Biometry 711: Categorical
Data Analysis
Summer 2015
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Instructor |
Elizabeth G Hill |
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Office |
118F Hollings
Cancer Center |
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Phone |
876-1115 |
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Email |
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Class schedule |
Monday and
Wednesday, 1pm - 3pm |
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Class dates |
Wednesday May 13th
- Wednesday July 29th |
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Location |
135 Cannon Place,
Room 301 |
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Website |
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Instructor Office
Hours |
By appointment |
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Teaching Assistant |
Chawarat
Rotejanaprasert |
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TA Email |
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TA Office Hours |
By appointment |
Text: Categorical Data
Analysis, Third Edition, Alan Agresti, John Wiley & Sons,
2013. ISBN 978-0-470-46963-5
Course Description: Biometry 711 (Categorical Data Analysis) covers the theoretical
underpinnings and analysis methods for categorical and discrete data. The tentative course outline includes
topics from: Chapters 1 - 3 (contingency tables analysis and inference);
Chapters 4 - 7 (logistic regression and alternative modeling approaches for
binary data); Chapter 8 (models for multinomial response data); and Chapter 11
(models for matched pairs data). Additional topics may be added, time
permitting.
Grading: There will be four
homework assignments, each worth 12.5% of your grade. In lieu of exams, there
will be two projects. The first project will be worth 20% of your grade. The
final project will be worth 30% of your grade. Late homework is accepted, but
at a penalty. Homework turned in late on the day it is due receives 3/4 credit.
Homework turned in late the day after it is due receives 1/2 credit. Homework
turned in two days after it is due receives 1/4 credit. Homework more than two
days late receives no credit. Additional information about the projects will be
distributed at a later time. Currently, I anticipate the first project will be
assigned in mid-June and due in early July. The final project will be assigned
at the completion of the course and will serve as the course's capstone
project.
Important Dates:
Monday, May 25th, Memorial Day - No Class
Monday, June 29th - No Class
Friday, August 14th - Final Project due
CGS academic calendar - http://academicdepartments.musc.edu/esl/em/records/forms/11_calendar_13-18.pdf
CDA website: http://www.stat.ufl.edu/~aa/cda/cda.html
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Day |
Date |
Topic |
Text References |
Handouts |
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W |
May 13th |
Introduction |
CDA 1.1, 1.2 |
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M |
May 18th |
Introduction (cont.) |
CDA 1.3, 1.4 |
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W |
May 20th |
Introduction (cont.) |
CDA 1.5, 16.6 |
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M |
May 25th |
Describing Contingency Tables |
CDA 2.1, 2.2 |
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|
W |
May 27th |
Describing Contingency Tables (cont.) |
CDA 2.3, 2.4 |
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M |
June 1st |
Inference for two-way tables |
CDA 3.1, 3.2 |
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|
W |
June 3rd |
Inference for two-way tables (cont.) |
CDA 3.3, 3.4 |
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M |
June 8th |
Inference for two-way tables (cont.); GLM introduction |
CDA 3.5, 4.1 - 4.3 |
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W |
June 10th |
Fitting the GLM - IRWLS |
CDA 4.4, 4.6 |
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M |
June 15th |
Fitting the GLM - Fisher Scoring; Review of logistic regression |
CDA Chapter 5 |
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W |
June 17th |
GLM GOF - Deviance; Grouped and ungrouped logistic regression |
CDA 4.5 |
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M |
June 22nd |
GLM GOF - HL test, ROC curves, residual analysis |
CDA 5.2, 6.2, 6.3 |
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W |
June 24th |
Assessing linearity in the logit, multivariable fractional
polynomials |
|
Dichotomizing
continuous variables in regression, SIM article, 2006 Royston and Altman
fractional polynomials JRSSC paper, 1994 Sauerbrei et al. comparison
of FP software CSDA article, 2006 R documentation
for mfp library Assessing linearity in the logit for logistic regression and use
of fractional polynomials (R) |
|
W |
July 1st |
AIC, Pearson/Deviance residuals and diagnostic plots,
Quasi-complete separation |
CDA 6.1.6, 4.5.6, 6.2, 6.5 |
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PROJECT 1 - Due Monday July 20th |
||||
|
M |
July 6th |
Poisson Regression, Overdispersed
models for count data - Quasi-likelihood and Negative Binomial models |
CDA 4.2, 4.7, 14.4 |
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|
W |
July 8th |
Zero-inflated models - Hurdle models, ZIP models and ZINB models |
Guest lecture by Dr. Neelon |
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M |
July 13th |
High Throughput Sequencing (HTS) Data Analysis |
Guest lecture by Dr. Chung |
Nucleic Acids
Research article |
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W |
July 15th |
Generalized logit models |
CDA 8.1 |
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|
M |
July 20th |
Proportional odds models |
CDA 8.2 |
Low birthweight data codesheet Low birthweight data (sas7bdat) |
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W |
July 22nd |
Quasi-likelihood theory |
CDA 12.2, 12.3 |
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F |
July 24th |
GEE theory |
CDA 12.2, 12.3 |
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M |
July 27th |
GEE applications |
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|
|
W |
July 29th |
GEE GOF |
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PROJECT 2 - Due Monday August 17th, 9AM |
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References
1.
An Introduction to
Categorical Data Analysis, Second Edition. A. Agresti. John Wiley & Sons, 2007.
2.
Analysis of Ordinal
Categorical Data, Second Edition. A. Agresti.
John Wiley & Sons, 2010.
3.
Statistical Methods
for Rates and Proportions, Third Edition. J. Fleiss, B.
Levin and M.C. Paik. John Wiley & Sons, 2003.
4.
Applied Logistic
Regression, Third Edition. D.W. Hosmer, S. Lemeshow and R.X. Sturdivant. John Wiley & Sons, 2013.
5.
Regression Modeling
Strategies. F.E. Harrell. Springer-Verlag, 2001.
6.
Generalized Linear
Models, Second Edition. P. McCullagh
and J.A. Nelder. Chapman & Hall, 1989.
7.
The Statistical
Evaluation of Medical Tests for Classification and Prediction. M.S. Pepe. Oxford
University Press, 2003.
8.
The Elements of
Statistical Learning, Second Edition. T. Hastie, R. Tibshirani and J. Friedman. Springer-Verlag,
2009.