11  Assessment 1

A project with a qmd file showing basic reproducible report skills

11.1 Instructions

Your task is to write the outline structure of a published paper in your field in a reproducible quarto script. The paper should contain at least one image and one table (ideally small). The report must contain the following:

• A project structure with all needed files
• A setup code chunk that loads the tidyverse
• Before the abstract, use inline R to include the version of R you are using, as well as a bibliographic reference to the original paper
• All section headers and subheaders that are present in the paper (i.e., Abstract, Introduction, Methods, Results, Discussion, Author Notes, References)
• Copy the abstract as a paragraph, using markdown syntax for any text formatting
• Include one relevant image from the paper (you can screenshot it from the PDF) with the figure caption in the appropriate section
• Cross reference the image in the text with automatic figure numbering . You can copy a sentence from the original text that references the figure, or make up a sentence of your own to reference them.
• Copy sentences with least two bibliographic citations from the paper, including the citations via reproducible techniques
• Automatically display these citations in the reference section using reproducible techniques
• Customise the YAML header to:
  • a table of contents
  • use a non-default theme of your choosing
  • hide all code chunks
• The quarto file should be renderable by the marker

See this report for an example.

11.2 AI Declaration

It is School policy to include this specific AI declaration in any work that allows the use of generative AI. You can copy the code below and include it at the end of your assessment.

### Generative AI Declaration

Indicate [YES] or [NO] to all statements below to show how you have used generative AI tools in this assignment. You MUST declare all use of AI and take responsibility for the content of the assignment. We consider it a misuse of generative AI if you do not declare all uses, including initial exploration of the subject, literature searching, writing and editing, corrections for grammar and spelling, as well as any other tasks from the course.

* [YES/NO] Do you take full responsibility for the content of this submission, ensuring its adherence to academic integrity standards and compliance with University and subject-specific regulations regarding generative AI use as detailed in the assessment information sheet?

Did you use AI for:

* [YES/NO] General learning about a topic 
* [YES/NO] Idea generation or scoping of topic or research question
* [YES/NO] Searching and consulting the scientific literature
* [YES/NO] Summarising or explaining primary sources like journal articles
* [YES/NO] Planning the overall structure of a piece of work?
* [YES/NO] Translation of your own text from another language into English
* [YES/NO] Rephrasing your own text at sentence level
* [YES/NO] Language editing for spelling, grammar, clarity or tone
* [YES/NO] Referencing support, for example checking or producing citations, DOIs or formatting
* [YES/NO] Analysis support, for example statistical or qualitative analysis advice or interpreting output
* [YES/NO] Coding assistance, for example writing or debugging code
* [YES/NO] Visuals or media support, for example figures, diagrams, slide layout or transcription of my own * recordings
* [YES/NO] Something else (explain below)
* [YES/NO] Avoided use of AI tools in any way to assist with this assignment or my learning of the topic

11.3 Submission

• Covers: chapters 1 and 2
• Worth: 10%
• Do not put your name in your report; use your student ID as the author.
• Please submit a zip file containing:
  1. the .rproj file
  2. your reproducible script, named report1_studentID.qmd
  3. any additional files necessary to reproduce your report (e.g., images or bibliography files),
  4. the rendered html report, named report1_studentID.html.

11.4 Marking Rubric

You will receive green/amber/red lights for each of 11 elements, and a generic feedback document explaining common issues. Each rubric element is weighted equally.

• Green: Perfect or nearly perfect
• Amber: Needs some improvement
• Red: Incorrect or absent

Elements	Green	Amber	Red
project structure
setup code chunk
section headers
paragraph
image
cross reference
inline R
citations
references
YAML header
renderable

Total: 0/22