Biostat 540 Lecture Files -- 2008

General
- Overview of Each Day = a log of what was covered in class (refresh)
- Link to Lecture Material 2007
Week 1
- 01 Apr 2008 Notes: Introduction
- 01 Apr 2008 TLC Data used to illustrate naive analysis
- 01 Apr 2008 tlc-naive-do.txt STATA do file for naive analysis
Week 2
- 08 Apr 2008 Notes: Analysis of CF Data --- Analysis of CF Data using STATA with "derived variable" and mixed model approaches.
- 08 Apr 2008 NewCFkids.data --- example longitudinal data set
- 08 Apr 2008 NewCFkids.txt --- documentation
- 08 Apr 2008 Information on Cystic Fibrosis --- from Mayo Clinic
- 08 Apr 2008 cfkids-do.txt --- STATA code for EDA
- 08 Apr 2008 cfkids-derived-do.txt --- STATA code for derived variable analysis
- 08 Apr 2008 cfkids-lmm-gee-do.txt --- STATA analysis using mixed models and GEE.
- 08 Apr 2008 Link to GLLAMM Information
- 08 Apr 2008 MultiLevel-Glossary.pdf -- an article that lists common terms and provides a brief description for each term.
- 10 Apr 2008 FixedRandomEffects.pdf -- a brief discussion of Fixed and Random effects in a multilevel model.
- 10 Apr 2008 Edwards (2000) -- introduction of mixed model methods for pediatricians!
- 10 Apr 2008 Twiss et al. (2006) -- example of mixed model analysis
- 10 Apr 2008 Schaedel et al. (2002) -- example of mixed model
- 10 Apr 2008 Corey et al. (1997) -- mixed model analysis of CF that incorporated death time.
Week 3
- 15 Apr 2008 Notes: Linear Mixed Models -- methods --- inference and estimation for linear mixed models (S+/R illustration).
- 15 Apr 2008 cfkids-CDA-NewLMM.q --- Analysis of CF Data using S+ / R and lme function
- 15 Apr 2008 Notes: Linear Mixed Models -- SAS --- analysis using SAS, and comparison of different covariance matrices.
- 15 Apr 2008 cfkids-sas.txt --- SAS code for regression analysis
- 17 Apr 2008 NewCFkids-SAS.data --- data to read in to SAS for regression analysis
- 17 Apr 2008 Link to some UW SAS training documents -- thanks Caleb!!!
- 17 Apr 2008 Link to PROC MIXED example from SAS
- 17 Apr 2008 Link to SAS documentation -- then search for "MIXED" -- thanks Tanya!!!
- 17 Apr 2008 Littell, Pendergast, and Natarajan (2000) -- Tutorial paper on covariance models and SAS
Week 4
- 22 Apr 2008 Notes: Mean Models
- 22 Apr 2008 tlc-raw.txt -- TLC Data -- example of balanced longitudinal data.
- 22 Apr 2008 tlc.txt -- Documentation for the TLC data
- 22 Apr 2008 General description of the TLC study
- 22 Apr 2008 Press release about TLC study
- 22 Apr 2008 Background information on chelation
- 22 Apr 2008 tlc-sas.txt -- SAS analysis file for the TLC data
- 22 Apr 2008 tlc-lst.txt -- SAS output, with the addition of separate covariance matrices for the two treatment groups.
- 24 Apr 2008 Fitzmaurice (2001) "A Conundrum in the Analysis of Change"
- 24 Apr 2008 Fitzmaurice (2000) "Regression to the Mean"
Week 5
- 29 Apr 2008 tlc-do.txt STATA analysis file for TLC data (pre-post analyses)
- 29 Apr 2008 DiagraExample.q S+/R file for generating the Diagra example data.
- 29 Apr 2008 GroupTime-Sim.q S+/R file for simulations that compare OLS and WLS estimators in terms of their mean and variance.
