Section outline


  • Course Introduction & Conceptual Frameworks for Causal Inference

    Introduction to the course; models/heuristics for causal inference in epidemiology; discussion of counterfactuals and identifiability criteria; ideal randomized experiments; conditional randomization

    Faculty: June Chan, Rebecca Graff

    • Required Reading (please read PRIOR to watching the lectures):

      Chapter 1, Hernán & Robins, Causal Inference Book, online

    • Recommended Reading:

      Chapter 2, Hernán & Robins, Causal Inference Book, online

    • Optional Reading:

      1. Chapter 3, Hernán & Robins, Causal Inference Book, online
      2. Chapter 2, Rothman, Greenland, & Lash, 2008

    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Intro to EPI 207 W21 revised Media Resource
    • Conceptual Frameworks for Causal Inference - Part 1 Media Resource
    • Conceptual Frameworks for Causal Inference - Part 2 Media Resource
    • Bradford Hill (Optional) Media Resource
    • Sufficient & Component Cause (Optional) Media Resource
    • Session Slides:

    • Two word clouds from first day of class File
    • Session Audio/Video Recording (access restricted to registered students):

    • Class Recording - Week 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, January 21, 2021 at the beginning of lecture

    • Article to Read for HW - Jain, et al. JAMA 2015 File
      Not available unless: You belong to Registered Students Only
    • Watch pre-recorded lecture on DAGs

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

    • Miscellaneous:

  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez

  • DAGs

    How to draw and use directed acyclic graphs; d-separation; DAGs to represent common biases in epidemiology; limitations of DAGs

    Faculty:  Rebecca Graff


    • Required Reading (please read PRIOR to watching the lectures):

      1. Chapter 2, Hernán & Robins, Causal Inference Book, online (if you didn't already read it for Week 1)
      2. Chapter 6, Hernán & Robins, Causal Inference Book, online

    • Optional Reading:

      1. Chapters 7.1-7.4, 8.1-8.5, and 9, Hernán & Robins, Causal Inference Book, online
      2. Chapter 12, Rothman, Greenland, & Lash, 2008
      3. "Using Causal Diagrams to Understand Common Problems in Social Epidemiology", M Glymour. chapter 18 in Methods in Social Epidemiology, 2nd edn. (2017) Oakes and Kaufman eds. Wiley (This is an updated and somewhat friendlier version of the chapter in Modern Epi). http://publicifsv.sund.ku.dk/~nk/epiF14/Glymour_DAGs.pdf

      4. Hernán MA, Hernández-Díaz S, Robins JM. A structural approach to selection bias. Epidemiology. 2004 Sep 1;15(5):615-25. (This was a very influential paper that reconceptualized how we think about selection bias). https://www.ncbi.nlm.nih.gov/pubmed/15308962 

      5. VanderWeele TJ, Hernán MA. Results on differential and dependent measurement error of the exposure and the outcome using signed directed acyclic graphs. American journal of epidemiology. 2012 May 8;175(12):1303-10. https://www.ncbi.nlm.nih.gov/pubmed/22569106

    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Directed Acyclic Graphs - Part 1 Media Resource
    • Session Slides:

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

    • Class Recording - Week 2 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, January 28, 2021 at the beginning of lecture

    • Article to Read for HW - Hernan, et al. Ann Neurol 2001 File
      Not available unless: You belong to Registered Students Only
    • Assignment Answer Key (access restricted to registered students):

    • Directed Acyclic Graphs Homework Answer Key File
      Not available unless: You belong to a group in Registered Students Only
  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez

  • Homework #1 Review: Conceptual Frameworks for Causal Inference

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez

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

    • Class Recording - Week 3 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, January 28, 2021 at the beginning of lecture

    • Watch pre-recorded lectures on Target Trials

  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Homework #2 Review: DAGs

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez

  • Target Trials


    Strengths and limitations of randomized clinical trials; similarities and differences between components of randomized clinical trials and observational studies; application of using a “target trial” to make causal inferences from cohort studies.

