Biostat 540 Lecture Files -- 2018

General
- Overview of Each Day = a log of what was covered in class (refresh)
Outlines
Week 1
- 27 Mar 2018 Notes: Introduction
- 29 Mar 2018 Additional diagrams for notes
- 29 Mar 2018 TLC Data used to illustrate naive analysis
- 29 Mar 2018 tlc-naive-do.txt STATA do file for naive analysis
- 29 Mar 2018 Two Lines with Annotation for LMM
Week 2
- 03 Apr 2018 Notes: Analysis of CF Data --- Analysis of CF Data using STATA with "derived variable" and mixed model approaches.
- 03 Apr 2018 NewCFkids.data --- example longitudinal data set
- 03 Apr 2018 NewCFkids.txt --- documentation
- 03 Apr 2018 Information on Cystic Fibrosis --- from Mayo Clinic
- 03 Apr 2018 --- R Analysis and Results
  - R-CFdataAnalysis-R.txt
  - R-CFdataAnalysis.html
- 03 Apr 2018 --- STATA Analysis and Results
  - cfkids-do.txt --- STATA code for EDA
  - cfkids-derived-do.txt --- STATA code for derived variable analysis
  - cfkids-lmm-gee-do.txt --- STATA analysis using mixed models and GEE.
  - Link to GLLAMM Information
- 03 Apr 2018 MultiLevel-Glossary.pdf -- an article that lists common terms and provides a brief description for each term.
- 05 Apr 2018 FixedRandomEffects.pdf -- a brief discussion of Fixed and Random effects in a multilevel model.
- 05 Apr 2018 Edwards (2000) -- introduction of mixed model methods for pediatricians!
- 05 Apr 2018 French and Heagerty (2008) -- tutorial on longitudinal analysis of policy change
- 05 Apr 2018 Twiss et al. (2006) -- example of mixed model analysis
- 05 Apr 2018 Schaedel et al. (2002) -- example of mixed model
- 05 Apr 2018 Corey et al. (1997) -- mixed model analysis of CF that incorporated death time.
Week 3
- 10 Apr 2018 Notes: Linear Mixed Models -- methods --- inference and estimation for linear mixed models (S+/R illustration).
- 10 Apr 2018 Notes: Linear Mixed Models -- R --- analysis using R, and comparison of different covariance matrices.
- 10 Apr 2018 --- Analysis of CF Data using R and lme function
  - cfkids-CDA-NewLMM.q -- R analysis file
  - cfkids-CDA-NewLMM-out.txt -- Results
- 10 Apr 2018 Notes: Linear Mixed Models -- SAS --- analysis using SAS, and comparison of different covariance matrices.
- 10 Apr 2018 cfkids-sas.txt --- SAS code for regression analysis
- 12 Apr 2018 NewCFkids-SAS.data --- data to read in to SAS for regression analysis
- 12 Apr 2018 Link to some UW SAS training documents -- thanks Caleb!!!
- 12 Apr 2018 Link to SAS documentation -- then search for "MIXED" -- thanks Tanya!!!
- 12 Apr 2018 Littell, Pendergast, and Natarajan (2000) -- Tutorial paper on covariance models and SAS
Week 4
- 17 Apr 2018 Notes: Mean Models
- 17 Apr 2018 tlc-raw.txt -- TLC Data -- example of balanced longitudinal data.
- 17 Apr 2018 tlc.txt -- Documentation for the TLC data
- 17 Apr 2018 General description of the TLC study
- 17 Apr 2018 Background information on chelation
- 17 Apr 2018 tlc-sas.txt -- SAS analysis file for the TLC data
- 17 Apr 2018 tlc-lst.txt -- SAS output, with the addition of separate covariance matrices for the two treatment groups.
