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EPI 204: Clinical Epidemiology (Fall 2021)

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Section outline

  • General

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    • Clinical Epidemiology 

      EPI 204 Fall 2021 (3 units).

      Course Director: Michael A. Kohn, MD, MPP.

      Professor, Epidemiology & Biostatistics 

      Course Director Emeritus: Thomas B. Newman, MD, MPH
      Professor Emeritus, Epidemiology & Biostatistics and Pediatrics 
    • EPI204 Forum
    • News forum

    • Problem-writing Assignment:

    • Problem-Writing Assignment (due Monday 11/14 11:59 pm)m) File
    • Problem-writing Assignment -- upload here

      Collaboration with 1 or 2 other classmates on this assignment is permitted and even encouraged.  List the people you worked with, but for record-keeping purposes, each member of the team must upload a separate copy of the problem.

      If possible, please either include a link to the paper(s) on which your problem is based or upload a pdf of the paper.

      1.  Please NAME your problem file using this convention:

      [Last name of student author closest to the beginning of the alphabet]_ + Ch_ + [Chapter numbers of EBD-2 where material is covered]_ + [a word or two about the topic].

      Example: John Brown, Sally Green and Joe Black wrote a problem about brain tumors that has material about ROC curves (Chapter 3) and spectrum bias (Chapter 4).  ALL THREE STUDENTS IN THE GROUP would name their problem: "Black_Ch3_4_Brain_tumors.doc".  (If you want to add a date at the end, that's fine.)

      2.  Please name the pdfs of any included articles on which your problem is based starting exactly the same way.  If the article was by Gold et al from JAMA in 2019, you could name it

      "Black_Ch3_4_Brain_tumors_Gold_JAMA_2019.pdf"

      THANK YOU!


    • Required reading --Evidence-Based Diagnosis: an Introduction to Clinical Epidemiology, 2nd Ed. File

      (You don't need to download the Word document, it has this same information.)

      Evidence-Based Diagnosis: an Introduction to Clinical Epidemiology, 2nd Ed.

      Thomas B Newman and Michael A Kohn

      Illustrated by Martina Steurer

       We think the book is well worth buying, but you can download it free from Cambridge University Press if you go through the UCSF Library.  Here's a link.

      From there, click on 

      Cambridge University Press online books

      You should see a green check for "Access."  Then "select all" on the left side and download a zip file. 

       


  • Tuesday, September 14, 2021; 8:45 AM - 10:15 AM

    Course introduction; Diagnostic process and measures of interobserver agreement

    Introduction to the course and how we will teach it; testing to refine probabilities and guide decisions; concordance, unweighted Kappa, linear and quadratic weighted Kappa

    Faculty:  Michael Kohn

    No Large-Group Discussion (LGD).  LGDs start on Tuesday 9/21.


    The first small group will be Thursday 9/16 at 1:15 pm.  In that small group, we will review Problem Set #0 (not to turn in) and play the Kappa Game.  Prior to that small group meeting, please watch Lecture 1, read Chapters 1 and 5 (pages 110 - 121), and do Problem Set #0, which is not to submit. 

    All subsequent problem sets (#1 - #9) should be uploaded on the CLE prior by 1:15 pm on Thursday, starting with Problem Set #1 on 9/23.



    • Lecture Slides:

    • Lec 1 Part 1 Overview diagnosis 2021-0725 File
    • Lec 1 Part 2 Kappa 2021 File

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

      Note: The live recordings sometimes omit the on-screen pointer/cursor or display it with a lag.  From the audio, it is clear that I am pointing at something with my mouse, but you can't see it on the video.  This is especially problematic during the Excel and Stata demonstrations.  I tried to make it a bit better by adding annotations to the video.

