BIOS 543 Week 1 Lecture 1 Notes

Each TA will provide 3 hours of office hours each week
AM and PM hours 5 days per week (as much as schedules allow)
Office hours will be in-person or via Zoom
In addition to the TAs, the instructor is available to meet during:
- TTH 5:20-6:20 pm, or by appointment (in person or via Zoom)

There will be five (5) homework assignments that will count for $75\%$ of your grade
You will have a minimum of 1 week for every homework assignment
Most assignments will have a written component
This is where the IMRaD information module in Canvas will be useful as you WILL provide your write-up in IMRaD format

There is a single final comprehensive exam that will count for $25\%$ of your final grade
The format of this final exam has not been determined
Assignment Type and Grade Ranges (summary):
- Homework (5): $75\%$ of final grade
- Final Examination (1): $25\%$ of final grade
- Letter Grade ranges:
- $A: 90\% \leq \text{Grade} \leq 100\%$
- B: 80\% \leq \text{Grade} < 90\%
- C: 70\% \leq \text{Grade} < 80\%
- F: \text{Grade} < 70\%

Some modules include reading assignments as well as videos
Please read the assigned material before the week begins
Links to the videos are posted in the modules; the ones appropriate for each lecture are presented before the PowerPoint they apply to
You may want to go through the PowerPoint before watching the videos so you have an idea of what to expect

I EXPECT that you will review materials BEFORE class:
- This includes watching any videos, reading assignments, and reviewing posted slides to be prepared to ask questions
I EXPECT that you will review materials from PREVIOUS weeks regularly
This is not a “listen to me lecture and then put everything away until the next class” course
I EXPECT that you will utilize the TAs and their office hours; they are there to help you gain a deeper understanding of material and help with coding in R
If you cannot meet with a TA, email the instructor to arrange a meeting

If you need an extension for a homework assignment, request the extension a MINIMUM of $24\text{ hours}$ BEFORE the due date
Extensions will be granted for valid reasons
You MUST request the extension at least $24\text{ hours}$ in advance of the due date
You are expected to take this course as seriously as any other course you are taking (or as seriously as your job if you work while taking classes)

Are there any questions regarding TAs, Grading, Course Materials, or instructor expectations for the course?

Process steps (from page 14):
- 1. Generate Hypothesis
- 2. Design Study to test Hypothesis
- 3. Collect Data
- 4. Analyze Data
- 5. Interpret Data
- 6a. Publish or conduct next experiment
- 6b. Refine or Expand Hypothesis
Common pitfalls (associated with poor practice):
- Poor/incomplete methods description
- Low statistical power
- Failure to consider confounders
- Unintended bias
- Cherry picking / phishing
- Inappropriate methods
- P-hacking
- Model biases
- Over/under-optimism
- Failure to assess measurement quality (Internal Validity)
Source attribution: Mohanish Deshmukh, T32 Co-Director, Medical Sciences Training Program, UNC Chapel Hill
Topic: The Scientific Process

Definitions:
- Replication and Reproducibility: there is much disagreement and confusion; definitions are sometimes swapped
- 1. Taking someone else’s specimens, data, code, etc., and obtaining identical results
- 2. Using someone else’s approach and obtaining sufficiently similar results
Most definitions distinguish: (1) Replication and (2) Reproducibility
Science is deemed not replicable or reproducible when original results cannot be obtained or approximated
Peng RD (2009) Reproducible research and biostatistics. Biostatistics 10(3): 405-408

Causes (per page 16):
- Public Perception: Fraud or Deceitful Behavior
- Overemphasis on P-Values
Actual Culprits:
- Isolated Sub-Populations/small Samples
- Poor/Overly-simple Methods
- “Hero Ball”/Poor Teamwork
- Poorly Oriented Goals
- Confirming hunches
- Proving hunches
Solutions and goals:
- Research Goals SHOULD NOT Be: Find “your” answer; Prove/justify new drug/intervention/etc.
- Research Goals SHOULD Be: Find “THE” answer; Seek TRUTH, not glory; Act reproducibly and justifiably; Reduce uncertainty
Justification and Methodology:
- Scientific Method requires: Objectivity of Study Outcomes; Clinical Equipoise; If Methods/Findings aren’t reproducible, results are invalid; Sound Methods → Sound Conclusions