Disability and COVID-19 Reproduction

Sep-28 : In this lesson, we will reanalyze county-level association of disability and COVID-19.

The purpose of this lab is to reanalyze Chakraborty (2021) and finalize a reproduction report.

Procedure

• identify an error, uncertain decision, or opportunity for improving reproducibility or study design. Everyone can contribute to the following on this reproduction:
  1. The final choropleth map has a mistaken parameter causing it to only use half of the available color ramp
  2. Improve the formatting of the missing data table with Kable and/or KableExtra functions and/or by transposing the table to vertical orientation.
  3. Integrate Emily’s discussion and any new results that have yet to be discussed into a new discussion section. There’s no need to repeat information found earlier in the report. Rather, this is a chance to synthesize the findings presented earlier and think about their implications.
  4. Separate a conclusions section from the discussion that concludes whether the reproduction attempt was successful, and what the implications are for how the original study contributes to scientific knowledge.
  5. Move the “rationale for the updated report” section to the very end
• write a plan for modifications in markdown, including:
  1. title and author (yourself)
  2. description of modification(s) with rationale(s)
  3. plan for visualizing/comparing/interpreting of results
  4. save as docs/reports/<name>-analysis-plan.md, e.g. docs/reports/holler-analysis-plan.md
  5. commit the plan and push to GitHub
  6. this is a small-scale version of a preregistration
• modify the main 01-Rpr-Chakraborty.Rmd analysis plan & code to address the issue identified above
• implement the change in code
• interpret the results of your change(s) in the rmarkdown report
• knit a new study report html form. See this video
• enable GitHub Pages on the repository to serve the html version of the report to the web. (see previous video)
• write a blog post highlighting what you have learned from and contributed to with this reproduction and reanalysis study. In particular, please address these questions:
  • What have you learned from doing a reproduction study?
  • Has the reproduction deviated from the original study in any way?
  • If so, are the deviations improvements or errors?
  • Are there opportunities to further improve the study’s research design, reproducibility, or reproducibility for teaching purposes?
  • Are there opportunities to design meaningful replication studies to further test any theories established by this study?
  • Keep in mind, a blog post is for highlights : aim for a post to be a short and impactful advertisement for the full study… no more than two paragraphs.
• Link to your full study from the blog post

Timeline

• Thursday, September 28 Class: Draft analysis plan of proposed changes and plans for interpreting the changes
• Thursday, September 28 Lab: Finalize analysis plan and commit the plan to GitHub
• Before Thursday, October 5 Lab: Commit finalized analysis report and blog post to GitHub

General types of improvements/contributions

• If a process is difficult to understand or visualize, break it down into smaller steps and visualize intermediary outputs
• Improve data visualizations to better understand the study
• Choose a subjective or questionable research decision and try an alternative
• Fix any errors or investigate any uncertainties you discover
• Improve computational efficiency or coding style efficiency

Suggested markdown for analysis plan

# Planned revisions to reproduction of ....

Author: First name, Last name

## Analysis

Enumerate and justify changes to analytical plan here

## Results

Describe how changes will be visualized / compared here

## Discussion

Describe how you will interpret the results of your changes here.
For example, in hypothetical terms, if my new/revised map shows ---, it will mean that ---.

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