    • Lecture 1 Segment 1 -- Ch 1 material on diagnosis and testing (12:55) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 1 Segment 2 -- Ch 5 material on kappa (unweighted) (22:45) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 1 Segment 3 -- Ch 5 material on weighted kappa (27:15) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 1 Segment 4 Ch 5 What affects kappa? What's a good kappa? (4:41) Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading:

    • Evidence-Based Diagnosis, 2nd Edition (EBD-2): Chapter 1, & Chapter 5 (pp 121-130 on reliability of continuous measurements is optional)

    • Optional video and material on kappa for more than 2 raters:

    • Melanoma pathology: example of agreement among multiple raters (2:35) Media Resource
      Not available unless: You belong to Registered students only

    • This video briefly introduces our example of multi-rater kappa, a study of the inter-rater reliability of histopathologists reviewing 37 slides for melanoma vs. benign melanocytic nevus.  See EBD-2 Appendix 5A -Multirater Kappa.

    • Study Using Multirater Kappa (Melanoma vs. Melanocytic Nevus) File
    • MultiraterKappa Datasets File

    • Optional Reading:

    • Kohn (2013) Understanding Evidence-Based Diagnosis File
      Not available unless: Your ID number contains 02

    • Resources:

    • Kappa Game Data Instructions and Collection Form File
    • Excel File for Calculating Kappa
    • Calculating kappa with Stata File
    • GraphPad Online Kappa Calculator URL

    • Assignments:

    • We will play the "Kappa Game" at the first Small Group Discussion on September 16.  Please try to view the lecture videos and and do the required reading in preparation for the Sept. 16 session.

    • Problem Set #0 -- Understanding Diagnosis (will not be graded) File

      Unlike Problem Sets #1-10, Problem Set #0 will not be graded.  We will discuss it in the Sept. 16 Small Group Discussion sections.

    • Problem Set #0 with Answers File

    • Assignment due date: 9/23/21 at 1:15 PM

    • Problem set #1 (Due 9/23/2021 at 1:15 PM) File
    • Upload Problem Set #1 Assignment

      Use the link above to upload Problem Set #1 by 1:15 PM on September 23. 

      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):

    • PSet #1 Answer Key File
      Not available unless: You belong to Registered students only

  • Thursday, September 16, 2021; 1:15 PM - 2:45 PM

    Small Group Discussion (see roster below for your section assignment)

    Kappa Game

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) File
      Not available unless: You belong to a group in Registered Students Only

  • Tuesday, September 21, 2021; 8:45 AM - 10:15 PM

    Course introduction; Diagnostic process and measures of interobserver agreement

    This Large Group Discussion will cover the Chapter 1 material on diagnosis and Chapter 5 material on kappa.  The lecture slides and video are all with the 9/14 syllabus entry.  We put them there so that you would see them BEFORE the first small group on Thursday 9/16, since that session is spent playing the Kappa Game.

    Faculty:  Michael Kohn



    • Lecture Slides: (See 9/14)


    • Lecture Audio/Video Recording (See 9/14):

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.  (All materials for this session are posted under 9/15.)

    • Zoom Recording of Large Group Discussion (Access restricted to registered students):

    • Recording of Interactive Large Group 9/21/2021 (Problem set 0 and Kappa) Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading (See 9/14):

    • Assignments:  See the syllabus entries for 9/14.  HW #1 is due 9/23 at 1:15 pm.

  • Wednesday, September 22, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

  • Thursday, September 23, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and Problem Set #1

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) (copy) File
      Not available unless: You belong to a group in Registered Students Only

  • Tuesday, September 28, 2021; 8:45 AM - 10:15 AM

    LGD: 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

    • Lecture Slides:

    • Lec 2 Dichotomous tests 2021-0921 File

      Note:  This PPT file is almost identical to the one I used for the recorded lecture.  The only differences are:

      • In the speaker notes I corrected how I misspoke in the recorded lecture on slides 6 and  40. 