- 19 Apr 2018 Fitzmaurice (2001) "A Conundrum in the Analysis of Change"
- 19 Apr 2018 Fitzmaurice (2000) "Regression to the Mean"
Week 5
- 24 Apr 2018 --- R Analysis and Results
  - R-TLCdataAnalysis-R.txt R analysis file for TLC data using mixed model and GEE
  - R-TLCdataAnalysis.html R results
- 24 Apr 2018 --- STATA Analysis and Results
  - tlc-mixed-do.txt STATA analysis file for TLC data using mixed model and GEE
  - tlc-do.txt STATA analysis file for TLC data (pre-post analyses)
- 24 Apr 2018 DiagraExample.q S+/R file for generating the Diagra example data.
- 24 Apr 2018 RegressionToTheMean-figure.pdf figure for PvDaM data example
- 24 Apr 2018 GroupTime-Sim.q S+/R file for simulations that compare OLS and WLS estimators in terms of their mean and variance.
- 26 Apr 2018 TopekaFEV1-data.txt Topeka FEV1 data
- 26 Apr 2018 TopekaFEV1.txt Topeka FEV1 documentation
- 26 Apr 2018 --- R Analysis and Results
  - R-TopekaFEVdataAnalyiss-Rmd.txt R markdown analysis file for Topeka FEV1 data
  - R-TopekaFEVdataAnalysis.html R analysis results for Topeka FEV1 data
- 26 Apr 2018 --- STATA Analysis and Results (in course notes)
  - TopekaFEV1-do.txt STATA analysis file for Topeka FEV1 data
  - TopekaFEV1-plots-do.txt STATA analysis file for Topeka FEV1 data
- 26 Apr 2018 --- SAS Analysis and Results
  - TopekaFEV1-sas.txt example of SAS program
  - TopekaFEV1-lst.txt SAS output file (run on mead)
- 26 Apr 2018 Some Facts about Linear Mixed Models
Week 6
- 01 May 2018 Notes: Categorical Data and GEE
- 01 May 2018 HivnetWide-data.txt HIVNET Informed Consent data
- 01 May 2018 HivnetWide-doc.txt HIVNET Informed Consent Data -- Documentation
- 01 May 2018 Coletti-2003JAIDS.pdf published analysis of knowledge items
- 01 May 2018 -- R Analysis and Results
  - hivnet-CDA-geese.R R Analysis file
  - hivnet-CDA-geese-out.txt R output
- 01 May 2018 -- STATA and SAS Analysis
  - HivnetIC-do.txt STATA Analysis file
  - HivnetIC-sas.txt SAS Analysis file
- 03 May 2018 vonEhrenstein (2006) AJE -- Example GEE analysis
- 03 May 2018 Dobkin (2006) J CLin Pain -- Example GEE analysis
- 03 May 2018 Savitz (2006) Epidemiology -- Example GEE analysis
- 03 May 2018 ThallWide.raw Seizure data
- 03 May 2018 -- STATA and R Analyses
  - thallGEE-do.txt --- STATA analysis file
  - thall-gee.R --- R analysis file (with jackknife)!
  - thall-gee-out.txt --- R results
- 03 May 2018 Hanley-2003AJE.pdf -- discussion of GEE ideas (weighted estimation) for epidemiologists
- 03 May 2018 Model Specification for Longitudinal Count Data -- summary document written in support of analysis plans for a device used to treat seizures
Week 7
- 08 May 2018 Notes: Missing Data
- 08 May 2018 Missing Data Diagrams
- 08 May 2018 Marder and Meibach (1994): Published PANSS data results
- 08 May 2018 -- Comprehensive mixed models using SAS
  - 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.
  - panss-lst.txt -- SAS results.
- 10 May 2018 -- STATA analysis using IPW and PMM
  - panss-ipw.do ----- STATA "do" file for analysis of PANSS data using inverse probability weights (IPW).
  - panss-ipw.log ----- STATA log file showing analysis results.
  - panss-pmm.do ----- STATA "do" file for analysis of PANSS data using pattern mixture model (PMM).
  - panss-pmm.log ----- STATA log file showing analysis results.
- 10 May 2018 -- R analysis using LMM, MI, IPW, PMM
  - R-MissingData.R --- R command file for analyses
  - R-MissingData.Rmd --- R markdown file for analyses
  - R-MissingData.html --- R results
  - R-MissingData-Supplement.Rmd --- R markdown file for analyses
  - R-MissingData-Supplement.html --- R results
- 10 May 2018 Niaua et al. (2002) ----- paper that illustrates use of pattern mixture models.
