EPI 204: Clinical Epidemiology (Fall 2019)
Section outline
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Use the link above to upload the problem-writing assignment by 11:59 pm on Thursday 11/14.
You must be logged in to use the upload link.
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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-
Watch URL
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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.
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Skip from "Reiliability of Continuous Measurements" on Page 12 up to "Using studies of reliability from the literature" on Page 21.
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").
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In section on 9/19, 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.
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Kohn (2013) Understanding Evidence-Based Diagnosis File
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Small Group Discussion Section 1
Review of Chapter 1 (Reason for a Diagnosis) problems and "Kappa Game"
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Due 9/26 at 1 pm. Upload to CLE.
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Use the link above to upload Problem Set #1 by 1 pm on 9/27 (this should have said 9/26, but we will accept late homework).
You must be logged in to upload your assignment.
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Problem Set #1 (M.Laker Section) Assignment
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PSet 1 Answer Key File
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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 Regret graphs to understand testing and treatment thresholdsFaculty: Thomas Newman
Location: Mission Hall 1400-
Watch URL
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2019 Lecture .MP4 URL
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EBD-2 Ch 2 -- Dichotomous tests File
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Testing Threshold Derivations File
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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/
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Small Group Discussion Section 2
Review HW-1 (Kappa) Problems
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Upload Problem Set #2 to the above link by 1 pm on Thursday 10/3.
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PSet2 Answer Key File
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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-
This version has one sheet for demo and one with the formulas
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Watch URL
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2019 Lecture .mp4 URL
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Small Group Discussion Section 3
Review HW-2 (Dichotomous Tests)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Due 10/10/2019, 1:00 pm.
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PSet #3 Answer Key File
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Office Hours
Location: MH-2500
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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-
Watch URL
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2019 Lecture .mp4 URL
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Kohn Carpenter Newman -- Understanding the Direction of Bias in Studies of Diagnostic Test Accuracy File
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Mehta 2009 J Hepatol Exceeding the limits of liver histology markers File
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Moyer 2000 APAM AccuracyJaundice File
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Small Group Discussion Section 4
Review HW-3 (Multi-level Tests)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Due 10/17 1 pm
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Pset 4 Answer Key File
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Office Hours
Location: online or +1 669 900 6833 (Meeting ID: 758 106 231)
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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-
Watch URL
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2019 Lecture .mp4 URL
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Vickers_Net_Benefit_BMJ_2016.pdf File
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Kerr 2015 Decision Curves File
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Small Group Discussion Section 5
Review HW-4 (Bias in Test Accuracy Studies)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Problem Set #5 includes 4 problems. The first 3 are in the posted file above. The complete 4-problem document is below.
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The complete Problem Set 5 has 4 problems.
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Office Hours
Location: MH-2500
https://ucsf.zoom.us/j/186412472Meeting ID: 186 412 472Telephone:US: +1 669 900 6833or +1 646 558 8656 -
Lecture 6: Combining Tests and Multivariable Risk Models
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-
Watch URL
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2019 Lecture .mp4 URL
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Small Group Discussion Section 6
Review HW-5 (Evaluating Risk Predictions)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108 -
Office Hours
Location: online or +1 669 900 6833 (Meeting ID: 758 106 231)
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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: Martina Steurer
Location: Mission Hall 1400-
Watch URL
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2019 Lecture .mp4 URL
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LeNoury 2015 BMJ Restoring Study 329 File
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Newman 2004 NEJM Antidepressant Perspective File
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Stempel 2016 NEJM AUSTRI study Advair v fluticasone alone File
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Stolker 2014 Circulation rethinking composite endpoints in clinical trials File
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Ciani 2013 BMJ Surrogate vs patient relevant outcomes File
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Miner 2017 Am J Gastro Pecanatide for chronic constipation File
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Small Group Discussion Section 7
Review HW-6 (Combining Tests)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108 -
Office Hours
Location: MH 2500 and online or +1 669 900 6833 (Meeting ID: 758 106 231)
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Lecture 8: P-Values and Confidence Intervals / Alternatives to RCTs
Faculty: Thomas Newman
Location: Mission Hall 1400-
Watch URL
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2019 Lecture .mp4 URL
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Goodman S 2008 Seminars Hematol Dirty Dozen P Value fallacies File
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Laptook 2017 JAMA Effect of therapeutic hypothermia after 6 hours Bayesian example File
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Quintana 2017 JAMA Bayesian analysis. Using prior information to interpret results of clinical trials File
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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
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Goodman, S. Toward evidence-based medical statistics. 1: The P value fallacy. Annals of Internal Medicine 1999; 130: 995-1004 File
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Goodman, S. Toward evidence-based medical statistics. 2: The Bayes factor. Annals of Internal Medicine 1999; 130: 1005-1013 File
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Newman, T. If almost nothing goes wrong, is almost everything all right? JAMA 1995; 274: 1013 File
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Goodman S 2013 Circulation Are we there yet File
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Ray 2006 American Journal of Epidemiology New User DEsigns File
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Small Group Discussion Section 8
Review HW-7 (RCTs)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Problem Set #8 (M.Laker Section) Assignment
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Office Hours
Location: online or +1 669 900 6833 (Meeting ID: 758 106 231)
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Reminder: Problem-writing assignment due at midnight. See top of Syllabus.
Lecture 9: 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-
Watch URL
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2014 Lecture (Watch) URL
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2019 Lecture .mp4 URL
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Merenstein D. Winners & Losers. JAMA 2004;291:242-5 File
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Heath 2014 BMJ Role of fear in overdiagnosis File
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Heath 2013 BMJ Overdiagnosis When good intentions meet vested interests File
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Newman 2016 JAMA IM Lipid screening in children-low value care File
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Annas 1995 NEJM Reframing the Debate on Healthcare by replacing Metaphors File
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Tilman 2014 Nature Global diets link environmental sustainability and human health File
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Small Group Discussion Section 9
Review HW-8 (P-Values, Confidence Intervals)
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108 -
Office Hours
Location: MH 2500 and online or +1 669 900 6833 (Meeting ID: 758 106 231)
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Lecture 10: Cognitive Biases / Course Review
Faculty: Michael Kohn
Location: Mission Hall 1400-
2018 Lecture Watch (2019 students should watch this) URL
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Newman, TB. The Power of Stories over Statistics.BMJ. 2003;327(7429):1424-7 File
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Small Group Discussion Section 10
Review HW-9 Screening
Faculty: Charles Murphy, Adrian Whelan, Sandeep Brar, Marta San Luciano Palenzuela, Miriam Laker, Kerstin Kolodzie, Martina Steurer, Tom Newman, Michael Kohn
Location: Murphy MH-2105, Whelan MH-2106, Brar MH-2107, San Luciano Palenzuela MH-2108-
Problem Set #9 (M.Laker Section) Assignment
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Lecture 11: Final Exam Review
Faculty: Michael KohnLocation: Mission Hall 1400
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Watch URL
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2019 Lecture .mp4 URL
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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.