      • The substantive difference is that I (TN) made logical error on slide 57 and in my discussion of it in the lecture recording, which is corrected on the slide and in the speaker notes for that slide.  If you want a challenge, try watching the lecture to see if you notice the error before finding the answer in slide 57 of this PPT.



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

    • Lecture 2 -- Dichotomous Tests (1:17:35) URL

      Tom Newman explains dichtomous tests: sensitivity, specificity, positive/negative predictive value, and more.

      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Large Group Discussion (Access restricted to registered students):

    • Recording of Zoom Large Group Discussion 9/28/2021 Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading:

    •  EBD-2:  Chapter 2, Dichotomous Tests

    • Optional Reading:

    • Regret graph calculator URL
    • LR Slide Rule URL
    • Cost-Benefit X Graph and calcs MAK File

      This is the Excel version of the Regret Graph Calculator available at https://ebd-2.net/regret-calculator/


      Not available unless: Your ID number contains 02

    • Assignments: Problem Set #2, Dichotomous Tests

    • PSet2 Dichotomous tests 2021-0923 File

    • Assignment due date: 9/30/2021 at 1:15 PM

    • Upload Problem Set #2 Assignment
    • Upload Problem Set #2 (M.Laker section) Assignment
      Not available unless: You belong to M. Laker

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

    • PSet #2 Answer Key File
      Not available unless: You belong to Registered students only

  • Wednesday, September 29, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

  • Thursday, September 30, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) File
      Not available unless: You belong to a group in Registered Students Only

  • Tuesday, October 5, 2021; 8:45 AM - 10:15 AM

    LGD: Continuous Tests

    ROC Curves, multilevel  likelihood ratios and the relationship between them; how dichotmozing tests wastes information; the Walking Man approach to ROC curves; choosing cutoffs

    Faculty:  Michael Kohn

    • Lecture Slides:

    • Multilevel_tests_Lecture_2020.1001.pptx File
    • MultiLevelAndContinuousTestsExcelDemo.xlsx File

      This version has one sheet for demo and one with the formulas

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

    • Lecture 3 Segment 1 -- Multilevel Tests -- Why not make the test dichotomous? (13:34) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 3 Segment 2 -- the ROC Curve (17:45) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 3 Segment 3 -- Interval Likelihood Ratios (22:34) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 3 Segment 4 -- What test result should prompt treatment? (11:29) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 3 Segment 5 -- computer-drawn ROC curves (33:30) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • 2020 (!) Zoom Recording of Large Group Discussion 10/6/2020 (1:31:00) Media Resource

      0:00 – Intro set up

      3:00 – Michael: Review of material covered in the first 4 segments

      10:45 – Michael: “Walking Man” approach to understanding computer-drawn ROC curves

      46:30 – Student questions

      1:03:30 – Tom: problem on using BNP to diagnose peripartum congestive heart failure (CHF)

      Includes a detailed discussion of a published ROC table and why NOT to report LR(+) and LR(-) at each of multiple cutoffs.

      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Large Group Discussion (Access restricted to registered students):

    • Large Group Discussion Zoom Recording 10/5/2021 Audio and Shared Screen Only Media Resource

      I tried downloading the Zoom recording that includes only the shared screen and audio, not the gallery of faces.  It's a bit odd because, when I'm not sharing my screen, there is no video. 

    • Required Reading:

    • EBD-2, Chapter 3

    • Optional Reading:

    • M.A. Kohn, Key concepts in clinical epidemiology: reporting on the accuracy of continuous tests, Journal of Clinical Epidemiology, https:// doi.org/ 10.1016/ j.jclinepi.2021.07.012 File
      Not available unless: You belong to Registered students only

    • Assignments:  Problem Set #3, Multi-level Tests

    • Problem set #3 File

    • Assignment Due Date: 10/07/21 at 1:15 PM

    • Problem Set #3 Assignment

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

    • PSet #3 Answer Key File
      Not available unless: You belong to Registered students only

  • Wednesday, October 6, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

     

