Welcome: From Correlation to Causation

# From Correlation to Causation

**Session 1**

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## 👋

##  Lucy D'Agostino McGowan

&nbsp; [mcgowald@wfu.edu](mailto:mcgowald@wfu.edu) 
 &nbsp; Wed 11a-12p
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Everything you will need will be posted at:

# [bit.ly/sta-679-s22](http://bit.ly/sta-679-s22)
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# Correlation v Causation

# Correlation v Causation

<img src="01-welcome_files/figure-html/unnamed-chunk-1-1.png" width="504" style="display: block; margin: auto;" />
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# Correlation v Causation

<img src="01-welcome_files/figure-html/unnamed-chunk-2-1.png" width="504" style="display: block; margin: auto;" />
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# Correlation v Causation

<img src="01-welcome_files/figure-html/unnamed-chunk-3-1.png" width="504" style="display: block; margin: auto;" />
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# Correlation v Causation

<img src="01-welcome_files/figure-html/unnamed-chunk-4-1.png" width="504" style="display: block; margin: auto;" />
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# Correlation v Causation

.box-inv-1.medium[ice cream sales, crime]

.box-inv-1.medium[smoking, lung cancer]

.box-inv-1.medium[coffee, cancer]

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# <svg aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M624 416H381.54c-.74 19.81-14.71 32-32.74 32H288c-18.69 0-33.02-17.47-32.77-32H16c-8.8 0-16 7.2-16 16v16c0 35.2 28.8 64 64 64h512c35.2 0 64-28.8 64-64v-16c0-8.8-7.2-16-16-16zM576 48c0-26.4-21.6-48-48-48H112C85.6 0 64 21.6 64 48v336h512V48zm-64 272H128V64h384v256z"/></svg> Application Exercise

.box-inv-1.medium[Causal assumptions]

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# Sir Austin Bradford Hill

Epidemiologist created a list of guidelines for evaluating whether there is evidence of a causal relationship

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# Strength

.center[
<figure>
 <img src = "https://imgs.xkcd.com/comics/boyfriend.png" height = "50%">
</figure>
]
.pull-right[.tiny[https://xkcd.com/539/]]

* How big is the effect you are seeing?

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* Note: Hill suggests that huge effects can suggest causality, however this does not mean small effects cannot

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# Consistency

.pull-left[
<figure>
 <img src = "https://imgs.xkcd.com/comics/the_difference.png" width = "45%">
</figure>
.tiny[https://xkcd.com/242/]
]

* Can your analysis be reproduced?

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* Has anyone been able to replicate your findings?

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# Specificity

.pull-left[
<figure>
 <img src = "https://imgs.xkcd.com/comics/cells_2x.png" width = "55%">
</figure>
.tiny[https://xkcd.com/1217/]
]

* Can the association be pinpointed to a specific cause with no other plausible explanation?

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* I appreciate Hill’s caveat here, *“if specificity exists we may be able to draw conclusions without hesitation; if it is not apparent, we are not thereby necessarily left sitting irresolutely on the fence.”*

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# Temporality

.center[
![](https://imgs.xkcd.com/comics/cell_phones.png)
]
.pull-right[.tiny[https://xkcd.com/925/]]

* Causes need to occur before effects

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# Biological gradient

.pull-left[
<figure>
 <img src = "https://imgs.xkcd.com/comics/ballmer_peak.png" width = "95%">
</figure>
.tiny[https://xkcd.com/323/]
]

* "Dose effect"

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* Does increasing an exposure yield a change in the outcome?

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# Plausibility

.center[
![](https://imgs.xkcd.com/comics/extrapolating.png)
]
.pull-right[.tiny[https://xkcd.com/605/]]

* Does the causal relationship make sense?

* *This is also a tricky one since plausibility depends on knowledge at the time.*

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# Coherence

.center[
<figure> 
 <img src="https://imgs.xkcd.com/comics/bridge_2x.png" width = "70%">
</figure>
]
.pull-right[.tiny[https://xkcd.com/1170/]]

* Similar to plausibility, is there a logical argument that can be made by/to experts in the field regarding causality.

* Does it fit into the understanding of the field (*this should have caveats too…the field could be wrong!*).

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# Experiment

.pull-left[
<figure> 
 <img src = "https://imgs.xkcd.com/comics/blind_trials_2x.png" width = "65%">
</figure>
.tiny[https://xkcd.com/1462/]
]

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* If a controlled experiment can take place, this can strengthen the argument for causality

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# Analogy

.pull-left[
<figure>
 <img src = "https://imgs.xkcd.com/comics/significant.png" width = "60%">
</figure>
.tiny[https://xkcd.com/882/]
]

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* Have we seen a similar effect from a similar exposure?

