Section outline

  • General

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  • Thursday, September 20, 2018; 8:45 AM - 10:15 AM

    Lecture 1: Course overview, the diagnostic process, and measures of interobserver agreement

    Introduction to the course and how we will teach it.

    Evidence-Based Medicine: 1) refining disease probabilities; 2) quantifying  treatment effects. 

    Diagnosis: assigning the right name to a patient's illness versus using test results to guide treatment decisions.

    Inter-rater agreement: concordance, unweighted Kappa, linear and quadratic-weighted Kappa.

    Faculty:  Michael Kohn

    Location:  Mission Hall 1400

    • Prospectus:

    • Session Slides:

    • Lec 1 Overview diagnosis kappa 2018-0918 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to Registered students only
    • Lecture 1 from 2017 URL

      1:09:30 Weighted kappa.

      1:27:00 What's a good kappa?

      On a laptop or desktop you should be able to play back at 2X speed.  This does not appear to work on a mobile device.  If you use 2X, you can watch from 1:09 to the end of the lecture in 10 minutes.

      Not available unless: You belong to Registered students only

    • Required Reading from Evidence-Based Diagnosis, 2nd Edition (EBD-2), which hasn't been published.

      Chapter 0 (Preface), Chapter 1, & Chapter 5 (posted below as Word documents)

    • EBD-2 Ch 0 -- Preface File
    • EBD 2 Ch 1 -- Introduction Understanding diagnosis and diagnostic testing File
    • 5 Reliability and Measurement Error 2018-1004 File

      Skip from "Reiliability of Continuous Measurements" on Page 15 up to "Using studies of reliability from the literature" on Page 27.

      This section covers Bland-Altman plots (which you will cover later this quarter in Epi 203) and calibration (which we will cover in Session 5 on "Evaluating Predictions").


    • Problem Set # 0:  Think about answers to the Ch 1 exercises posted below.  (You do not need to turn them in.)

       

    • Problem Set # 0 -- Understanding Diagnosis File

      In section on 10/20, we will discuss these questions.  Try to think about them and jot down some notes for yourself, but we won't be collecting or grading your answers.

    • Assignment Answer Key (Access restricted to registered students):

    • Optional Reading:

    • Multi-Rater Kappa File
    • Kohn (2013) Understanding Evidence-Based Diagnosis File

    • Resources:

    • Martina Stuerer Clinical Epi Lecture Notes lectures 1-3 corrected 2016-1013 File
    • Martina Stuerer Clinical Epi Lecture Notes lectures 4-8 corrected 2016-1013 File
    • EBD-1 Errata-As of 2015-0915 File
    • TBN's Document Repository website URL

  • Thursday, September 20, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 1

    Review of Chapter 1 (Reason for a Diagnosis) problems and "Kappa Game"

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108

    • Resources:

    • Kappa Game Data Collection Form File
    • Appendix 5-1 calculating kappa with Stata File
    • GraphPad Online Kappa Calculator URL

    • Problem Set #1, Inter-rater Agreement, due 9/27/18 at 1:00 PM

    • Problem Set #1 -- Kappa File
    • Problem Set #1 Assignment

      Use the link above to upload Problem Set #1 by 1 pm on 9/27.

      You must be logged in to upload your assignment.

    • Problem Set #1 (M.Laker Section) Assignment
      Not available unless: You belong to M Laker

    • Assignment Answer Key (Access restricted to registered students):

  • Thursday, September 27, 2018; 8:45 AM - 10:15 AM

    Lecture 2: Dichotomous Tests
    Sensitivity, specificity, predictive value, prior and posterior probability; 2x2 table method for getting posterior probability; probability and odds;  likelihood ratios, the likelihood ratio slide rule, false-positive and false negative confusion; use of X-graphs to understand testing and treatment thresholds

    Faculty:  Thomas Newman

    Location:  Mission Hall 1400

    • Session Slides:

    • Lec 2 Dichotomous tests 2018-0926 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading for EBD-2, which hasn't been published yet:

      Chapter 2, Dichotomous Tests (posted below as a Word document)

    • EBD-2 Ch 2 -- Dichotomous tests File

    • Optional Reading:

    • Testing Threshold Derivations File
    • Cost-Benefit X Graph and calcs for Chapter 3 MAK File

  • Thursday, September 27, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 2

    Review HW-1 (Kappa) Problems

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


      

    • Problem Set #2, Dichotomous Tests, due 10/4/2018 at 1:00 PM

    • Problem Set #2 File
    • Upload Problem Set #2 Assignment

      Upload Problem Set #2 to the above link by 1 pm on Thursday 10/4.