  • Thursday, October 7, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) (copy) (copy) (copy) File
      Not available unless: You belong to a group in Registered Students Only

  • Tuesday, October 12, 2021; 8:45 AM - 10:15 AM

    Bias in Test Accuracy Studies / Systematic Reviews of Test Accuracy Studies
    Common biases: incorporation bias, verification bias, double gold-standard bias, spectrum bias;  Prevalence, spectrum bias and nonindependence; checklist vs systematic approach to critical appraisal of studies of diagnostic tests

    Faculty:  Tom Newman

    • Lecture Slides:

    • Lec 4 Studies of Dx Tests 2020-1007 rev 2021 File

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

    • TN Studies of Diagnostic Test Accuracy Lecture PART 1 (56:24) 2020-1008 URL
      Not available unless: You belong to a group in Registered Students Only
    • TN Studies of Diagnostic Test Accuracy Lecture PART 2 (41:32) 2020-1008 URL
      Not available unless: You belong to a group in Registered Students Only
    • MAK GRACE Module 1 on Sampling Frame in Diagnostic Test Accuracy Studies Media Resource

      GRACE (Guidelines for Reasonable and Appropriate Care in the Emergency Department) is a project of the Society for Academic Emergency Medicine.  They asked me (Michael) to record a series of videos on how to evaluate studies of diagnostic test acccuracy (DTA studies).  I have recorded two modules so far and am posting them here.

      Here is the link for the GRACE project:

      https://www.saem.org/publications/academic-emergency-medicine/grace


      Not available unless: You belong to Registered students only
    • MAK GRACE Module 2 - Incorporation, Partial Verification, and Differential Verification Bias Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of LGD 10/12/2021 Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading:

    • EBD-2, Chapter 4

    • Optional Reading:

    • Kohn MA Sampling Frame and Partial Verification Bias File

      Manuscript under review by the Journal of Clinical Epidemiology

      Not available unless: You belong to Registered students only
    • Kohn Carpenter Newman -- Understanding the Direction of Bias in Studies of Diagnostic Test Accuracy File
      Not available unless: You belong to Registered students only

    • Assignments: Homework assignment #4, Bias in Test Accuracy Studies

    • Problem Set #4 File

      Due 10/14/2021 at 1:15 pm.

    • Assignment Due Date: 10/15/20 at 1:15 PM

    • Problem Set #4 (Upload) Assignment


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

    • PSet 4 Answer Key File
      Not available unless: You belong to Registered students only

  • Wednesday, October 13, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

  • Thursday, October 14, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) File
      Not available unless: You belong to Registered students only

  • Tuesday, October 19, 2021; 8:45 AM - 10:15 AM

    LGD: Risk Prediction Models
    Prediction models: differences from diagnostic tests; calibration and discrimination; comparing predictions; value of prognostic information.

    Faculty:  Michael Kohn

    • Lecture Slides:

    • PPT for 2021 Lecture 5 on Risk Prediction File

      The 2021 Lecture 5 on risk prediction is pre-recorded.  The 2019 lecture was recorded live as given on 10/17/2019.

      We are making both the 2019 and 2021 lectures available to you.

      This is the PPT for the 2021 version.  The notation changes that I hand-wrote while recording the lecture have been incorporated into the slides.  Also, the rounding problems have been corrected.

    • PPT for 2019 Lecture 5 Risk Prediction File

      This is the PPT for the 2019 version of Lecture 5 on Risk Prediction Models as given live on 10/17/2019.  

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

    • 2021 Lecture 5 Segment 1 - Calibration (33:16) Media Resource
      Not available unless: You belong to Registered students only
    • Supplement to EBD-2 Chapter 6 on Calibration Error (Word document) File

      This is the material covered in Lecture 5 Segment 1.

