Semester project submission

Completing the semester project entails two steps:

  1. Classroom presentation of your work (Week of April 28 (Updated))
  2. Submit final Semester Project report (push to Git and archive the repository on Zenodo).

Details for both are provided below.

Presentation

  • Each student is allotted 16 minutes– approx. 12 minutes for your talk, and approx. 4 for questions from classmates

  • The presentation should be made using quarto, and formatted as a revealjs slide deck (see this link for instructions).

  • The content of the presentation should cover:

    • The motivation of the original study
    • A summary of the approach and results from the original study
    • What data and code was made available by the authors
    • Your approach for replication. E.g. what was the biggest hurdle? What went more smoothly than you anticipated?
    • Your code for reproduction, including comments so that it can be easily understood by someone looking to replicate your work. (If code takes too long to compile, OK to set eval = F)
    • What you learned about replication from this process
    • What is one tool you learned about during your replication exercise that you feel others in the class would find useful?

1 Note that talks at the Ecological Society of America and at some other conferences last 12 minutes each, so you can think of this as practice!

Writeup

You are encouraged to use your submission for Activity 4 as the first draft for this final writeup.

Content

Your final project submission should be structured as follows:

Background: Two to three paragraph overview of the science you are trying to achieve. (For undergraduates, a shorter Background might suffice). This paragraph should include a ≥ 10 citations to key papers in the field that motivate the research question.

Process: One to two paragraph narrative describing the process that you followed to complete your replication. For graduate students, this could mean describing the process you followed for retrieving the raw data sets, any confusions you felt regarding the methods of the original paper, and a summary of what you have and have not been able to reproduce so far. For undergraduate students, this could mean describing the process you undertook to understand the dataset you are working with, any visualizations you considered creating but ultimately rejected, etc. This section should include citations to each of the packages currently being used in the project.

Reproducible research code: Next, your status report show include any code you have written so far to reproduce parts of your analysis. You should aim to create at least two plots or analyses similar to work presented in the paper you are working on. For most students, this will be in the format of R code chunks with their associated outputs; if your project entails substantial coding outside of R, please meet with me to discuss options.

Learning and takeaways: This should be a two to three paragraph reflection on the replication process. Your response should address the following themes: - What aspect of this exercise was most instructive, and what aspect was most frustrating? - How do you anticipate applying the lessons you learned from this activity to your own research process? - Refer back to your responses to Question 1 in Activity 2 from earlier in the semester. Have any of your responses to those questions evolved over the course of this semester? How?

Formatting

Formatting guidelines from Activity 4 remain in place:

  • All elements of the document must be double spaced.
  • The document should include page numbers and line numbers for all of the “core” content (i.e. everything except title and your name)
  • In-text citations and the bibliography must follow the formatting guidelines of the journal The American Naturalist.
  • The different sections outlined above (Background, Process, Reproducible Research Code, Learning) must each have their own sub-heading within the PDF.

2 Note that this stylesheet is available at this link: https://github.com/citation-style-language/styles/tree/master

Submission

Until now, you have submitted activities by pushing them to Gitlab. As this is your final submission for this semester, completing your semester project submission will require one more step: archiving your project replication repository on Zenodo, such that it is assigned a persistent DOI. Steps for completing this archival are available here.