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      Effective March 9, 2020:  In deference to the coronavirus outbreak, we will not be holding in-person activities for this course at Mission Hall.  Instead, all activities will be implemented via online mechanisms.  The Course Director will be providing additional information, and the relevant changes will be updated on the respective dates on this CLE page.

      Tuesday Office Hour Zoom Link: https://ucsf.zoom.us/j/897527765 or +1 669 900 6833 (Meeting ID: 891 527 765)

      Thursday Homework Review/Lecture Zoom Link: https://ucsf.zoom.us/j/591075194 or +1 669 900 6833 (Meeting ID: 591 075 194)


      Epidemiologic Methods II


      EPI 207 Winter 2020 (3 units)


      Course Director:

    • Forum for students to post questions and materials.

    • Session Slides:

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

  • Lecture: Introduction & Study Design (COH & RCT) (In-Person Lecture)

    Introduction to the course, strengths and limitations of randomized clinical trials, similarities and differences between components of randomized clinical trials and observational studies, and application of using a “target trial” to make causal inferences from cohort studies.

    Faculty:  June Chan

    Location:  
    Mission Hall 1407

    • Prospectus:

    • Please note - these slides were updated on Jan 8, 2020, to reflect a change in the calendar (office hours at 8:30 on Tuesday's instead of 9am; swapping topics on Feb 6 and 13). As stated in the video, please check the CLE for latest schedule updates. We did NOT update the video (below), only these slides.

    • This short video describes course objectives, format, resources, and expectations. Please review before the first day of class.

      1/8/20 - Please note the slide of the course calendar in this video was UPDATED on Jan 8th; the one in the video is outdated. Please see CLE for latest schedule.

    • Session Slides:

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

    • Required Reading:

      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.

    • Lawson KA. Multivitamin Use and Risk of Prostate cancer in the National Institutes of Health-AARP Diet and Health Study. JNCI 99:754-764, 2007 File
      Not available unless: Your ID number contains 02
    • Assignment:

    • Note - this assignment was slightly modified on Jan 9, at 5:30pm. There is a very slight (hopefully helpful) wording clarification on q6 only.  This edit will also be posted on the forum.

    • Assignment Due Date: January 16, 2020 at the beginning of class

    • Watch pre-recorded lecture for Matching/Ca-Co/Case-Only Designs

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

    • HW 1 Intro Coh HW Ques KEY 2020 FINAL to post File
      Not available unless: You belong to Registered Students Only
  • Lecture: Matching in Observational Studies - Pre-Recorded, View on Own BEFORE Jan. 16

    This lecture will review matching, including the purpose of matching, matching in cohort, case-control, and case-only studies.

    Faculty:  Erin Van Blarigan

    • Session Slides:

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

    • Intro to Matching Part 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Intro to Matching Part 2 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Intro to Matching Part 3 Media Resource
      Not available unless: You belong to a group in Registered Students Only
  • Office Hours: Intro/RCTs/Target Trial/Coh

    Faculty: Dan Kelly

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)


  • Homework #1 Review: RCTs/Target Trial/Coh

    Faculty: Dan Kelly

    Location: Mission Hall 1407

  • Lecture: Matching in Observational Studies (Remote Live Lecture)

    This lecture will review matching, including the purpose of matching, matching in cohort, case-control, and case-only studies.

    Faculty:  Erin Van Blarigan

    Location:  Mission Hall 1407

    • Session Slides:

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

    • Required Reading:

           Chapter 8 AND pages 171-182 (optional 283-288). Rothman/Greenland/Lash, 2008, 3rd edition, Case-Control Studies

            Poynter JN, Gruber SB, Higgins PD, Almog R, Bonner JD, Rennert HS, Low M, Greenson JK, Rennert G. Statins and the risk of colorectal cancer. N Engl J Med. 2005 May, PubMed PMID: 15917383. https://www.ncbi.nlm.nih.gov/pubmed/?term=15917383


    • HW7 assigned reading statins and crc in nejm File
      Not available unless: Your ID number contains 02
    • Optional Reading:

    • Hernan IJE 2013 Matching and Causal Diagrams File
      Not available unless: Your ID number contains 02
    • Pearce 2016bmj matching File
      Not available unless: Your ID number contains 02
    • Forest fire smoke and Cardiac ehp.1408436 Matching lec File
      Not available unless: Your ID number contains 02
    • Assignment:

    • Assignment Due Date: January 23, 2020 at the beginning of lecture

    • Watch pre-recorded lecture on Causal Inference

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

    • HW2 2020 Matching CaCo FINAL Ans Key to POST File
      Not available unless: You belong to a group in Registered Students Only
  • Lecture: Causal Inference  - Pre-Recorded, View on Own BEFORE Jan. 23

    Models/heuristics for causal inference in epidemiology; discussion of counterfactuals and identifiability criteria; ideal randomized experiments

    Faculty:  Rebecca Graff

  • Office Hours: Matching/Ca-co/Case-only Designs

    Faculty:  Shelley DeVost

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Homework #2 Review: Matching/Ca-Co/Case-Only Designs