    • 2021 Lecture 5 Segment 2 -- Net Benefit and Decision Curves (40:50) Media Resource
      Not available unless: You belong to Registered students only
    • 2019 Lecture 5 Risk Model -- Recorded Live on 10/17/2019 (1:26:25) Media Resource
      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Live Large Group Discussion (Access restricted to registered students):

    • Zoom Recording of Large Group 10/19/2021 Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading:

      EBD-2, Chapter 6

    • Supplement to EBD-2 Chapter 6 on Calibration Error (Word document) File

      Duplicate posting under Required Reading.  This is the material covered in Lecture 5, Segment 1.

    • Optional Reading:

    • Vickers_Net_Benefit_BMJ_2016.pdf File
      Not available unless: Your ID number contains 02
    • Kerr 2015 Decision Curves File
      Not available unless: Your ID number contains 02

    • Assignments: Homework assignment #5, Evaluating Risk Predictions

    • Problem Set 5 -- Risk Prediction File

    • Assignment due date:  10/21/21 at 1:15 PM

    • Problem Set #5 Upload Assignment


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

    • Pset 5 Risk Prediction Key File
      Not available unless: You belong to Registered students only
    • MeteorologistsBrier.do File

      Stata do-file to create a dataset with meteorologist predictions and (rain) outcomes for HW#6, Problem 1, then run Brier command.

    • MeteorologistFrequencies.xls File
    • meteorologists.dta File

  • Wednesday, October 20, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

      Location (Access restricted to registered students):  Zoom URL

  • Thursday, October 21, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) File
      Not available unless: You belong to Registered students only

  • Tuesday, October 26, 2021; 8:45 AM - 10:15 AM

    LGD: Combining Tests and Multivariable Risk Models
    Combining tests/diagnostic models:Importance of test non-independence; recursive partitioning; logistic regression; importance of validation separate from derivation

    Faculty:  Michael Kohn

    • Lecture Slides:

    • Lecture 6 Part 1 -- Test Non-Independence File
    • Lecture 6 Part 2 -- Classification Trees, Logistic Regression, Variable Selection File

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

    • Lecture 6 Segment 1 -- Test Non-independence (29:28) Media Resource
      Not available unless: You belong to Registered students only
    • Lecture 6 Segment 2 Classification Trees and Logistic Regression (36:51) Media Resource
      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Large Group Discussion 10/26/2021 Media Resource
      Not available unless: You belong to Registered students only

    • Optional Reading:

    • Assignments: Homework Assignment #6, Combining Tests

    • Problem Set #6 File

    • Assignment Due Date:  10/28/2021 at 1:15 PM

    • Problem Set #6 Upload Assignment

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

    • PSet 6 Answer Key File

  • Wednesday, October 27, 2021; 1:00 - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL


  • Thursday, October 28, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) (copy) File
      Not available unless: You belong to Registered students only

  • Tuesday, November 2, 2021; 8:45 AM - 10:45 AM

    LGD: Quantifying the benefits and harms of treatments using RCTS / Alternatives to 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:  Thomas Newman

    • Lecture Slides:

    • Newman RCTs lecture 2020-1027 with 2021 Speaker notes File

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

    • Lecture 7 Part 1, (Introduction and critical appraisal of RCTs; 37:52) 2020-1028 URL
      Not available unless: You belong to Registered students only
    • Lecture 7, Part 2 (Quantifying treatment effects; 42:33) 2020-1028 URL
      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Large Group Discussion 11/2/2021 Media Resource
      Not available unless: You belong to Registered students only

    • Required Reading: 

      EBD-2: Chapter 8

    • RCT EquationSheet File

      This is an expanded version of Table 8.1 created by Nicole Rodriquez.

    • 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
      Not available unless: Your ID number contains 02
    • Ciani 2013 BMJ Surrogate vs patient relevant outcomes File
      Not available unless: Your ID number contains 02
    • Miner 2017 Am J Gastro Pecanatide for chronic constipation File
      Not available unless: Your ID number contains 02

    • Resources:

    • How Do We Know What We Know? Recording of TN lecture on industry-sponsored research and marketing. [52:16] URL

      This recording has some of the same examples as the lecture on Chapter 8; feel free to skip around.

