MSCI Biostatistics II Course Schedule -- February 2024

Key:
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
Thurs 1 Zoom Course Webpage
Syllabus
Key Concepts
Glossary
A17.1-17.7, A17.10-1
B10-B10.5
H2.4.7
Simple Linear & Nonparametric Regression Getting Started
  2 Zoom A18, B10.6
B9.4-9.9
Multiple Linear Regression
R rms Package
HW 1 abd17-lion: lion age from nose
Mon 5 Zoom B10.7-10.10 " HW 2  
  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
Mon 12 Zoom H3, H4-4.1.2 Missing Data, Multivariable Modeling Strategies HW 6
HW 7 (optional)
support: missing data
nhgh: basic diagnostics
  13 Zoom H4.3-4.7.2, 4.7.5-4.7.7 Variable Selection, Overfitting, Shrinkage, Collinearity, Data Reduction HW 8 nhgh: data reduction
support: variable clustering
  14 Zoom H4.9-5.1.1, this Influential Observations, Comparing Models, Improving Practice, Strategies, Describing the Fitted Model   nhgh
  15 Zoom H5.1.2, 5.1.3, H5.2-5.4, (omit 5.5), B10.10 Performance Indexes, Relative Explained Variation, Bootstrap, Validation, Bootstrapping Ranks HW 9
framingham: outliers
framingham: internal validation
  16 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
  Mon 19 Zoom Student led discussion of papers HW 10 Final project statistical analysis plan finished
  20 Zoom A17.9, H10-10.5, 10.8-10.10, NNT Final project analysis file finished
Binary Logistic Models, NNT
   
  21 Zoom B6.10.3, B13.6.2-13.7 (brief), blog, blog, H11 " + Case Study   support: ordinal predictors
  22 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
  23 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
Mon 26 Zoom Review and catch-up
  27 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
   
  28 Zoom B15, Advantages, Efficiency, H22 Analysis of Serial Measurements
Ordinal Longitudinal Data
  29 Zoom Student Presentations of Final Project Final Project


Biostat2Stata : Stata code for in-class examples, 2022
Topic revision: r230 - 26 Feb 2024, FrankHarrell
 

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