    • Assignment Answer Key (Access restricted to registered students):

    • PSet2 Dichotomous tests w Answers 2018.1004 File
      Not available unless: You belong to Registered students only

  • Thursday, October 4, 2018; 8:45 AM - 10:15 AM

    Lecture 3: Multilevel and continuous tests
    ROC Curves, interval likelihood ratios, and the relationship between them; how making multilevel tests dichotomous wastes information; choosing cutoffs, the Walking Man approach to the "non-parametric" ROC curve.

    Faculty:  Michael Kohn

    Location:  Mission Hall 1400

    • Session Slides:

    • Multilevel_tests_Lecture_With_Youdens_Index_and_Audience_Response.pptx File
    • MultiLevelAndContinuousTestsExcelDemo.xlsx File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading EBD-2 (which hasn't been published yet):

      EBD-2, Chapter 3 (posted below as a Word document)

    • EBD-2 Ch 3 -- Multi-level tests File

  • Thursday October 4, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 3

    Review HW-2 (Dichotomous Tests)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


    • Problem Set #3, Multi-level Tests, due 10/11/18 at 1:00 PM

    • Epi 204 PSet3 (Updated 10/5 11 am) File
    • Problem Set 3 (Upload) Assignment

    • Assignment Answer Key (Access restricted to registered students):

  • Thursday, October 11, 2018; 8:45 AM - 10:15 AM

    Lecture 4: Studies of Diagnostic Tests
    Common biases in test accuracy studies: incorporation bias, verification bias, double gold-standard bias, spectrum bias;  Prevalence, spectrum bias, and nonindependence; going beyond checklists and estimating the direction of bias.

    Faculty:  Tom Newman

    Location:  Mission Hall 1400

  • Thursday, October 11, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 4

    Review HW-3 (Multi-level Tests)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


    • Homework assignment #4, Bias in Test Accuracy Studies, due 10/18/18 at 1:00 PM

    • Epi 204 - PSet4 No Answers 2018.1011 File
    • Problem Set #4 (Upload) Assignment

      Due 10/18/2018 at 1 pm.

    • Assignment Answer Key (Access restricted to registered students):

  • Thursday, October 18, 2018; 8:45 AM - 10:15 AM

    Lecture 5: Evaluating Risk Predictions
    Risk predictions: differences from diagnostic tests; calibration and discrimination; comparing predictions; net benefit calculation; decision curves.

    Faculty:  Michael Kohn

    Location:  Mission Hall 1400

    • Session Slides:

    • Lecture 5 Risk Prediction.pptx File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading EBD-2:

      EBD-2, Chapter 6 (Posted below as a Word document)

    • EBD-2 Ch 6 -- Risk Predictions File

    • Optional Reading:

    • Vickers_Net_Benefit_BMJ_2016.pdf File
    • Kerr 2015 Decision Curves File

  • Thursday, October 18, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 5

    Review HW-4 (Bias in Test Accuracy Studies)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108

    • Homework assignment #5, Evaluating Risk Predictions, due 10/25/18 at 1:00 PM

      (The file below is a placeholder.  The real assignment will be posted before 6 pm.)

    • Problem Set #5 File
    • Poblem Set #5 Upload Assignment

    • Assignment Answer Key (Access restricted to registered students):

  • Thursday, October 25, 2018; 8:45 AM - 10:15 AM

    Lecture 6: Combining Tests and Multivariable Decision Rules
    Combining tests/diagnostic models:  Test non-independence conditional on D+/D-; recursive partitioning; logistic regression; importance of validation separate from derivation. 

    Faculty:  Michael Kohn

    Location: Mission Hall 1400

    • Session Slides:

    • Lecture 6 Combining Tests and Multivariate Decision Rules File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

      EBD-2, Ch 7 Combining Tests and Multivariable Decision Rules (posted below)

    • EBD-2 Ch 7 -- Multiple Tests and Multivariable Decision Rules File
    • Box 7.3 Revised 2018-1101 File

    • Optional Reading:

  • Thursday, October 25, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 6

    Review HW-5 (Prognostic Tests)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


    • Homework Assignment #6, Combining Tests, due 11/1/2018 at 1:00 PM

    • Problem Set #6 File
    • Problem Set #6 Upload Assignment

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, October 26, 2018; 2:45 PM - 4:15 PM

    Office Hours

    Location:   online or +1 669 900 6833 (Meeting ID: 438 568 050)  

  • Tuesday, October 30, 2018: 12:00 PM - 1:00 PM

    Office Hours

    Location:  MH-1106 and online or +1 669 900 6833 (Meeting ID: 982 195 831)

      

     

  • Thursday, November 1, 2018; 8:45 AM - 10:45 AM

    Lecture 7: Quantifying the benefits and harms of treatments using RCTS
    RCT checklist; importance of baseline incidence; measures of effect size: Relative risk (RR), relative risk reduction (RRR), Odds ratio (OR), Absolute risk reduction (ARR), Number needed to treat (NNT);   "Back of the Envelope Cost Effectiveness Analysis" 

    Faculty:  Shabnam Peyvandi

    Location:  Mission Hall 1400

    • Session Slides:

    • Lecture 7 -- Quantifyng Treatment Effects Using RCTs File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading from Evidence-Based Diagnosis, 2nd Edition (EBD-2), which hasn't been published.

