EPI 207: Epidemiologic Methods II (Winter 2020)
Section outline
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Forum for students to post questions and materials.
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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-
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.
Uploaded 01/8/20, 16:49 -
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1/8/20 - Please note the slide of the course calendar in this video was UPDATED on Jan 8th; the one in the video is outdated.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.
Uploaded 01/4/20, 13:40 -
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
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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.
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HW 1 Intro Coh HW Ques KEY 2020 FINAL to post File
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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
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Intro to Matching Part 1 Media Resource
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Intro to Matching Part 2 Media Resource
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Intro to Matching Part 3 Media Resource
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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)
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Homework #1 Review: RCTs/Target Trial/Coh
Faculty: Dan Kelly
Location: Mission Hall 1407
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Uploaded 01/16/20, 16:52
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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
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Uploaded 01/16/20, 15:16
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HW7 assigned reading statins and crc in nejm File
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Hernan IJE 2013 Matching and Causal Diagrams File
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Pearce 2016bmj matching File
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Forest fire smoke and Cardiac ehp.1408436 Matching lec File
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HW2 2020 Matching CaCo FINAL Ans Key to POST File
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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 experimentsFaculty: Rebecca Graff
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Causal Inference Part 2 updated Media Resource
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Causal Inference Part 3 Media Resource
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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)
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Homework #2 Review: Matching/Ca-Co/Case-Only Designs
Faculty: Shelley DeVost
Location: Mission Hall 1407
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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
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Article to read for Causal Inf HW Jain et al JAMA 2015 File
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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
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VanderWeele TJ. Invited Commentary: The Continuing Need for Suggicient cause Model Today. AJE 185:11:1041-1043,2017 File
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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.
Uploaded 01/30/20, 17:48
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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
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Office Hours: Causal Inference
Faculty: Dan Kelly
Location: Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)
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Homework #3 Review: Causal Inference
Faculty: Dan Kelly
Location: Mission Hall 1407
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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
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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)
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Office Hours: Person Time & Bias
Faculty: June Chan
Location: online or +1 669 900 6833 (Meeting ID: 891 527 765)
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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 -
Office Hours: DAG's
Faculty: Shelley DeVost
Location: Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)
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Homework #4 Review: Person Time & Bias
Faculty: Dan Kelly and June Chan
Location: Mission Hall 1407
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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)
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Homework #5 Review: DAGs
Faculty: Michelle DeVost
Location: Mission Hall 1407
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Lecture: Interaction/Effect Modification (In-Person Lecture)
Faculty: June Chan and Francois Rerolle
Location: Mission Hall 1407
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Part 1 Intro Interaction EffMod winter 2019 Media Resource
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Part 2a_rec_Model Coeff_Interaction EffMod v2 Media Resource
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Part 2b_rec_Model Coeff_Interaction EffMod v2 Media Resource
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Part4 rec Presenting EffMod winter 2019 REDO 190227 Media Resource
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Part5 rec Interaction EffMod winter 2019 v2 Media Resource
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VanderWeele.InteractionTutorial 2014 clean to post File
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Knol et al Int J Epid 2007 Interaction on Additive Scale File
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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.
Uploaded 02/20/20, 17:02 -
HW6 interaction Ques Answ w2020 key to POST final File
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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)
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Homework #6 Review: Interaction/Effect Modification
Faculty: Dan Kelly
Location: Mission Hall 1407
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Office Hours: General Catch Up
Faculty: Dan Kelly
Location: Mission Hall 3700 and online or +1 669 900 6833 (Meeting ID: 891 527 765)
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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)
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Orsini article for QBA HW File
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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
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Hernán MA, Hernández-Díaz S, Robins JM. A structural approach to selection bias. Epidemiology. 2004;15(5):615-625. File
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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
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Last TL, et al. Good practices for quantitative bias analysis. International Journal of Epidemiology. 2014;43(6):1969-1985. File
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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#
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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
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300312 WrapUp with markings and NEW slides after Review FileUploaded 03/12/20, 23:14
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Final exam will be posted by 5:00pm 3/12 with due date of Thursday, March 26th, 2020 @ 11:59pm.
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200316 Final Exam Ques only to Post-v2a FileUploaded 03/16/20, 10:38
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Satia et al AJE 2009 BetaCarotene and Lung CA in VITAL File
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RIVUR Dataset for Q12_13_14 FINAL Exam File
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Jain et al MMR and ASD Supplemental Content JAMA 2015 File
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200426 Final Exam KEY v2a To POST FileUploaded 05/3/20, 13:20