    Faculty:  Shelley DeVost

    Location:  Mission Hall 1407

  • Lecture: Causal Inference (In-Person Lecture)

    Models/heuristics for causal inference in epidemiology; discussion of counterfactuals and identifiability criteria; ideal randomized experiments”

    Faculty:  Rebecca Graff

    Location: Mission Hall 1407

    • Session slides:

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

    • Required Reading:

      Chapters 1 and 2, Hernán & Robins, Causal Inference Book, online

    • Article to read for Causal Inf HW Jain et al JAMA 2015 File
      Not available unless: You belong to Registered Students Only
    • Optional Reading:

      1. Chapter 3, Hernán & Robins, Causal Inference Book, online

      2. Chapter 2, Rothman, Greenland, & Lash, 2008

      3. “Applying the Bradford Hill criteria in the 21st century: how data integration has changed causal inference in molecular epidemiology” Fedak et al. Emerging Themes in Epidemiology. 2015

      https://ete-online.biomedcentral.com/articles/10.1186/s12982-015-0037-4

      4. “Invited Commentary: The Continuing Need for the Sufficient Cause Model Today.” Tyler J. VanderWeele. AJE 2017.


    • Fedak KM. Applying the Bradford Hill criteria in the 21st century: how data integration has changed causal inference in molecular epidemiology. Emerg Themes Epidemiol. 12:14:1-9, 2015 File
      Not available unless: Your ID number contains 02
    • VanderWeele TJ. Invited Commentary: The Continuing Need for Suggicient cause Model Today. AJE 185:11:1041-1043,2017 File
      Not available unless: Your ID number contains 02
    • Assignment:

    • Assignment Due Date: January 30, 2020 at the beginning of lecture

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

    • Causal Inference HW3 KEY W2020 Final to post v2 File

      Small edits made from key originally posted at 3:30 - i.e., In q7b, after the tree diagrams, the 2x2 table for the pseudo-population was missing, though it is the same as the one obtained using the 2x2 table method beneath it. The interpretation statements have also now been made the same, across q7, as mentioned in class and to avoid confusion. We have updated this now and re-posted (v2), in case you wish to download again.

      Not available unless: You belong to Registered Students Only
  • Lecture: Person-time and Bias  - Pre-Recorded, View on Own BEFORE Jan. 30

    View Parts 1-3 of Person-time and Bias lecture (listed on Jan 30) BEFORE coming to class on Jan 30, 2020.

     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

  • Office Hours: Causal Inference

    Faculty:  Dan Kelly

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Homework #3 Review: Causal Inference

    Faculty:  Dan Kelly

    Location:  Mission Hall 1407

  • 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

    Location: Mission Hall 1407

  • Office Hours: Person Time & Bias

    Faculty: June Chan

    Location:  online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Lecture: DAGS (In-Person Lecture)

    We will review how to draw and use Directed Acyclic Graphs.  This will cover applying the d-separation rule, identifying sufficient and minimally sufficient sets, and DAGs to represent common biases in epidemiology.  We will consider representations of alternative study designs and how these representations help identify potential design problems.  Finally, we will discuss limitations of DAGs and controversies about the usefulness of DAGs.

    Faculty:  Rebecca Graff

    Location:  
    Mission Hall 1407

    • Session Slides:

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

    • Required Reading:

      Chapter 12, Rothman, Greenland, & Lash 3rd Edition

      Hernán MA, Zhang SM, Rueda-deCastro AM, Colditz GA, Speizer FE, Ascherio A. Cigarette smoking and the incidence of Parkinson’s disease in two prospective studies. Ann Neurol. 2001 Dec;50(6):780-6. PMID: 11761476.

    • Optional Reading:

      Ch. 6-9 - Hernán MA & Robins JM, Causal Inference book – What if, online text book (Nov. 2019 version)

       "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

       Glymour MM, Weuve J, Berkman LF, Kawachi I, Robins JM. When is baseline adjustment useful in analyses of change? An example with education and cognitive change. American journal of epidemiology. 2005 Aug 1;162(3):267-78. (This is an illustration of a particular problem that could helpfully be represented with DAGs) https://www.ncbi.nlm.nih.gov/pubmed/15987729

      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 

      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

    • Assignment

    • Watch pre-recorded lecture on Interaction/Effect Modification

    • Assignment Due Date: February 20, 2020 at the beginning of lecture

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

  • Office Hours: DAG's

    Faculty:  Shelley DeVost

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Homework #4 Review: Person Time & Bias

    Faculty:  Dan Kelly and June Chan

    Location:  Mission Hall 1407

  • Lecture: Interaction/Effect Modification - Pre-Recorded, View on Own BEFORE Feb. 20

    BEFORE class on Feb. 20, 2020, please view/review Parts 1-4 of Interaction/Effect Modification (listed on Feb. 20). 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 2/20. In the live lecture on 2/20, we will also be focusing on discussing interaction using the counterfactual framework.