    Faculty:  June Chan

    • Required Reading (please read PRIOR to watching the lectures):

      Rothman, Greenland and Lash 2008 (RGL), Modern Epidemiology, Ch. 6 (focus on RCT and COH) skim Chapter 7. Please note, RGL Chapter 7 will also be assigned for a future lecture on Person Time/Bias in Cohorts.


    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Target Trials - Part 1 Media Resource
    • There is no recording associated with the Target Trials - Part 2 slides. Please just review the slides.

    • Target Trials - Part 3 Media Resource
    • Session Slides:

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

    • Class Recording - Week 4 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, February 4, 2021 at the beginning of lecture

    • Article to Read for HW - Lawson, et al. J Natl Cancer Inst 2007 File
      Not available unless: You belong to a group in Registered Students Only
    • EPID 207 W21 Target Trials HW Questions File
      Not available unless: You belong to Registered Students Only
    • Watch pre-recorded lecture on Matching in Observational Studies

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

    • 210203 EPI207 RCT Coh Target Trials KEY ONLY to POST File
      Not available unless: You belong to Registered Students Only
  • Office Hours: 

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Homework #3 Review: Target Trials

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez

  • Matching in Observational Studies

    Purpose of matching; matching in cohort and case-control studies; case-crossover studies

    Faculty:  Rebecca Graff

    • Required Reading (please read PRIOR to watching the lectures):

      Chapter 8, pages 171-182, and page 605 Rothman, Greenland, & Lash, 2008


    • Optional Reading:

      Pages 283-288, Rothman, Greenland, & Lash, 2008


    • Mansournia, et al. Int J Epidemiol 2013 File
      Not available unless: You belong to a group in Registered Students Only
    • Pearce BMJ 2016 File
      Not available unless: You belong to a group in Registered Students Only
    • Dennekamp, et al. Environ Health Perspect 2015 File
      Not available unless: You belong to a group in Registered Students Only
    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Matching in Observational Studies - Part 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Matching in Observational studies - Part 2 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Matching in Observational Studies - Part 3 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Session Slides:

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

    • Class Recording - Week 5 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, February 11, 2021 at the beginning of lecture

    • Article to Read for HW - Poynter, et al. N Engl J Med 2005 File
      Not available unless: You belong to a group in Registered Students Only
    • Watch pre-recorded lecture on Interaction/Effect Modification

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

    • Matching in Observational Studies Homework Answer Key File
      Not available unless: You belong to a group in Registered Students Only
  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Homework #4 Review: Matching

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Lecture: Interaction/Effect Modification

    Faculty: June Chan 

    BEFORE class on Feb. 11, 2021, please do the readings and view/review Parts 1-4 of Interaction/Effect Modification (listed on Feb. 11). You are responsible for the material in all parts, however note that Parts 1, 2a, and 2b may be more of a “review” for some. In particular, parts 2a and 2b may have been recently covered by Dr. Shiboski in BIO208. For these sections, you may wish to skim the slides, to ensure that you are familiar with the material but may opt not to watch the video lectures. Part 3 is a slide deck of definitions only (no video), and we will review some of this during the live lecture on 2/11. In the live lecture on 2/11, we will also be focusing on discussing interaction using the counterfactual framework.

    • Required Reading:

      VandeerWeele & Knol, “A Tutorial on Interaction”, Epidemiol Methods 2014, PARTS 1.1-1.7 only (parts 1.8, 1.9 and 2 are optional)

      Chapter 5, p. 71-76 (the rest of the chapter is optional) Rothman/Greenland/Lash 2008, Modern Epidemiology 3rd edition


    • VanderWeele.InteractionTutorial 2014 clean to post File
      Not available unless: Your ID number contains 02
    • Optional Reading:

      Hernan & Robins, Causal Inference online book, Ch. 4.1-4.3 and Ch. 5.1-5.3


    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Part 1 Intro Interaction EffMod winter 2019 Media Resource
    • Part 2a_rec_Model Coeff_Interaction EffMod v2 Media Resource
    • Part 2b_rec_Model Coeff_Interaction EffMod v2 Media Resource
    • No video for Part 3
    • Part4 rec Presenting EffMod winter 2019 REDO 190227 Media Resource
    • Part 6 AFTER live lec Part 5_EPID207 W21 Intro to Interaction App by Francois Rerolle_Recorded Lec Media Resource
      Not available unless: You belong to Registered Students Only
    • Session Slides:

    • In_Class_Int EM_Updates Parts 3_4 AND Live Part5 Counterfactual Framework File
      Not available unless: You belong to Registered Students Only
    • No slides for Part 6, recorded lecture by Francois Rerolle; video only
    • Part7 OPTIONAL Appendix NOT Recorded Interaction EffMod File
      Not available unless: You belong to Registered Students Only
    • Session Audio/Video Recording (Access restricted to registered students):

    • Class Recording - Week 6 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, February 18, 2021 at the beginning of lecture. Note, for this HW assignment, you will need to access the online "app" below.

      https://francoisrerolle.shinyapps.io/epi_207_interaction_app/

    • EM and Interaction HW Ques W21 File
      Not available unless: You belong to Registered Students Only
    • Dataset for Interaction HW File
      Not available unless: You belong to Registered Students Only
    • Watch pre-recorded lectures on Person-time and Bias

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

    • 210218 W21 Interaction HW Answ Key to POST File
      Not available unless: You belong to a group in Registered Students Only
  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Lecture: Person-time and Bias (In-Person Lecture)

    Fixed vs. open cohorts; the dynamic allocation of person-time in longitudinal cohorts; patient or survivor cohorts; particular bias issues discussed in the setting of patient cohorts (including selection bias, immortal-person time bias, measurement error bias, confounding by indication, and residual confounding); and how emulation of a target trial may help avoid some of these biases.

    Faculty: June Chan

    View Parts 1-3 of Person-time and Bias lecture BEFORE coming to class on Feb 18, 2021.


    • Required Reading (please read PRIOR to watching the lectures):

      Chapter 7, Rothman, Greenland, & Lash 3rd Edition

    • Recommended Reading:

      Optional Reading:

      Emilsson L, García-Albéniz X, Logan RW, Caniglia EC, Kalager M, Hernán MA. Examining Bias in Studies of Statin Treatment and Survival in Patients With Cancer. JAMA Oncol. 2018, PubMed PMID: 28822996. https://www.ncbi.nlm.nih.gov/pubmed/28822996 



    • For those interested in a bit more background information on survival analysis, please see this chapter written by Dr. McCulloch for the UCSF medical students, in 2016. We are sharing this supplemental information with his permission. Please note there may be internal references in this chapter to other texts from that course, which are not relevant for EPI207. (citation: Ch. 65 of the UCSF SOM Mechanisms, Methods, and Malignancy syllabus, 2016, copyright UC Regents)

    • Recorded Lectures (please watch PRIOR to class):

      Access restricted to registered students

    • Session Slides:

    • 200130 InClass Exercise Ques withANSWERS File
      Not available unless: You belong to Registered Students Only
    • Session Audio/Video Recording (Access restricted to registered students):

    • Class Recording - Week 7 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Assignment:

      Due Thursday, February 25, 2021 at the beginning of lecture

    • HW PT Bias Ques to Post W21 File
      Not available unless: You belong to Registered Students Only
    • Choe, K.S., et al, Aspirin use and the risk of prostate cancer mortality in men treated with prostatectomy or radiotherapy. 2012, Journal of Clinical Oncology, 30(28), pp.3540-3544.


