Checkpoint 4

There is a template RMarkdown file called README.Rmd to start from in the initial Github Repo from Github Classroom.

For this checkpoint, I want you to work on your own, generating ideas by yourself so that when you work with your partner, you’ll have twice the ideas.

Github Setup

To create a shared repository (for you and me), go to https://classroom.github.com/a/UJTKr-k2. Once that repository is created, you’ll want to add the Rmd template file to this repository (with some existing data files). You can do this by setting it up with Github Desktop (my recommendation) or by uploading existing files.

Data Context

1. Read the following two journal articles about the ACTIVE study.

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934012/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055506/

Write 3-5 sentence reflection about this study.

Also, add the citations of these papers to the Library.bib file in the Github Repo by going to https://www.bioinformatics.org/texmed/ and typing the PMC numbers from the article addresses. Click on bibtex and copy the @Article{key, …} text below into the Library.bib file. Then provide Bibtex citations in a reference section at the end of this homework by citing the article in your summary by [@key]. For example, I could write about misspecification of the covariance matrix in mixture models and refer to my paper [@heggeseth_impact_2013].

ANSWER:

Research Question

2. Develop a “linear regression” research question you’d like to explore about aging related to the clinical trial.

Outcome Ideas: Reasoning, Memory, Speed of Processing, Functional Outcomes

Predictors: Treatment Group, Years, Baseline Age, Gender, Baseline Values [of any outcome], Interactions, Reasoning, Memory, Speed of Processing, Functional Outcomes

ANSWER:

3. Load in the ACTIVE study data and come up with two high quality graphs that provide insight about your research question.

ANSWER:

source('Cleaning.R') #Open Cleaning.R to see the data cleaning steps to create a long format dataset & more info about each variable
head(activeLong)

Models

4. Use those graphs to inform fitting a series of linear models (using lm) predicting the outcome of your choice (as it relates to your research question). Make sure to consider interactions (whether the effect is the same within treatment groups). Provide code and output for one model that you feel is informative about your research question.

ANSWER:

5. Write about 500 words of what you learn from fitting those models. Make sure you interpret the coefficients accurately and in context.

ANSWER:

References