      Chapter 8 (posted below as a Word document)

    • EBD2-Ch8 Quantifying treatment effects 2018-1203 File

    • Optional Reading:

    • LeNoury 2015 BMJ Restoring Study 329 File
      Not available unless: You belong to a group in Registered Students Only
    • Newman 2004 NEJM Antidepressant Perspective File
      Not available unless: You belong to a group in Registered Students Only
    • Stempel 2016 NEJM AUSTRI study Advair v fluticasone alone File
      Not available unless: You belong to a group in Registered Students Only
    • Stolker 2014 Circulation rethinking composite endpoints in clinical trials File
    • Ciani 2013 BMJ Surrogate vs patient relevant outcomes File
    • Miner 2017 Am J Gastro Pecanatide for chronic constipation File

    • Resources:

  • Thursday, November 1, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 7

    Review HW-6 (Combining Tests)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


    • Optional Reading:

    • Homework Assignment #7 (RCTs) Due 1 pm on 11/8/2018

    • Problem Set #7 File
    • Problem Set #7 (Upload) Assignment

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, November 6, 2018; 12:00 PM - 1:00 PM

    Office Hours

    Location:  MH-1106 and online or +1 669 900 6833 (Meeting ID: 982 195 831)

      

     

  • Thursday, November 8, 2018; 8:45 AM - 10:15 AM

    Lecture 8: Screening Tests
    Need for a more critical approach for screening tests, risk factor vs disease screening; biases in observational studies of screening: lead time bias, length time bias, volunteer bias, stage migration bias, pseudodisease; randomized trials of screening

    Faculty:  Martina Steurer-Muller
     
    Location:  Mission Hall 1400

    • Session Slides:

    • Lec 8 Screening (Martina) File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only
    • 2014 Lecture (Watch) URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

      EBD-2 Chapter 10 -- Screening

    • EBD2 Ch 10 Screening File

    • Optional Reading:

    • Merenstein D. Winners & Losers. JAMA 2004;291:242-5 File
      Not available unless: You belong to a group in Registered Students Only
    • Woloshin et al. Cancer Screening Campaigns — Getting Past Uninformative Persuasion. NEJM 2012; 367:1677-1679 URL
    • Heath 2014 BMJ Role of fear in overdiagnosis File
      Not available unless: You belong to a group in Registered Students Only
    • Heath 2013 BMJ Overdiagnosis When good intentions meet vested interests File
      Not available unless: You belong to a group in Registered Students Only
    • We're #37. (Song celebrating US Healthcare Ranking by Paul Hipp) URL
    • Newman 2016 JAMA IM Lipid screening in children-low value care File
      Not available unless: You belong to a group in Registered Students Only
    • Annas 1995 NEJM Reframing the Debate on Healthcare by replacing Metaphors File
    • Tilman 2014 Nature Global diets link environmental sustainability and human health File
      Not available unless: You belong to a group in Registered Students Only

  • Thursday, November 8, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 8

    Review HW-7 (RCTs)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


    • Homework Assignment #8, Screening, Due 11/9/2017 1 pm: 

    • Problem Set #8 Screening File
    • Problem Set #8 (Upload) Assignment
    • Problem Set #8 (M.Laker Section) Assignment
      Not available unless: You belong to M Laker

    • Assignment Answer Key (Access restricted to registered students):

  • Tuesday, November 13, 2018; 12:00 PM - 1:00 PM

    Office Hours

    Location:  MH-1106 and online or +1 669 900 6833 (Meeting ID: 982 195 831)

      

     

  • Thursday, November 15, 2018; 8:45 AM - 10:15 AM

    Lecture 9: P-Values and Confidence Intervals / Alternatives to RCTs

    Faculty:  Thomas Newman

    Location:      Mission Hall 1400

    • Session Slides:

    • Lec 8 Alternatives To RCTs and P-values 2018-1203 File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

      EBD-2, Ch 9 and 11

    • EBD-2 Chapter 9 Alternatives to RCTs (Updated 11-18-2018) File

      This version of the chapter has some modifications to the section on propensity scores, pages 8-12.