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

    • W21 PT Bias KEY to post File
      Not available unless: You belong to Registered Students Only
  • Homework #5 Review: Effect Modification/Interaction

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Lecture: DAGs for Advanced Challenges to Validity

    Faculty: June Chan and Rebecca Graff

    • Session Slides:

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

    • Class Recording - Week 8 Media Resource
      Not available unless: You belong to a group in Registered Students Only
  • Homework #6 Review: Person-Time/Bias

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Quantitative Bias Analysis (QBA) 

    The focus of this workshop is methods for conducting quantitative bias analysis in epidemiologic research. We will first provide a brief introduction to confounding, information bias, and selection bias using causal diagrams. Next, we will discuss deterministic and probabilistic bias analysis. Dr. Mayeda will discuss examples of specific biases in her own work on determinants of cognitive decline in older adults. At the end of the workshop, participants should walk away with an understanding of the motivations behind quantitative bias analysis and how to use tools for conducting quantitative bias analysis.

    The first two hours will contain the material for which students in EPI207 are responsible; the last hour is optional for the class.

    Faculty:  Elizabeth Rose Mayeda


    • Optional Reading:


    • Mayeda ER, et al. A simulation platform for quantifying survival bias: an application to research on determinants of cognitive decline. American Journal of Epidemiology. 2016 Sep 1;184(5):378-87. File
      Not available unless: You belong to Registered Students Only
    • Hernán MA, Hernández-Díaz S, Robins JM. A structural approach to selection bias. Epidemiology. 2004;15(5):615-625. File
      Not available unless: You belong to Registered Students Only
    • Fox MP, Lash TL, Greenland S. A method to automate probabilistic sensitivity analyses of misclassified binary variables. International journal of epidemiology. 2005;34(6):1370-1376. File
      Not available unless: You belong to Registered Students Only
    • Last TL, et al. Good practices for quantitative bias analysis. International Journal of Epidemiology. 2014;43(6):1969-1985. File
      Not available unless: You belong to Registered Students Only
    • Session Slides:

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

    • Class Recording QBA Workshop W21 Media Resource
      Not available unless: You belong to Registered Students Only
    • Assignment:

      Due Thursday, March 11, 2021 at the beginning of lecture

    • Orsini article for QBA HW File
      Not available unless: You belong to Registered Students Only
    • Assignment Answer Key (access restricted to registered students):

    • QBA Homework Answer Key File
      Not available unless: You belong to Registered Students Only
  • Office Hours

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Homework #7 Review: QBA

    Instructors: Alice Guan, Eduardo Santiago-Rodriguez


  • Wrap Up

    Faculty: June Chan, Rebecca Graff

    • Optional Reading:


    • Emilsson et al JAMA 2018 Bias in Studies of Statins and Cancer URL
      Not available unless: You belong to Registered Students Only
    • Chan et al JAMA 2018_Commentary Statins & Overall and CA survival URL
      Not available unless: You belong to Registered Students Only
    • Stefan MS Orig Article JAMA 21 Antibiotics and Asthma with potential IM Time bias URL
      Not available unless: You belong to Registered Students Only
    • Newman T Comment on Stefan MS_JAMA 21 IM Time Bias_Antibiotics_Asthma URL
      Not available unless: You belong to Registered Students Only
    • Stefan MS et al JAMA 21 Retraction and Replacement URL
      Not available unless: You belong to Registered Students Only
    • Session Slides:

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

    • Class Recording Wrap-up / Review Media Resource
      Not available unless: You belong to Registered Students Only
  • The final exam will be posted by 5:00pm on Thursday, 3/11 and be due by Friday, 3/19 at 11:59pm.

    • Assignment:

      Due Friday, March 19, 2021 at 11:59pm

    • 2021 Epi 207 Final Exam Questions v2 File
      Not available unless: You belong to Registered Students Only
    • Satia, et al. Am J Epidemiol 2009 (Q1-Q4) File
      Not available unless: You belong to Registered Students Only
    • Jain, et al. JAMA 2015 Supplement (Q8) File
      Not available unless: You belong to Registered Students Only
    • RIVUR Dataset (Q9) File
      Not available unless: You belong to Registered Students Only
    • Assignment Answer Key (access restricted to registered students):

    • 2021 Epi 207 Final Exam Answer Key File