MSCI Biostatistics II Course Schedule -- February 2023

A = Whitlock and Schluter (text)
B = Biostatistics for Biomedical Research (handout) - Some of the chapters include audio narration and video
H = Harrell (text) and the corresponding chapter in RMS Handouts

Homework assignments are here

To fetch scripts for in-class Examples and copy them into the RStudio script editor pane:
  • Point to the RStudio command console (usually lower left pane)
  • Run require(Hmisc) to load the getRs function
  • Run getRs('xxx.qmd', put='rstudio') where the script file name xxx is replaced by the name given in the Examples column below

Date Room Material to read/watch
prior to class
Session Topics Assignments Examples
Wed 1 Zoom Course Webpage
Key Concepts
A17.1-17.7, A17.10-1
Simple Linear & Nonparametric Regression Getting Started
  2 Zoom A18, B10.6
Multiple Linear Regression
R rms Package
HW 1 abd17-lion: lion age from nose
  3 Zoom B10.7-10.10 " HW 2  
Mon 6 Zoom B13-13.6.1, 13.13 Analysis of Covariance in Randomized Studies HW 3 abd18-molerats: mole rats
  7 Zoom Hxiii, H1, H2-2.3.1, classification blog Regression Modeling Strategies: Introduction Exercise: ID the model
Final project dataset in hand
abd18-molerats: chunk tests
cat-pred: categorical predictors, taking control of contrasts
  8 Zoom H2.3.2-2.4.1-2.4.6 demos Methods for Multivariable Models HW 4 splinex: polynomial and spline fitting
  9 Zoom H2.4.8-2.7.2 (omit 2.5.1), 2.8 " HW 5 support: nonlinear relationships
  10 Zoom H3 (brief), H4-4.1, 4.3-4.4 Missing Data (brief), Multivariable Modeling Strategies HW 6 support: missing data
nhgh: basic diagnostics
Mon 13 Zoom H4.6 (brief), 4.7-4.12.3 and this. Skip 4.7.3-4 " HW 7 (optional)
HW 8
nhgh: data reduction
support: variable clustering
  14 Zoom H5-5.4, (omit 5.5), B10.10 Model Interpretation and Validation HW 9
Final project analysis file finished
framingham: outliers
framingham: internal validation
  15 Zoom H5.6, B6.8, 6.9, 6.10-6.10.2, A17.9 Relative Effect Measures, Introduction to LRM Prep for critique Simple Logistic
acath: binary logistic 2
  16 Zoom   Student led discussion of papers HW 10  
  17 Zoom A17.9, H10-10.5, 10.8-10.10, NNT Binary Logistic Models, NNT    
Mon 20 Zoom B6.10.3, B13.6.2-13.7, blog, blog, H11 " + Case Study Analysis plan for final project support: ordinal predictors
  21 Zoom H12, HTE, HTE, B19, More Analyses of Diagnostic Yield,
Simple Decision Analysis
Binary Logistic Model Case Study, Risk-based diagnostic research, ROC curves, HTE HW 11 Bayes and this
  22 Zoom B4.1.2, B5.12.4-.5, Power, B7.6-7.7, H13.1-13.3, 13.4.3, 13.4.5, 13.4.7, H14.1 and Table 14.1, 14.2, H15-15.2, 15.5.2, Figure 15.15, 15.16 Proportional Odds Ordinal Logistic Models HW 12 (Optional)
HW 13
simhiv: ordinal regression
  23 Zoom H17.1-17.3, 17.5.1,
H18.1, 18.3-18.3.6, H20-20.1.5, 20.3, 20.7, H21
Survival Analysis
Cox Model
  24 Zoom B15, Advantages, Efficiency, H22 Analysis of Serial Measurements
Ordinal Longitudinal Data
Mon 27 Zoom Student Presentations of Final Project Final Project
  28 Zoom Student Presentations of Final Project Final Project

Biostat2Stata : Stata code for in-class examples, 2022
Topic revision: r224 - 15 May 2023, FrankHarrell

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