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# Class details

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# Create a GitHub account

Go to https://github.com/, and create an account (unless you already have one). Tips for selecting a username:1

.tiny[
- Incorporate your actual name! People like to know who they’re dealing with. Also makes your username easier for people to guess or remember.
- Reuse your username from other contexts if you can, e.g., Twitter or Slack.
- Pick a username you will be comfortable revealing to your future boss.
- Shorter is better than longer.
- Be as unique as possible in as few characters as possible. In some settings GitHub auto-completes or suggests usernames.
- Make it timeless. Don’t highlight your current university, employer, or place of residence.
- Avoid words laden with special meaning in programming, like `NA`.
]

.footnote[ [1] Source: [Happy git with R](http://happygitwithr.com/github-acct.html#username-advice) by Jenny Bryan.]

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# Download R and RStudio

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# Let's take a tour - class website

- Concepts introduced:
  - How to find slides
  - How to find assignments
  - How to get help
  - How to find policies
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# Course structure and policies
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# Class meetings

- Interactive
- Some lectures, lots of learn-by-doing
- Bring your laptop to class every day

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# Diversity & Inclusiveness:

- Intent: Students from all diverse backgrounds and perspectives be well-served by this course, that students' learning needs be addressed both in and out of class, and that the diversity that the students bring to this class be viewed as a resource, strength and benefit. It is my intent to present materials and activities that are respectful of diversity: gender identity, sexuality, disability, age, socioeconomic status, ethnicity, race, nationality, religion, and culture. Let me know ways to improve the effectiveness of the course for you personally, or for other students or student groups.

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# Diversity & Inclusiveness:

- If you feel like your performance in the class is being impacted by your experiences outside of class, please don't hesitate to come and talk with me. I want to be a resource for you. If you prefer to speak with someone outside of the course, your academic dean is an excellent resource. 
- I (like many people) am still in the process of learning about diverse perspectives and identities. If something was said in class (by anyone) that made you feel uncomfortable, please talk to me about it.

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# Disability Policy

Students with disabilities who believe that they may need accommodations in the class are encouraged to contact Learning Assistance Center & Disability Services at 336-758-5929 or [lacds@wfu.edu](mailto:lacds@wfu.edu) as soon as possible to better ensure that such accommodations are implemented in a timely fashion.

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# How to get help

All course discussion will be via GitHub: [sta-679-s22/discussion](https://github.com/sta-679-s22/discussion/discussions/) 
    
- See course policies for tips on posting questions.
- For personal and grade related questions, use email.

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# How to get help

- Go to https://github.com/sta-679-s22/discussion/discussions/ and bookmark this page.
- In the issues tab find the issue created by Dr. D'Agostino McGowan (`@LucyMcGowan`) and click on it to view it.
- Respond to it with a hello, or something else. Feel free to add some code formatted text, inline surrounded by a single backtick or on a new line surrounded by three backtics, or a hyperlink. Or try bolding or italicizing. You could also tag someone if you know their GitHub username. Your post doesn't have to be meaningful.

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# How to get help

- Hit Comment when you're done.
- Read the "How to get help" section on the course policies page.

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# How to get help

#### Math & Stats center

* Located in Kirby Hall 117
* Make an appointment:  [https://mathandstatscenter.wfu.edu/](https://mathandstatscenter.wfu.edu/)

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# Academic integrity

Adhere to the Wake Forest Honor Code. Academic dishonesty will not be tolerated.

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# Sharing/reusing code

* There are many online resources for sharing code (for example, StackOverflow) - you **may** use these resources but **must explicitly cite** where you have obtained code (both code you used directly and "paraphrased" code / code used as inspiration). Any reused code that is not explicitly cited will be treated as plagiarism.
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# Sharing/reusing code

* You **may** discuss the content of assignments with others in this class. If you do so, please acknowledge your collaborator(s) at the top of your assignment, for example: "Collaborators: Gertrude Cox, Florence Nightingale David". Failure to acknowledge collaborators will result in a grade of 0. You **may not** copy code and/or answers **directly** from another student. If you copy someone else's work, both parties will receive a grade of 0.
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* Rather than copying someone else's work, ask for help. You are not alone in this course!

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# Course components:

- Reflections
- Application exercises: Usually start in class and finish in teams by the next class period, check/no check
- Assessment
- Lab: start in class,
- Midterm
- Final Projects

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# Grading

Component             | Weight
----------------------|----------------
Reflections | 5%  
Application exercises | 10%  
Midterm | 15%  
Assessments | 20%  
Labs | 30%  
Final Project | 20%

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# Late/missed work policy

- Late work policy for homework and lab assignments:
    - late, but within 24 hours of due date/time: -50%
    - any later: no credit

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# Next Class

* Getting to know you / tech set up

Please book a 10 minute slot with me here:

[bit.ly/sta-679-appt](https://bit.ly/sta-679-appt)