
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M Jan 26 |
Inferences and assumption checking in SLR |
R code | Ch 6 | |
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W Jan 28 |
SLR Diagnostics |
R code | ||
| M Feb 2 | Diagnostics (continued);Correlation; Intro to Multiple Linear Regression | lect5.ppt | R code | Ch 5 |
| W Feb 4 | Hypothesis testing in LR | lect6.ppt | R code | Ch 2, Ch 6 |
| M Feb 9 | MLR | Ch 2, Ch 6 | ||
| W Feb 11 | Forms for predictors | lect7.ppt | R code | Ch 8 |
| M Feb 16 | interactions | lect8.ppt | R code | Ch 7 |
| W Feb 18 | F-tests and ANOVA | lect9.ppt | R code | |
| M Feb 23 | F-tests and Coefficients of Determination | lect10.ppt | R code | Ch 7 |
| W Feb 25 | Multicollinearity | lect11.ppt | R code | Ch 7 |
| M Mar 2 | MLR Model Building | lect12.ppt | R code | Ch 9 |
| W Mar 4 | MLR: final comments | lect13.ppt | R code | Ch 10 |
| M Mar 9 | NO CLASSES: SPRING BREAK! | |||
| W Mar 11 | NO CLASSES: SPRING BREAK! | |||
| M Mar 16 |
no class! Instructor at meeting in TX |
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| W Mar 18 | MLR final comments | (see W Mar 4) | ||
| M Mar 23 | Introduction to logistic regression | lect14.ppt | R code | Ch 14 |
| W Mar 25 | Inference and link functions | lect15.ppt | R code | |
| M Mar 30 | Likelihood ratio tests and deviance | |||
| W Apr 1 | Goodness of fit, Information criteria, | lect16.ppt | R code, Stata do | |
| M Apr 6 | ROC Analysis | (see lect16) | ||
| W Apr 8 | Logistic regression for case control studies | lect17.ppt | ||
| M Apr 13 | Catch up day | |||
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W Apr 15 |
Logistic regression for matched case control studies | class canceled | enjoy doing your taxes! | |
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M Apr 20 |
Introduction to survival data | lect18.ppt |
http://jslhr.asha.org/cgi/reprint/42/2/432 http://www.walkerbioscience.com/pdfs/Survival%20analysis.pdf |
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| W Apr 22 | Survival analysis | lect19.ppt | ||
| M Apr 27 | Cox regression | lect20.ppt | R code | |
| W Apr 29 | Exam 2 |
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/