- 01 May 2008 TopekaFEV1.raw Topeka FEV1 data
- 01 May 2008 TopekaFEV1.txt Topeka FEV1 documentation
- 01 May 2008 TopekaFEV1-do.txt STATA analysis file for Topeka FEV1 data
- 01 May 2008 TopekaFEV1-sas.txt example of SAS program
- 01 May 2008 TopekaFEV1-lst.txt SAS output file (run on mead)
- 01 May 2008 TopekaFEV1-plots-do.txt STATA analysis file for Topeka FEV1 data
Week 6
- 01 May 2008 Notes: Categorical Data and GEE
- 01 May 2008 HivnetWide.raw HIVNET Informed Consent data
- 01 May 2008 HivnetWide.txt HIVNET Informed Consent Data -- Documentation
- 01 May 2008 Coletti-2003JAIDS.pdf published analysis of knowledge items
- 06 May 2008 HivnetIC-do.txt STATA Analysis file
- 06 May 2008 HivnetIC-sas.txt SAS Analysis file
- 08 May 2008 vonEhrenstein (2006) AJE -- Example GEE analysis
- 08 May 2008 Dobkin (2006) J CLin Pain -- Example GEE analysis
- 08 May 2008 Savitz (2006) Epidemiology -- Example GEE analysis
- 08 May 2008 ThallWide.raw Seizure data
- 08 May 2008 thallGEE-do.txt STATA analysis file
- 08 May 2008 Hanley-2003AJE.pdf -- discussion of GEE ideas (weighted estimation) for epidemiologists
Week 7
- 13 May 2008 Notes: Missing Data
- 15 May 2008 panss-sas.txt -- SAS file for the analysis of the PANSS data. This shows both different choices for the covariance model, and linear and dummy variable models for the mean.
- 13 May 2008 panss-lst.txt -- SAS results.
- 15 May 2008 Niaua et al. (2002) ----- paper that illustrates use of pattern mixture models.
  - Table 5 (Results)
- 15 May 2008 Leon et al. (2006) ----- paper that overviews issues/methods for data with attrition.
- 15 May 2008 panss-ipw.do ----- STATA "do" file for analysis of PANSS data using inverse probability weights (IPW).
- 15 May 2008 panss-ipw.log ----- STATA log file showing analysis results.
Week 8
- 20 May 2008 Dufouil-Neurology200.pdf -- article that nicely discusses their use of inverse probability weighting to handle drop-out
- 20 May 2008 panss-pmm.do ----- STATA "do" file for analysis of PANSS data using pattern mixture model (PMM).
- 20 May 2008 panss-pmm.log ----- STATA log file showing analysis results.
- 20 May 2008 Notes: Generalized Linear Mixed Models
- 20 May 2008 HivnetIC-glmm-do.txt --- STATA analysis file for conditional logistic regression and GLMM.
- 20 May 2008 hivnet-sas.txt --- SAS analysis file for GEE and GLMM.
- 20 May 2008 hivnet-lst.txt --- SAS output.
- 20 May 2008 Pebley-Demography1996.pdf -- article that uses multi-level logistic regression
- 20 May 2008 StatisticalIssues.pdf -- tutorial that uses multi-level logistic regression to estimate hospital-specific random effects after adjusting for the patient case-mix.
Week 9
- 27 May 2008 MultiLevel.pdf Notes: Multi-Level Models
- 27 May 2008 MultiLevel-Glossary.pdf -- article that explains terms commonly used.
- 27 May 2008 DiezRoux-EpiRev.pdf -- recent review article that discusses major issues.
- 27 May 2008 Kinmonth-BMJ1998.pdf -- article that discusses community randomized trials that we analyze in lecture notes (data and programs below).
- 27 May 2008 sheff.raw -- data.
- 27 May 2008 sheffield-stata9-do.txt -- STATA analysis file.
- 27 May 2008 sheffield-sas.txt -- SAS analysis file.
- 27 May 2008 Singer-JEBS1998.pdf -- article that discussess SAS PROC MIXED and multilevel models.
- 27 May 2008 Kahn-NEJM2006.pdf -- example multilevel analysis evaluating hospital volume and patient outcomes.
Week 10
- 03 June 2008 Notes: Time-dependent Covariates
- 03 June 2008 Bodnar-2004AJE.pdf -- article that overviews and illustrates the use of marginal structural models for analysis of longitudinal data with time-dependent confounding.
- 03 June 2008 Mortimer-2002EurRespJ.pdf -- article that uses distributed lag models for longitudinal analysis of the effect of pollution on asthmatic children(!)
- 03 June 2008 Bell-2004JAMA.pdf -- article that uses both single lag and distributed lag models for mortality count time series analysis of pollution effects.