Biostat 537 Lecture Files -- 2009

LINK TO LECTURE VIDEO/AUDIO ---- Click Here

• General
  • Overview of Each Day = a log of what was covered in class (refresh)

  • Lecture Web Page from 2006 = a look at what was covered in 2006

• Week 1
  • 06 Jan 2009 Notes: Introduction 1 -- Longitudinal Studies

  • 06 Jan 2009 Notes: Introduction 2 -- Survival Data

  • 08 Jan 2009 Notes: One Sample Summaries

  • 08 Jan 2009 Herpes.raw Example Data.
  • 08 Jan 2009 Herpes.doc Data Documentation.
  • 08 Jan 2009 Published Article ----- details of the study and primary results.

  • 08 Jan 2009 HerpesDiscrete-do.txt STATA Do File
  • 08 Jan 2009 HerpesParametric-do.txt STATA Do File
  • 08 Jan 2009 HerpesKM-do.txt STATA Do File

• Week 2
  • 13 Jan 2009 Notes: Testing Survival Curves (updated on 20 Jan 2009)

  • 13 Jan 2009 HerpesLogRank-do.txt STATA Do file

  • 15 Jan 2009 LogRankSim.q -- an S+/R file to simulate data and evaluate various 2-sample tests.

  • 15 Jan 2009 Kernel Density Estimator -- discussion, and links to both an applet showing the estimate of a density function, with different bandwidths and/or kernels, and an on-line (using R) calculator (SEE end of section).

• Week 3
  • 20 Jan 2009 Notes: Intro to Cox Regression

  • 20 Jan 2009 HerpesCoxRegn-do.txt STATA Do file

  • 22 Jan 2009 Notes: Cox Regression Summaries and Stratified Cox Regression

  • 22 Jan 2009 HerpesCoxS0-do.txt -- STATA do file
  • 22 Jan 2009 HerpesCoxStrata-do.txt -- STATA do file

• Week 4
  • 27 Jan 2009 Midterm (in-class) 2008 -- some example questions for QUIZ (Note: some topics in this example we have not done yet since the 2008 midterm was later than our first 2009 quiz)
  • 27 Jan 2009 QUIZ Hand-out of Formulae -- this will be handed out with the QUIZ next week.

  • 27 Jan 2009 Midterm (take home) Exam 2006 -- an example of the take-home midterm exam
  • 27 Jan 2009 ColonDoc.txt -- documentation
  • 27 Jan 2009 ColonData.txt -- data
  • 27 Jan 2009 comments on midterm -- updated comments as needed.
    • 27 Jan 2009 Master List of Comments for Midterms

    • 27 Jan 2009 NEJM article that presents these results (approx)

    • 27 Jan 2009 Example Student Analysis -- (1)
    • 27 Jan 2009 Example Student Analysis -- (2)
    • 27 Jan 2009 Example Student Analysis -- (3)

  • 27 Jan 2009 Friberg et al. (1997) -- some comments on Analysis and Reporting

  • 29 Jan 2009 Notes: Competing Risks

  • 29 Jan 2009 Veronesi et al. (1995) -- article that presents analysis of competing risks

  • 29 Jan 2009 cmprsk.pdf -- documentation / description of S+/R package to create cumulative incidence curves.

  • 29 Jan 2000 stcompet -- Stata module to estimate cumulative incidence.
  • 29 Jan 2009 Coviello (2004) STATA Journal -- paper that describes cumulative incidence estimation using STATA

• Week 5
  • 03 Feb 2009 Notes: Left Truncation

  • 03 Feb 2009 nickel-do.txt -- STATA example analysis.
  • 03 Feb 2009 nickel.raw -- Example data.
  • 03 Feb 2009 Kaldor-JNCI1986.pdf -- published analysis of cohort.

  • 05 Feb 2009 BreslowDay-nickel.pdf -- Breslow & Day's presentation of nickel refiners analysis.
  • 05 Feb 2009 Korn-AJE1997.pdf -- an Am J Epi paper discussing choice of time scales.

  • 05 Feb 2009 Notes: Checking PH Assumption

  • 05 Feb 2009 HerpesPHcheck-do.txt -- STATA example analysis.

  • 05 Feb 2009 addicts-do.txt -- STATA example analysis.
  • 05 Feb 2009 addicts.raw -- Example data.

• Week 6
  • 10 Feb 2009 Notes: Time-dependent Covariates

  • 10 Feb 2009 HerpesTVC-do.txt ---- STATA example using herpes data

  • 10 Feb 2009 Sears (2008) J. Occ. Rehab. ---- papers that uses "tvc" idea to synthesize analysis of work-loss duration (J. Sears was 2006 student!)

  • 10 Feb 2009 heart-do.txt ---- STATA example using time-dependent covariate.
  • 10 Feb 2009 heart.raw ---- Data

  • 12 Feb 2009 heart2-do.txt ---- STATA example using START and STOP times for the multiple records per person.

• Week 7
  • 17 Feb 2009 Scribner-CancerResearch1983.pdf -- example presented in the notes on pp. 423--431.

  • 17 Feb 2009 Notes: Model Specification and Checking

  • 17 Feb 2009 mayo-do.txt ---- STATA example analysis of Mayo PBC data
  • 17 Feb 2009 mayo.raw ---- Mayo PBC data

  • 19 Feb 2009 Hernan (2000) Epidemiology ---- article about time-dependent covariates and marginal structural models.

• Week 8
  • 24 Feb 2009 Notes: Predictive Models

  • 24 Feb 2009 mayoAIC-do.txt ---- STATA example analysis of Mayo PBC data
  • 24 Feb 2009 mayoROC-do.txt ---- STATA example analysis of Mayo PBC data

  • 26 Feb 2009 Final (in-class) 2005
  • 26 Feb 2009 QUIZ Hand-out of Formulae -- this will be handed out with the QUIZ.

• Week 9
  • 03 Mar 2009 Notes: Alternative Epidemiologic Designs

  • 03 Mar 2009 Essebag-2003AmHeartJ.pdf ---- article that overviews nested case-control designs, and comments on case-cohort designs.
  • 03 Mar 2009 Wacholder-1991Epidemiology.pdf ---- article that compares nested case-control and case-cohort designs in terms of practical issues.

  • 03 Mar 2009 McShane-JClinOnc2005.pdf ---- article that gives analysis / presentation guidelines for evaluating prognostic tumor markers.

  • 05 Mar 2009 Notes: Intro Poisson Regression

  • 05 Mar 2009 thall-do.txt ---- STATA code for the analysis of the seizure treatment trial data.
  • 05 Mar 2009 ThallWide.raw ---- Progabide and Seizures data

• Week 10
  • 10 Mar 2009 Notes: Poisson Regression and Grouped Survival Data

  • 10 Mar 2009 mayoPoisson-do.txt ---- analysis of Tx for the Mayo PBC Data
  • 10 Mar 2009 MayoTimeDepData.raw ---- Mayo PBC Data expanded into multiple time periods per subject

  • 12 Mar 2009 Notes: Grouped Survival Data -- Montana Example

  • 12 Mar 2009 montana-do.txt ---- analysis of the Montana Smelter Data

  • 12 Mar 2009 Arsenic deposition in the Puget Sound