    • Homework Assignment: Problem set #7 (RCTs)

    • Problem Set #7 File

    • Assignment due date:  11/05/2020 at 1:15 pm

    • Problem Set #7 (Upload) Assignment

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

    • Epi 204 PSET7 Answers File

  • Wednesday, November 3, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL


  • Thursday, November 4, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

  • Tuesday, November 9, 2021; 8:45 AM - 10:15 AM

    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

    • Lecture Slides:

    • epi screening 2019 handout File

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

    • Lecture 8 Screening (Recorded in 2019) Media Resource
      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Video of Large Group 11/9/2021 Media Resource
    • Medulloblastoma Problem File

      This is a problem on length- and lead-time bias that we were going to put on PSet#8, but it's too hard and requires a lot of clinical knowledge.   I tried to add some explanation and some additional pieces to make it easier.  Martina and Tom are planning to discuss it at large group discussion.   They have not reviewed my changes and may think I made things worse rather than better.

      Michael



    • Medulloblastoma Problem with Answers File

    • Required Reading:

      EBD2: Chapter 10

    • 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
      Not available unless: Your ID number contains 02
    • Tilman 2014 Nature Global diets link environmental sustainability and human health File
      Not available unless: You belong to a group in Registered Students Only
    • Welch 2019 NEJM Epidemiologic signatures cancer File

    • Assignment: Problem set #8: Alternatives to RCTs (Ch-9), P-Values and CIs (Ch 11),

    • Problem set #8 File

    • Assignment Due Date: 11/12/2020 1:15 pm: 

    • 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):

    • PSet #8 Answer Key File
      Not available unless: You belong to Registered students only

  • Wednesday, November 10, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

     

  • Friday NOT Thursday, November 12, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday 11/11, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

    • EPI 204 Section Assignment (includes Zoom Access Information) File

      Adam Zakaria's section has been re-distributed to the other 3 sections.  He has emailed you to assign you to one of Nicole, Anita (Michael), or Vidya (Tom).

      You may also attend Nasim's section on Thursday evening at 6 pm.

      Not available unless: You belong to Registered students only

  • Tuesday, November 16, 2021; 8:45 AM - 10:15 AM

    P-values and confidence intervals,  Alternatives to randomized trials

    Introduction and justification: why this Bayesian stuff is important and why we think you can handle it; what P-values and confidence intervals don' t mean; what they do mean; confidence intervals for negative studies and for proportions with small numerators.  Alternatives to RCTs: When randomized trials are and may not be needed; instrumental variables and natural experiments; measuring additonal predictor and outcome variables to estimate bias; propensity scores.

    Faculty:  Thomas Newman

    • Lecture Slides:

    • Lec 9 Alternatives To RCTs and P-values 2021-1115 File

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

    • Tom's 2019 Lecture on Alternatives to RCTS and P-values and CI (WATCH FOR 2020) URL
      Update for Slide 28: Vinay Prasad is in our department at UCSF now!
      Not available unless: You belong to Registered students only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Zoom Recording of Large Group 11/16/2021 Media Resource
      Not available unless: You belong to Registered students only
    • Chapter 9 and 11 ILG 2021-1115 File

    • Required Reading:

      EBD-2, Ch 9 and 11

    • Goodman S 2008 Seminars Hematol Dirty Dozen P Value fallacies File
      Not available unless: Your ID number contains 02

    • Optional Reading:

