Survival Analysis was taught Spring 2019 at Rice/GSBS by James Long and Nabihah Tayob. This website is no longer maintained but is available for reference purposes.

Instructor Contact

• name: James Long
• email: jp followed by my last name @mdanderson.org
• office: FCT 4.6082 (Pickens Academic Tower), email me to schedule meeting

Lecture Notes and Reading

Unless otherwise specified, all reading is from “Survival Analysis” by Klein and Moeschberger.

• February 27: Introduction to Cox Proportional Hazards Model
  • Suggested Reading: 8.1 - 8.3 in textbook
  • Lecture Notes html, markdown, R
  • Data Set kirc_small.RData
• March 1: Cox PH Breslow Partial Likelihood, Local and Global Tests
  • Suggested Reading: 8.4 - 8.5 in textbook
  • Lecture Notes html, markdown, R
• March 6: Model Building with Cox PH
  • Suggested Reading: 8.7 - 8.8 in textbook
  • Lecture Notes html, markdown, R
• March 8: Cox PH Regression Diagnostics
  • Suggested Reading: 11.1 - 11.4 in textbook
  • Lecture Notes html, markdown, R
• March 27: TCGA and High Dimensional Inference
  • Suggested Reading
    • Survival analysis with high-dimensional covariates
  • Lecture Notes html
  • TCGA KIRC Data Set
    • Assembling TCGA Data Set zip
    • Resulting R Data File RData
    • EDA with R Data File R
• March 29: Multiple Testing and Regularized Regression
  • Suggested Reading
    • Beta Uniform Mixture Model for Multiple Testing
    • Regularized Cox Models with glmnet
    • Glmnet Examples (see Cox section)
  • Lecture Notes html, markdown
• April 3 - April 5: Tuning Parameter Selection and Measuring Predictive Accuracy of Survival Models
  • Suggested Reading
    • On the C-Statistics for Evaluating Overall Adequacy of Risk Prediction Procedures with Censored Survival Data
  • Lecture Notes html, markdown, R
• April 10: Time Dependent Covariates
  • Suggested Reading: 9.1 - 9.2 in textbook
  • Lecture Notes html, markdown, R
• April 12: Estimation and Regression with Left Truncation
  • Suggested Reading: 4.6 and 9.4 in textbook
  • Lecture Notes html, markdown, R
• April 17: Bayesian Estimation of Discrete Survival Function without Censoring
  • Suggested Reading: 6.4 in textbook
  • Lecture Notes html, markdown, R
• April 19: Bayesian Estimation of Survival with Right Censoring, Metropolis MCMC
  • Lecture Notes html, markdown, R

Homeworks

• HW 4 on Chapter 8 due March 29 (solutions)
• HW 5 on Lectures 5-8 due April 12 (solutions)

Project

The project is due April 30. Project Description