  - Table 5 (Results)
- 10 May 2018 Leon et al. (2006) ----- paper that overviews issues/methods for data with attrition.
Week 8
- 15 May 2018 Dufouil-Neurology2000.pdf -- article that nicely discusses their use of inverse probability weighting to handle drop-out
- 15 May 2018 STATA-MICE-2011.pdf -- article that discusses one option for multiple imputation in STATA.
- 15 May 2018 How many imputations?
- 15 May 2018 Summary of Missing Data Approaches for Longitudinal Data
- 17 May 2018 Notes: Generalized Linear Mixed Models
- 17 May 2018 Generalized Linear Mixed Models -- Diagrams to augment notes
- 17 May 2018 HivnetIC-glmm-do.txt --- STATA analysis file for conditional logistic regression and GLMM.
- 17 May 2018 hivnet-sas.txt --- SAS analysis file for GEE and GLMM.
- 17 May 2018 hivnet-lst.txt --- SAS output.
- 17 May 2018 HivnetIC-glmm.q --- R analysis file for GLMM.
- 17 May 2018 HivnetIC-glmm-out.txt --- R output.
- 17 May 2018 Pebley-Demography1996.pdf -- article that uses multi-level logistic regression
- 17 May 2018 StatisticalIssues.pdf -- tutorial that uses multi-level logistic regression to estimate hospital-specific random effects after adjusting for the patient case-mix.
- 17 May 2018 Martin-2013-HSR.pdf -- example published in Health Services Research of logistic regression to estimate hospital-specific random effects after adjusting for the patient case-mix.
- 17 May 2018 MarginalConditionalOddsRatios.pdf -- simple example showing difference between marginal and conditional odds ratio
  - NonCollapse.q -- R program to create this example
Week 9
- 22 May 2018 MultiLevel.pdf Notes: Multi-Level Models
- 22 May 2018 MultiLevel-Glossary.pdf -- article that explains terms commonly used.
- 22 May 2018 DiezRoux-EpiRev.pdf -- recent review article that discusses major issues.
- 22 May 2018 Hubbard2010.pdf -- "To GEE, or not to GEE..."
- 22 May 2018 Cluster RCT Power / Sample Size -- interactive tool
- 22 May 2018 Kinmonth-BMJ1998.pdf -- article that discusses community randomized trials that we analyze in lecture notes (data and programs below).
- 22 May 2018 sheff.raw -- data.
- 22 May 2018 sheff-do.txt -- STATA analysis file.
- 22 May 2018 sheffield-sas.txt -- SAS analysis file.
- 22 May 2018 Singer-JEBS1998.pdf -- article that discussess SAS PROC MIXED and multilevel models.
- 22 May 2018 Kahn-NEJM2006.pdf -- example multilevel analysis evaluating hospital volume and patient outcomes.
- 24 May 2018 Neuhaus-Biometrics1998.pdf -- discussion of using derived predictors (X_ij - Xbar) and Xbar to separate "within-" and "between-" covariate effects.
Week 10
- 29 May 2018 Notes: Time-dependent Covariates #1
- 29 May 2018 Bodnar-2004AJE.pdf -- article that overviews and illustrates the use of marginal structural models for analysis of longitudinal data with time-dependent confounding.
- 29 May 2018 Mortimer-2002EurRespJ.pdf -- article that uses distributed lag models for longitudinal analysis of the effect of pollution on asthmatic children(!)
- 29 May 2018 Bell-2004JAMA.pdf -- article that uses both single lag and distributed lag models for mortality count time series analysis of pollution effects.
- 29 May 2018 HeagertyComstock-Biometrics2013.pdf -- article that overviews methods using lagged covariates
- 31 May 2018 Notes: Time Dependent Covariates #2
- 31 May 2018 Sitlani-SIM2012.pdf -- article that overviews methods for the analysis of longitudinal data with endogenous exposure timing