    • Laptook 2017 JAMA Effect of therapeutic hypothermia after 6 hours Bayesian example File
      Not available unless: Your ID number contains 02
    • Quintana 2017 JAMA Bayesian analysis. Using prior information to interpret results of clinical trials File
      Not available unless: Your ID number contains 02
    • 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
      Not available unless: Your ID number contains 02
    • Ray 2006 American Journal of Epidemiology New User DEsigns File
      Not available unless: Your ID number contains 02
    • Redelmeier 2001 AIM Survival in academy arard winners File
    • Sylvestre 2006 AIM Do Oscar winners live longer File

    • Assignment:  Problem set #9 - Alternatives to RCTs; P- values and confidence intervals


    • Problem Set #9 File

    • Assignment Due Date: 11/19/2020 at 1:15 PM

    • Problem Set #9 Upload Assignment


    • Problem Set #9 (M.Laker Section) Assignment
      Not available unless: You belong to M. Laker

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

    • PSet9 (chs 9 and 11) with Answers and changes 2021.1103.docx File
    • Newman 2021 JAMA IM LTE Possible Immortal Time Bias in Study of Antibiotics and Asthma File
    • Newman 2021 JAMA IM Antibiotics and asthma what have we learned Immortal Time Bias File

  • Wednesday, November 17, 2021; 1:00 PM - 2:30 PM

    Drop-in Help

    Course faculty are available to address questions

    Location (Access restricted to registered students):  Zoom URL

     

  • Thursday, November 18, 2021; 1:15 PM - 2:45 PM (Additional session: Thursday, 6:00 - 7:30 PM)

    Small Group Discussion (see roster for your section assignment)

    Review of prior lecture and problem set

    Faculty:  Vidya Eswaran, Anita Hargrave, Nicole Rodriguez, Nasim Sobhani, Adam Zakaria, Martina Steurer, Tom Newman, Alexis Beatty, and Michael Kohn
     
    Location (Access restricted to registered students): Zoom URL.

  • Tuesday, November 23, 2021 - No LGD - Thanksgiving Holiday

  • Thursday, November 25, 2021 - No Small Group - Thanksgiving Holiday

    Working on exam

  • Tuesday, November 30, 2021; 8:45 AM - 10:15 AM

    Cognitive Biases / Course Review
    Criticisms of evidence-based medicine; stories and statistics; psychology of medical decision making: heuristics used to estimate probability.  Course review.

    Faculty:  Michael Kohn

    • Lecture Slides:

    • Lecture 10 Cognitive Bias and Course Review File
    • Example Weighted Kappa Calculation File
    • CALFRAST File
    • Moderna Vaccine with NB Calculation File

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

    • 2020 (!) Course Review Zoom Video 12/1/2020 Media Resource

      2021 Students:  Note that this is last year's course review.

    • 2018 Lecture Cognitive Biases and Course Review (2021 students should watch this) URL
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Epi204 LGD and course review 11.30.2021 Media Resource

    • Required Reading:

      EBD, Chapter 12

    • Optional Reading:

    • Newman, TB. The Power of Stories over Statistics.BMJ. 2003;327(7429):1424-7 File
      Not available unless: Your ID number contains 02

    • Assignment: TAKE-HOME FINAL EXAM DUE MONDAY 12/6/21 11:59 PM

      The exam will be posted below by 2 pm on Tuesday 11/30/2021
    • Final EXAM epi 204 2021 File

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

      Do NOT collaborate with classmates.

    • EPI 204 Final Exam - upload Word doc here Assignment

      If possible, please upload as a Word .docx.  We will grade using "Track Changes".

      Due 12/6/21. 11:59 PM.

      Do NOT collaborate with classmates.

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

  • Wednesday, December 8, 2021; 1:00 PM - 2:45 PM

    Final Exam Review


    Faculty:  Michael Kohn


    • Zoom link (click on the word Zoom) or +1 669 900 6833 (Meeting ID: 945 0978 8609) (Password: 169414)

      Not available unless: You belong to Registered students only

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

    • Review of the Final Exam 12/8/2021 Media Resource
      Not available unless: You belong to Registered students only

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

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