    Faculty:  June Chan and Francois Rerolle
  • Office Hours: General catch-up

    Faculty:  Shelley DeVost

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Homework #5 Review: DAGs

    Faculty:  Michelle DeVost

    Location:  Mission Hall 1407

  • Lecture: Interaction/Effect Modification  (In-Person Lecture)

    Faculty: June Chan and Francois Rerolle

    Location: Mission Hall 1407

    • Session Slides (In-Person Lecture):

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

    • Session Slides/Video Recordings (Pre-Recorded):

      BEFORE class on Feb. 20, 2020, please view/review Parts 1-4 of Interaction/Effect Modification (listed on Feb. 20). 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 2/20. In the live lecture on 2/20, we will also be focusing on discussing interaction using the counterfactual framework.


    • 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
    • Part5 rec Interaction EffMod winter 2019 v2 Media Resource
    • 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


    • Knol et al Int J Epid 2007 Interaction on Additive Scale File
      Not available unless: Your ID number contains 02
    • Note, this HW assignment contains minor updates for q10-12 (as of 5pm on 2/20), per the notes on the Forum and as follow-up to the discussion in class. Please be sure to re-download this version.

    • Assignment Due Date: February 27, 2020 at the beginning of lecture

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

    • HW6 interaction Ques Answ w2020 key to POST final File
      Not available unless: You belong to a group in Registered Students Only
  • Optional Mini-Lab (STATA): Interaction/Effect Modification

    Faculty:  Dan Kelly

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Homework #6 Review: Interaction/Effect Modification

    Faculty:  Dan Kelly

    Location:  Mission Hall 1407

  • Office Hours: General Catch Up

    Faculty:  Dan Kelly

    Location:  Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)

  • Live Lecture: 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.

    Please RSVP to event: http://bit.ly/2OqttDh

    Faculty:  Elizabeth Rose Mayeda

    Location:  Mission Hall 1407  and online or +1 669 900 6833 (Meeting ID: 456 559 873)

    • Session Slides:

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

    • Required Reading:

      Orsini, N., Bellocco, R., Bottai, M., Wolk, A. and Greenland, S., 2008. A tool for deterministic and probabilistic sensitivity analysis of epidemiologic studies. Stata Journal, 8(1), pp.29-48.

      http://www.stata-journal.com/article.html?article=st0138


    • Orsini article for QBA HW File
      Not available unless: Your ID number contains 02
    • 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: Your ID number contains 02
    • Hernán MA, Hernández-Díaz S, Robins JM. A structural approach to selection bias. Epidemiology. 2004;15(5):615-625. File
      Not available unless: Your ID number contains 02
    • 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: Your ID number contains 02
    • Last TL, et al. Good practices for quantitative bias analysis. International Journal of Epidemiology. 2014;43(6):1969-1985. File
      Not available unless: Your ID number contains 02
    • Assignment:

    • Assignment Due Date: March 12, 2020 at the beginning of lecture

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

  • ONLINE OFFICE HOUR: QBA

    Faculty: Michelle DeVost

    Location:   Join from a PC, Mac, Linux, iOS or Android device: https://ucsf.zoom.us/j/891527765

    Meeting ID: 891 527 765

    Telephone:
    US: +1 669 900 6833
    or +1 646 558 8656

    iPhone single-tap (US Toll):
    +16699006833,,891527765# or +16465588656,,891527765#

  • Homework #7 Review: Quantitative Bias Analysis

    Faculty: Michelle DeVost

    Location: ZOOM ONLY

    Join from a PC, Mac, Linux, iOS or Android device:
    https://ucsf.zoom.us/j/591075194

    Meeting ID: 591 075 194

    Telephone:
    US: +1 669 900 6833
    or +1 646 558 8656

    iPhone single-tap (US Toll):
    +16699006833,,591075194# or +16465588656,,591075194#


  • Lecture: Wrap Up

    Faculty: June Chan

    Location: ZOOM ONLY

    Join from a PC, Mac, Linux, iOS or Android device: 
    https://ucsf.zoom.us/j/591075194 

    Meeting ID: 591 075 194 

    Telephone: 
    US: +1 669 900 6833 
    or +1 646 558 8656 

    iPhone single-tap (US Toll): 
    +16699006833,,591075194# or +16465588656,,591075194# 

    • Homework review & Wrap Up 3/12/20 Media Resource
      Not available unless: You belong to Registered Students Only
    • 300312 WrapUp with markings and NEW slides after Review File
      Not available unless: You belong to Registered Students Only
  • Final exam will be posted by 5:00pm 3/12 with due date of Thursday, March 26th, 2020 @ 11:59pm.

    • Take-Home Exam Assignment: Will by posted by 5pm
    • 200316 Final Exam Ques only to Post-v2a File
      Not available unless: You belong to Registered Students Only
    • Required Readings and other Resources:

    • Satia et al AJE 2009 BetaCarotene and Lung CA in VITAL File
      Not available unless: You belong to Registered Students Only
    • RIVUR Dataset for Q12_13_14 FINAL Exam File
      Not available unless: You belong to Registered Students Only
    • Jain et al MMR and ASD Supplemental Content JAMA 2015 File
      Not available unless: You belong to Registered Students Only
    • Final Exam Due Date: March 26, 2020 by 11:59 PM (23:59)

    • 200426 Final Exam KEY v2a To POST File