    • EBD2 Chapter 11 Understanding P values and CI 2018-1114 for posting File
    • Goodman S 2008 Seminars Hematol Dirty Dozen P Value fallacies File

    • Optional Reading:

    • Laptook 2017 JAMA Effect of therapeutic hypothermia after 6 hours Bayesian example File
    • Quintana 2017 JAMA Bayesian analysis. Using prior information to interpret results of clinical trials File
    • Browner WS, Newman TB. Are all significant P-values created equal? The analogy between diagnostic tests and clinical research. JAMA 1987;257:2459-63 File
      Not available unless: You belong to a group in Registered Students Only
    • Goodman, S. Toward evidence-based medical statistics. 1: The P value fallacy. Annals of Internal Medicine 1999; 130: 995-1004 File
      Not available unless: You belong to a group in Registered Students Only
    • Goodman, S. Toward evidence-based medical statistics. 2: The Bayes factor. Annals of Internal Medicine 1999; 130: 1005-1013 File
      Not available unless: You belong to a group in Registered Students Only
    • Newman, T. If almost nothing goes wrong, is almost everything all right? JAMA 1995; 274: 1013 File
      Not available unless: You belong to a group in Registered Students Only
    • Goodman S 2013 Circulation Are we there yet File
    • Ray 2006 American Journal of Epidemiology New User DEsigns File

  • Thursday, November 15, 2018; 1:00 PM - 2:30 PM

    Small Group Discussion Section 9

    Review HW-8 Screening

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Kolodzie MH-2105, Fergus MH-2106, McMahan MH-2107, Washington MH-2108


  • Monday, November 19, 2018; 2:00 PM - 3:00 PM

    Office Hours

    Location:  MH-2700 and online or +1 669 900 6833 (Meeting ID: 173 372 772)

      

     

  • Thursday, November 22 - No Class - Thanksgiving Holiday

  • Tuesday, November 27, 2018; 12:00 PM - 1:00 PM

    Office Hours

    Location:  MH-2800 and online or +1 669 900 6833 (Meeting ID: 982 195 831)

      

     

  • Thursday, November 29, 2018; 8:45 AM - 10:15 AM

    Lecture 10: Cognitive Biases / Course Review

    Faculty:  Michael Kohn

    Location:  Mission Hall 1400

    • Session Slides:

    • Lecture 10 Cognitive Bias and Course Review File
    • Example Weighted Kappa Calculation File
    • Example of going from ROC Table to LR Table File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Required Reading:

      EBD, Chapter 12

    • 12 EBD-2 Challenges for EBM (posted 11/27/2018) File

    • Optional Reading:

    • Rosenbaum 2014 NEJM Invisible risks File
      Not available unless: Your ID number contains 02
    • Newman, TB. The Power of Stories over Statistics.BMJ. 2003;327(7429):1424-7 File
      Not available unless: Your ID number contains 02
    • Newman TB, Maisels, MJ. Less Aggressive Treatment of Neonatal Jaundice and Reports of Kernicterus: Lessons About Practice Guidelines. Pediatrics 2000;105:242 File
      Not available unless: Your ID number contains 02
    • Newman TB, Johnston BD, Grossman DC. Effects and costs of requiring child-restraint systems for young children traveling on commercial airplanes.Arch Pediatr Adolesc Med. 2003 Oct;157(10):969-74 File
      Not available unless: Your ID number contains 02
    • Bishai D. Hearts and Minds and Child Restraints on Airplanes. Arch Peds Adol Med 2003;157:953 File
      Not available unless: Your ID number contains 02
    • Healy B. Who Says Whats Best? US News World Rept URL
    • Newman TB. Universal Bilirubin Screening, Guidelines and Evidence. Pediatrics 2009 File
      Not available unless: Your ID number contains 02

  • Thursday, November 29, 2018; 1:00 PM - 2:30 PM


    Small Group Discussion Section 10

    Review HW-9 (P-Values, Confidence Intervals)

    Faculty:  Kerstin Kolodzie, Ryan McMahan, Kirk Fergus. Samuel Washington, Martina Steurer-Mueller, Tom Newman, Michael Kohn, Vivian Avelino-Silva
     
    Location:  Selby MH-2106, Rodriguez MH-2107, Cage MH-2105, Peyvandi MH-2108

  • Thursday, December 6, 2018; 8:45 AM - 10:15 AM

    Lecture 11: Final Exam Review
     
    Faculty:  Michael Kohn

    Location: Mission Hall 1400

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to a group in Registered Students Only

    • Assignment: TAKE-HOME FINAL EXAM DUE THURS 12/6 8:45 AM

    • Final Exam (Due 12/6/2018 8:30 am) File

    • Note: I may post clarifications in response to forum posts!

    • EPI 204 Final Exam - upload PDF here if you are unable to attend class Assignment

      Please use this option if you are unable to attend this session.  Please upload as a .pdf such that all your formatting will be preserved.

      Due 8:30 am.

    • Final Examination Answer Key (Access restricted to registered students):

    • Final Exam Key File
      Not available unless: You belong to Registered students only

  • Thursday,December 6, 2018; 1:00 PM

    No Small Group